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Jamalizadeh Bahaabadi Z, Tavakoly Sany SB, Gheybi F, Gholoobi A, Meshkat Z, Rezayi M, Hatamluyi B. Electrochemical biosensor for rapid and sensitive monitoring of sulfadimethoxine based on nanoporous carbon and aptamer system. Food Chem 2024; 445:138787. [PMID: 38382254 DOI: 10.1016/j.foodchem.2024.138787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
In this study, a straightforward electrochemical aptasensor was developed to detect sulfadimethoxine (SDM). It included a glassy carbon electrode decorated by boron nitride quantum dots (BNQDs) and aptamer-functionalized nanoporous carbon (APT/CZ). CZ was first synthesized by calcinating a zeolitic imidazolate framework (ZIF-8). Then, the electroactive dye methylene blue (MB) was entrapped inside its pores. By attaching aptamer to the CZ surface, APT/CZ acted as a bioguard, which prevented the MB release. Therefore, the electrochemical signal of the entrapped MB was high in the absence of SDM. Introducing SDM caused the conformation of aptamers to change, and a large number of MB was released, which was removed by washing. Therefore, the detection strategy was done based on the change in the electrochemical signal intensity of MB. The aptasensor was applied to detect SDM at a concentration range of 10-17 to 10-7 M with a detection limit of 3.6 × 10-18 M.
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Affiliation(s)
- Zahra Jamalizadeh Bahaabadi
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyedeh Belin Tavakoly Sany
- Department of Health, Safety, and Environment Management, Faculty of Health, Mashhad University of Medical Sciences, Mashhad, Iran; Social Determinants of Health Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Fatemeh Gheybi
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Aida Gholoobi
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Meshkat
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Rezayi
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Behnaz Hatamluyi
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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2
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Fernandez Solis LN, Silva Junior GJ, Bertotti M, Angnes L, Pereira SV, Fernández-Baldo MA, Regiart M. Electrochemical microfluidic immunosensor with graphene-decorated gold nanoporous for T-2 mycotoxin detection. Talanta 2024; 273:125971. [PMID: 38521020 DOI: 10.1016/j.talanta.2024.125971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
T-2 is one of the most potent cytotoxic food-borne mycotoxins. In this work, we have developed and characterized an electrochemical microfluidic immunosensor for T-2 toxin quantification in wheat germ samples. T-2 toxin detection was carried out using a competitive immunoassay method based on monoclonal anti-T-2 antibodies immobilized on the poly(methyl methacrylate) (PMMA) microfluidic central channel. The platinum wire working electrode at the end of the channel was in situ modified by a single-step electrodeposition procedure with reduced graphene oxide (rGO)-nanoporous gold (NPG). T-2 toxin in the sample was allowed to compete with T-2-horseradish peroxidase (HRP) conjugated for the specific recognizing sites of immobilized anti-T-2 monoclonal antibodies. The HRP, in the presence of hydrogen peroxide (H2O2), catalyzes the oxidation of 4-tert-butylcatechol (4-TBC), whose back electrochemical reduction was detected on the nanostructured electrode at -0.15 V. Thus, at low T-2 concentrations in the sample, more enzymatically conjugated T-2 will bind to the capture antibodies, and, therefore, a higher current is expected. The detection limits found for electrochemical immunosensor, and commercial ELISA procedure were 0.10 μg kg-1 and 10 μg kg-1, and the intra- and inter-assay coefficients of variation were below 5.35% and 6.87%, respectively. Finally, our microfluidic immunosensor to T-2 toxin will significantly contribute to faster, direct, and secure in situ analysis in agricultural samples.
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Affiliation(s)
- Laura N Fernandez Solis
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Instituto de Química de San Luis, INQUISAL (UNSL - CONICET), Chacabuco 917, D5700BWS, San Luis, Argentina
| | - Gilberto J Silva Junior
- LSEME. Laboratório de Sensores Eletroquímicos e Métodos Eletroanalíticos. Institute of Chemistry, University of São Paulo, Av. Professor Lineu Prestes, 748, 05513-970, São Paulo - SP, Brazil
| | - Mauro Bertotti
- LSEME. Laboratório de Sensores Eletroquímicos e Métodos Eletroanalíticos. Institute of Chemistry, University of São Paulo, Av. Professor Lineu Prestes, 748, 05513-970, São Paulo - SP, Brazil
| | - Lúcio Angnes
- Laboratório de Automação e Instrumentação Analítica, Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Professor Lineu Prestes 748, 05508-000, São Paulo, Brazil
| | - Sirley V Pereira
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Instituto de Química de San Luis, INQUISAL (UNSL - CONICET), Chacabuco 917, D5700BWS, San Luis, Argentina
| | - Martín A Fernández-Baldo
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Instituto de Química de San Luis, INQUISAL (UNSL - CONICET), Chacabuco 917, D5700BWS, San Luis, Argentina.
| | - Matías Regiart
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Instituto de Química de San Luis, INQUISAL (UNSL - CONICET), Chacabuco 917, D5700BWS, San Luis, Argentina.
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3
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Pathak A, Verma N, Tripathi S, Mishra A, Poluri KM. Nanosensor based approaches for quantitative detection of heparin. Talanta 2024; 273:125873. [PMID: 38460425 DOI: 10.1016/j.talanta.2024.125873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/23/2024] [Accepted: 03/03/2024] [Indexed: 03/11/2024]
Abstract
Heparin, being a widely employed anticoagulant in numerus clinical complications, requires strict quantification and qualitative screening to ensure the safety of patients from potential threat of thrombocytopenia. However, the intricacy of heparin's chemical structures and low abundance hinders the precise monitoring of its level and quality in clinical settings. Conventional laboratory assays have limitations in sensitivity and specificity, necessitating the development of innovative approaches. In this context, nanosensors emerged as a promising solution due to enhanced sensitivity, selectivity, and ability to detect heparin even at low concentrations. This review delves into a range of sensing approaches including colorimetric, fluorometric, surface-enhanced Raman spectroscopy, and electrochemical techniques using different types of nanomaterials, thus providing insights of its principles, capabilities, and limitations. Moreover, integration of smart-phone with nanosensors for point of care diagnostics has also been explored. Additionally, recent advances in nanopore technologies, artificial intelligence (AI) and machine learning (ML) have been discussed offering specificity against contaminants present in heparin to ensure its quality. By consolidating current knowledge and highlighting the potential of nanosensors, this review aims to contribute to the advancement of efficient, reliable, and economical heparin detection methods providing improved patient care.
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Affiliation(s)
- Aakanksha Pathak
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Nishchay Verma
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Shweta Tripathi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, 342011, Rajasthan, India
| | - Krishna Mohan Poluri
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India; Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
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4
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Tian R, Ma W, Wang L, Xie W, Wang Y, Yin Y, Weng T, He S, Fang S, Liang L, Wang L, Wang D, Bai J. The combination of DNA nanostructures and materials for highly sensitive electrochemical detection. Bioelectrochemistry 2024; 157:108651. [PMID: 38281367 DOI: 10.1016/j.bioelechem.2024.108651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/30/2024]
Abstract
Due to the wide range of electrochemical devices available, DNA nanostructures and material-based technologies have been greatly broadened. They have been actively used to create a variety of beautiful nanostructures owing to their unmatched programmability. Currently, a variety of electrochemical devices have been used for rapid sensing of biomolecules and other diagnostic applications. Here, we provide a brief overview of recent advances in DNA-based biomolecular assays. Biosensing platform such as electrochemical biosensor, nanopore biosensor, and field-effect transistor biosensors (FET), which are equipped with aptamer, DNA walker, DNAzyme, DNA origami, and nanomaterials, has been developed for amplification detection. Under the optimal conditions, the proposed biosensor has good amplification detection performance. Further, we discussed the challenges of detection strategies in clinical applications and offered the prospect of this field.
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Affiliation(s)
- Rong Tian
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Wenhao Ma
- Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Lue Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
| | - Wanyi Xie
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Yunjiao Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Yajie Yin
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Ting Weng
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Shixuan He
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Shaoxi Fang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Liyuan Liang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Liang Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Deqiang Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Jingwei Bai
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
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5
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Mejias-Gomez O, Braghetto M, Sørensen MKD, Madsen AV, Guiu LS, Kristensen P, Pedersen LE, Goletz S. Deep mining of antibody phage-display selections using Oxford Nanopore Technologies and Dual Unique Molecular Identifiers. N Biotechnol 2024; 80:56-68. [PMID: 38354946 DOI: 10.1016/j.nbt.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/05/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
Antibody phage-display technology identifies antibody-antigen interactions through multiple panning rounds, but traditional screening gives no information on enrichment or diversity throughout the process. This results in the loss of valuable binders. Next Generation Sequencing can overcome this problem. We introduce a high accuracy long-read sequencing method based on the recent Oxford Nanopore Technologies (ONT) Q20 + chemistry in combination with dual unique molecular identifiers (UMIs) and an optimized bioinformatic analysis pipeline to monitor the selections. We identified binders from two single-domain antibody libraries selected against a model protein. Traditional colony-picking was compared with our ONT-UMI method. ONT-UMI enabled monitoring of diversity and enrichment before and after each selection round. By combining phage antibody selections with ONT-UMIs, deep mining of output selections is possible. The approach provides an alternative to traditional screening, enabling diversity quantification after each selection round and rare binder recovery, even when the dominating binder was > 99% abundant. Moreover, it can give insights on binding motifs for further affinity maturation and specificity optimizations. Our results demonstrate a platform for future data guided selection strategies.
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Affiliation(s)
- Oscar Mejias-Gomez
- Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marta Braghetto
- Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Morten Kielsgaard Dziegiel Sørensen
- Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andreas Visbech Madsen
- Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Laura Salse Guiu
- Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Section for Bioscience and Engineering, Aalborg University, Aalborg, Denmark
| | - Lasse Ebdrup Pedersen
- Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, Technical University of Denmark, Kongens Lyngby, Denmark.
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6
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Arora P, Zheng H, Munusamy S, Jahani R, Wang L, Guan X. Probe-assisted detection of Fe 3+ ions in a multi-functionalized nanopore. Biosens Bioelectron 2024; 251:116125. [PMID: 38359668 PMCID: PMC10922892 DOI: 10.1016/j.bios.2024.116125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 02/17/2024]
Abstract
Iron is an essential element that plays critical roles in many biological/metabolic processes, ranging from oxygen transport, mitochondrial respiration, to host defense and cell signaling. Maintaining an appropriate iron level in the body is vital to the human health. Iron deficiency or overload can cause life-threatening conditions. Thus, developing a new, rapid, cost-effective, and easy to use method for iron detection is significant not only for environmental monitoring but also for disease prevention. In this study, we report an innovative Fe3+ detection strategy by using both a ligand probe and an engineered nanopore with two binding sites. In our design, one binding site of the nanopore has a strong interaction with the ligand probe, while the other is more selective toward interfering species. Based on the difference in the number of ligand DTPMPA events in the absence and presence of ferric ions, micromolar concentrations of Fe3+ could be detected within minutes. Our method is selective: micromolar concentrations of Mg2+, Ca2+, Cd2+, Zn2+, Ni2+, Co2+, Mn2+, and Cu2+ would not interfere with the detection of ferric ions. Furthermore, Cu2+, Ni2+, Co2+, Zn2+, and Mn2+ produced current blockage events with quite different signatures from each other, enabling their simultaneous detection. In addition, simulated water and serum samples were successfully analyzed. The nanopore sensing strategy developed in this work should find useful application in the development of stochastic sensors for other substances, especially in situations where multi-analyte concurrent detection is desired.
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Affiliation(s)
- Pearl Arora
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Haiyan Zheng
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | | | - Rana Jahani
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
| | - Xiyun Guan
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA.
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7
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Chen Z, Xie X, Jia C, Zhong Q, Zhang Q, Luo D, Cao Y, Mu Y, Ren C. Concentration-Driven Evolution of Adaptive Artificial Ion Channels or Nanopores with Specific Anticancer Activities. Angew Chem Int Ed Engl 2024; 63:e202318811. [PMID: 38419371 DOI: 10.1002/anie.202318811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/16/2024] [Accepted: 02/28/2024] [Indexed: 03/02/2024]
Abstract
In nature, ceramides are a class of sphingolipids possessing a unique ability to self-assemble into protein-permeable channels with intriguing concentration-dependent adaptive channel cavities. However, within the realm of artificial ion channels, this interesting phenomenon is scarcely represented. Herein, we report on a novel class of adaptive artificial channels, Pn-TPPs, based on PEGylated cholic acids bearing triphenylphosphonium (TPP) groups as anion binding motifs. Interestingly, the molecules self-assemble into chloride ion channels at low concentrations while transforming into small molecule-permeable nanopores at high concentrations. Moreover, the TPP groups endow the molecules with mitochondria-targeting properties, enabling them to selectively drill holes on the mitochondrial membrane of cancer cells and subsequently trigger the caspase 9 apoptotic pathway. The anticancer efficacies of Pn-TPPs correlate with their abilities to form nanopores. Significantly, the most active ensembles formed by P5-TPP exhibits impressive anticancer activity against human liver cancer cells, with an IC50 value of 3.8 μM. While demonstrating similar anticancer performance to doxorubicin, P5-TPP exhibits a selectivity index surpassing that of doxorubicin by a factor of 16.8.
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Affiliation(s)
- Zhiqing Chen
- State Key Laboratory of Cellular Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
- Shenzhen Research Institute of, Xiamen University, Shenzhen, Guangdong, 518057, China
| | - Xiaopan Xie
- State Key Laboratory of Cellular Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
- Shenzhen Research Institute of, Xiamen University, Shenzhen, Guangdong, 518057, China
| | - Chunyan Jia
- State Key Laboratory of Cellular Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
- Shenzhen Research Institute of, Xiamen University, Shenzhen, Guangdong, 518057, China
| | - Qishuo Zhong
- State Key Laboratory of Cellular Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
- Shenzhen Research Institute of, Xiamen University, Shenzhen, Guangdong, 518057, China
| | - Qiuping Zhang
- State Key Laboratory of Cellular Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
- Shenzhen Research Institute of, Xiamen University, Shenzhen, Guangdong, 518057, China
| | - Daoxin Luo
- State Key Laboratory of Cellular Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
- Shenzhen Research Institute of, Xiamen University, Shenzhen, Guangdong, 518057, China
| | - Yin Cao
- State Key Laboratory of Cellular Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Changliang Ren
- State Key Laboratory of Cellular Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
- Shenzhen Research Institute of, Xiamen University, Shenzhen, Guangdong, 518057, China
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8
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Zhang X, Malle MG, Thomsen RP, Sørensen RS, Sørensen EW, Hatzakis NS, Kjems J. Deconvoluting the Effect of Cell-Penetrating Peptides for Enhanced and Controlled Insertion of Large-Scale DNA Nanopores. ACS Appl Mater Interfaces 2024; 16:18422-18433. [PMID: 38573069 DOI: 10.1021/acsami.3c18636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
DNA nanopores have emerged as powerful tools for molecular sensing, but the efficient insertion of large DNA nanopores into lipid membranes remains challenging. In this study, we investigate the potential of cell-penetrating peptides (CPPs), specifically SynB1 and GALA, to enhance the insertion efficiency of large DNA nanopores. We constructed SynB1- or GALA-functionalized DNA nanopores with an 11 nm inner diameter and visualized and quantified their membrane insertion using a TIRF microscopy-based single-liposome assay. The results demonstrated that incorporating an increasing number of SynB1 or GALA peptides into the DNA nanopore significantly enhanced the membrane perforation. Kinetic analysis revealed that the DNA nanopore scaffold played a role in prearranging the CPPs, which facilitated membrane interaction and pore formation. Notably, the use of pH-responsive GALA peptides allowed highly efficient and pH-controlled insertion of large DNA pores. Furthermore, single-channel recording elucidated that the insertion process of single GALA-modified nanopores into planar lipid bilayers was dynamic, likely forming transient large toroidal pores. Overall, our study highlights the potential of CPPs as insertion enhancers for DNA nanopores, which opens avenues for improved molecule sensing and the controlled release of cargo molecules.
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Affiliation(s)
- Xialin Zhang
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | - Rasmus P Thomsen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | | | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark
- Novonordisk Center for Protein Research, University of Copenhagen, Copenhagen 2100, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
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9
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Gonzalez Solveyra E, Perez Sirkin YA, Tagliazucchi M, Szleifer I. Orientational Pathways during Protein Translocation through Polymer-Modified Nanopores. ACS Nano 2024; 18:10427-10438. [PMID: 38556978 DOI: 10.1021/acsnano.3c11318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein translocation through nanopores holds significant promise for applications in biotechnology, biomolecular analysis, and medicine. However, the interpretation of signals generated by the translocation of the protein remains challenging. In this way, it is crucial to gain a comprehensive understanding on how macromolecules translocate through a nanopore and to identify what are the critical parameters that govern the process. In this study, we investigate the interplay between protein charge regulation, orientation, and nanopore surface modifications using a theoretical framework that allows us to explicitly take into account the acid-base reactions of the titrable amino acids in the proteins and in the polyelectrolytes grafted to the nanopore surface. Our goal is to thoroughly characterize the translocation process of different proteins (GFP, β-lactoglobulin, lysozyme, and RNase) through nanopores modified with weak polyacids. Our calculations show that the charge regulation mechanism exerts a profound effect on the translocation process. The pH-dependent interactions between proteins and charged polymers within the nanopore lead to diverse free energy landscapes with barriers, wells, and flat regions dictating translocation efficiency. Comparison of different proteins allows us to identify the significance of protein isoelectric point, size, and morphology in the translocation behavior. Taking advantage of these insights, we propose pH-responsive nanopores that can load proteins at one pH and release them at another, offering opportunities for controlled protein delivery, separation, and sensing applications.
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Affiliation(s)
- Estefania Gonzalez Solveyra
- Instituto de Nanosistemas, Universidad Nacional de San Martín-CONICET, San Martín, Buenos Aires B1650, Argentina
| | - Yamila A Perez Sirkin
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica Analítica y Química Física y CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE). Pabellón 2, Ciudad Universitaria, C1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - Mario Tagliazucchi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica Analítica y Química Física y CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE). Pabellón 2, Ciudad Universitaria, C1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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10
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Sampad MJN, Saiduzzaman SM, Walker ZJ, Wells TN, Wayment JX, Ong EM, Mdaki SD, Tamhankar MA, Yuzvinsky TD, Patterson JL, Hawkins AR, Schmidt H. Label-free and amplification-free viral RNA quantification from primate biofluids using a trapping-assisted optofluidic nanopore platform. Proc Natl Acad Sci U S A 2024; 121:e2400203121. [PMID: 38598338 DOI: 10.1073/pnas.2400203121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024] Open
Abstract
Viral outbreaks can cause widespread disruption, creating the need for diagnostic tools that provide high performance and sample versatility at the point of use with moderate complexity. Current gold standards such as PCR and rapid antigen tests fall short in one or more of these aspects. Here, we report a label-free and amplification-free nanopore sensor platform that overcomes these challenges via direct detection and quantification of viral RNA in clinical samples from a variety of biological fluids. The assay uses an optofluidic chip that combines optical waveguides with a fluidic channel and integrates a solid-state nanopore for sensing of individual biomolecules upon translocation through the pore. High specificity and low limit of detection are ensured by capturing RNA targets on microbeads and collecting them by optical trapping at the nanopore location where targets are released and rapidly detected. We use this device for longitudinal studies of the viral load progression for Zika and Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections in marmoset and baboon animal models, respectively. The up to million-fold trapping-based target concentration enhancement enables amplification-free RNA quantification across the clinically relevant concentration range down to the assay limit of RT-qPCR as well as cases in which PCR failed. The assay operates across all relevant biofluids, including semen, urine, and whole blood for Zika and nasopharyngeal and throat swab, rectal swab, and bronchoalveolar lavage for SARS-CoV-2. The versatility, performance, simplicity, and potential for full microfluidic integration of the amplification-free nanopore assay points toward a unique approach to molecular diagnostics for nucleic acids, proteins, and other targets.
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Affiliation(s)
| | - S M Saiduzzaman
- School of Engineering, University of California, Santa Cruz, CA 95064
| | - Zach J Walker
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT 84602
| | - Tanner N Wells
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT 84602
| | - Jesse X Wayment
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT 84602
| | - Ephraim M Ong
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT 84602
| | | | | | | | | | - Aaron R Hawkins
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT 84602
| | - Holger Schmidt
- School of Engineering, University of California, Santa Cruz, CA 95064
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11
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Rabolli CP, Naarmann-de Vries IS, Makarewich CA, Baskin KK, Dieterich C, Accornero F. Nanopore Detection of METTL3-Dependent m6A-Modified mRNA Reveals a New Mechanism Regulating Cardiomyocyte Mitochondrial Metabolism. Circulation 2024; 149:1319-1322. [PMID: 38620081 DOI: 10.1161/circulationaha.123.066473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Affiliation(s)
- Charles P Rabolli
- Departments of Physiology and Cell Biology (C.P.R., K.K.B., F.A.), The Ohio State University, Columbus
- Biomedical Engineering (C.P.R.), The Ohio State University, Columbus
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus (C.P.R., K.K.B., F.A.)
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI (C.P.R., F.A.)
| | - Isabel S Naarmann-de Vries
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology (I.S.N.-d.V., C.D.), University Hospital Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology; I.S.N.-d.V., C.D.), University Hospital Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany (I.S.N.-d.V., C.D.)
| | - Catherine A Makarewich
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, OH (C.A.M.)
- Department of Pediatrics, University of Cincinnati College of Medicine, OH (C.A.M.)
| | - Kedryn K Baskin
- Departments of Physiology and Cell Biology (C.P.R., K.K.B., F.A.), The Ohio State University, Columbus
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus (C.P.R., K.K.B., F.A.)
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology (I.S.N.-d.V., C.D.), University Hospital Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology; I.S.N.-d.V., C.D.), University Hospital Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany (I.S.N.-d.V., C.D.)
| | - Federica Accornero
- Departments of Physiology and Cell Biology (C.P.R., K.K.B., F.A.), The Ohio State University, Columbus
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus (C.P.R., K.K.B., F.A.)
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI (C.P.R., F.A.)
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12
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Chen H, Huang C, Liao Z, Ma X, Fan J. The Role of MXene Surface Terminations on Peptide Transportation in Nanopore Sensing. J Phys Chem Lett 2024; 15:3900-3906. [PMID: 38564363 DOI: 10.1021/acs.jpclett.4c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Nanopores with two-dimensional materials have various advantages in sensing, but the fast translocation of molecules hinders their scale-up applications. In this work, we investigate the influence of -F, -O, and -OH surface terminations on the translocation of peptides through MXene nanopores. We find that the longest dwell time always occurs when peptides pass through the Ti3C2O2 nanopores. This elongated dwell time is induced by the strongest interaction between peptides and the Ti3C2O2 membrane, in which the van der Waals interactions dominate. Compared to the other two MXene nanopores, the braking effect is indicated during the whole translocation process, which evidence the advantage of Ti3C2O2 in nanopore sensing. Our work demonstrates that membrane surface chemistry has a great influence on the translocation of peptides, which can be introduced in the design of nanopores for a better performance.
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Affiliation(s)
- Huan Chen
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Changxiong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Zhenyu Liao
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Xinyao Ma
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
- Department of Mechanical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
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13
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Kumar A, Bakli C, Chakraborty S. Ion-Solvent Interactions under Confinement Hold the Key to Tuning the DNA Translocation Speeds in Polyelectrolyte-Functionalized Nanopores. Langmuir 2024; 40:7300-7309. [PMID: 38536237 DOI: 10.1021/acs.langmuir.3c02816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
DNA sequencing and sensing using nanopore technology delves critically into the alterations in the measurable electrical signal as single-stranded DNA is drawn through a tiny passage. To make such precise measurements, however, slowing down the DNA in the tightly confined passage is a key requirement, which may be achieved by grafting the nanopore walls with a polyelectrolyte layer (PEL). This soft functional layer at the wall, under an off-design condition, however, may block the DNA passage completely, leading to the complete loss of output signal from the nanobio sensor. Whereas theoretical postulates have previously been put forward to explain the essential physics of DNA translocation in nanopores, these have turned out to be somewhat inadequate when confronted with the experimental findings on functionalized nanopores, including the prediction of the events of complete signal losses. Circumventing these constraints, herein we bring out a possible decisive role of the interplay between the inevitable variabilities in the ionic distribution along the nanopore axis due to its finite length as opposed to its idealized "infinite" limit as well as the differential permittivity of PEL and bulk solution that cannot be captured by the commonly used one-dimensional variant of the electrical double layer theory. Our analysis, for the first time, captures variations in the ionic concentration distribution across multidimensional physical space and delineates its impact on the DNA translocation characteristics that have hitherto remained unaddressed. Our results reveal possible complete blockages of DNA translocation as influenced by less-than-threshold permittivity values or greater-than-threshold grafting densities of the PEL. In addition, electrohydrodynamic blocking is witnessed due to the ion-selective nature of the nanopore at low ionic concentrations. Hence, our study establishes a functionally active regime over which the PEL layer in a finite-length nanopore facilitates controllable DNA translocation, enabling successful sequencing and sensing through the explicit modulation of translocation speed.
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Affiliation(s)
- Avinash Kumar
- Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Chirodeep Bakli
- Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Suman Chakraborty
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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Nie F, Ni P, Huang N, Zhang J, Wang Z, Xiao C, Luo F, Wang J. De novo diploid genome assembly using long noisy reads. Nat Commun 2024; 15:2964. [PMID: 38580638 PMCID: PMC10997618 DOI: 10.1038/s41467-024-47349-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
The high sequencing error rate has impeded the application of long noisy reads for diploid genome assembly. Most existing assemblers failed to generate high-quality phased assemblies using long noisy reads. Here, we present PECAT, a Phased Error Correction and Assembly Tool, for reconstructing diploid genomes from long noisy reads. We design a haplotype-aware error correction method that can retain heterozygote alleles while correcting sequencing errors. We combine a corrected read SNP caller and a raw read SNP caller to further improve the identification of inconsistent overlaps in the string graph. We use a grouping method to assign reads to different haplotype groups. PECAT efficiently assembles diploid genomes using Nanopore R9, PacBio CLR or Nanopore R10 reads only. PECAT generates more contiguous haplotype-specific contigs compared to other assemblers. Especially, PECAT achieves nearly haplotype-resolved assembly on B. taurus (Bison×Simmental) using Nanopore R9 reads and phase block NG50 with 59.4/58.0 Mb for HG002 using Nanopore R10 reads.
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Affiliation(s)
- Fan Nie
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- National Center for Applied Mathematics in Hunan and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, 411105, China
| | - Peng Ni
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Neng Huang
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Jun Zhang
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Zhenyu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University #7 Jinsui Road, Tianhe District, Guangzhou, China.
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC, 29634-0974, USA.
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China.
- Xiangjiang Laboratory, Changsha, 410205, China.
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China.
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15
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Chen BJ, Lin CH, Wu HY, Cai JJ, Chao DY. Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer. Microbiol Spectr 2024; 12:e0395423. [PMID: 38483513 DOI: 10.1128/spectrum.03954-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024] Open
Abstract
Coronaviruses (CoVs), including severe acute respiratory syndrome coronavirus 2, can infect a variety of mammalian and avian hosts with significant medical and economic consequences. During the life cycle of CoV, a coordinated series of subgenomic RNAs, including canonical subgenomic messenger RNA and non-canonical defective viral genomes (DVGs), are generated with different biological implications. Studies that adopted the Nanopore sequencer (ONT) to investigate the landscape and dynamics of viral RNA subgenomic transcriptomes applied arbitrary bioinformatics parameters without justification or experimental validation. The current study used bovine coronavirus (BCoV), which can be performed under biosafety level 2 for library construction and experimental validation using traditional colony polymerase chain reaction and Sanger sequencing. Four different ONT protocols, including RNA direct and cDNA direct sequencing with or without exonuclease treatment, were used to generate RNA transcriptomic libraries from BCoV-infected cell lysates. Through rigorously examining the k-mer, gap size, segment size, and bin size, the optimal cutoffs for the bioinformatic pipeline were determined to remove the sequence noise while keeping the informative DVG reads. The sensitivity and specificity of identifying DVG reads using the proposed pipeline can reach 82.6% and 99.6% under the k-mer size cutoff of 15. Exonuclease treatment reduced the abundance of RNA transcripts; however, it was not necessary for future library preparation. Additional recovery of clipped BCoV nucleotide sequences with experimental validation expands the landscape of the CoV discontinuous RNA transcriptome, whose biological function requires future investigation. The results of this study provide the benchmarks for library construction and bioinformatic parameters for studying the discontinuous CoV RNA transcriptome.IMPORTANCEFunctional defective viral genomic RNA, containing all the cis-acting elements required for translation or replication, may play different roles in triggering cell innate immune signaling, interfering with the canonical subgenomic messenger RNA transcription/translation or assisting in establishing persistence infection. This study does not only provide benchmarks for library construction and bioinformatic parameters for studying the discontinuous coronavirus RNA transcriptome but also reveals the complexity of the bovine coronavirus transcriptome, whose functional assays will be critical in future studies.
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Affiliation(s)
- Bo-Jia Chen
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
| | - Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - James J Cai
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Day-Yu Chao
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
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16
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Si W, Zhang Z, Chen J, Wu G, Zhang Y, Sha J. Protein Deceleration and Sequencing Using Si 3N 4-CNT Hybrid Nanopores. Chemphyschem 2024; 25:e202300866. [PMID: 38267372 DOI: 10.1002/cphc.202300866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 01/26/2024]
Abstract
Protein sequencing is crucial for understanding the complex mechanisms driving biological functions and is of utmost importance in molecular diagnostics and medication development. Nanopores have become an effective tool for single molecule sensing, however, the weak charge and non-uniform charge distribution of protein make capturing and sensing very challenging, which poses a significant obstacle to the development of nanopore-based protein sequencing. In this study, to facilitate capturing of the unfolded protein, highly charged peptide was employed in our simulations, we found that the velocity of unfolded peptide translocating through a hybrid nanopore composed of silicon nitride membrane and carbon nanotube is much slower compared to bare silicon nitride nanopore, it is due to the significant interaction between amino acids and the surface of carbon nanotube. Moreover, by introducing variations in the charge states at the boundaries of carbon nanotube nanopores, the competition and combination of the electrophoretic and electroosmotic flows through the nanopores could be controlled, we then successfully regulated the translocation velocity of unfolded proteins through the hybrid nanopores. The proposed hybrid nanopore effectively retards the translocation velocity of protein through it, facilitates the acquisition of ample information for accurate amino acid identification.
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Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Zhen Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Jiayi Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
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17
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Yeo D, Chan AHJ, Hiong KC, Ong J, Ng JY, Lim JM, Zhang W, Lim SR, Fernandez CJ, Wong AMS, Lee BPYH, Khoo MDY, Cheng TXW, Lim BTM, Yeo HHT, Tan MMQ, Sng WBG, Adam SS, Ang WF, How CB, Xie R, Wasser SK, Finch KN, Loo AHB, Yap HH, Leong CC, Er KBH. Uncovering the magnitude of African pangolin poaching with extensive nanopore DNA genotyping of seized scales. Conserv Biol 2024; 38:e14162. [PMID: 37551767 DOI: 10.1111/cobi.14162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/31/2023] [Accepted: 07/19/2023] [Indexed: 08/09/2023]
Abstract
Trade in pangolins is illegal, and yet tons of their scales and products are seized at various ports. These large seizures are challenging to process and comprehensively genotype for upstream provenance tracing and species identification for prosecution. We implemented a scalable DNA barcoding pipeline in which rapid DNA extraction and MinION sequencing were used to genotype a substantial proportion of pangolin scales subsampled from 2 record shipments seized in Singapore in 2019 (37.5 t). We used reference sequences to match the scales to phylogeographical regions of origin. In total, we identified 2346 cytochrome b (cytb) barcodes of white-bellied (Phataginus tricuspis) (from 1091 scales), black-bellied (Phataginus tetradactyla) (227 scales), and giant (Smutsia gigantea) (1028 scales) pangolins. Haplotype diversity was higher for P. tricuspis scales (121 haplotypes, 66 novel) than that for P. tetradactyla (22 haplotypes, 15 novel) and S. gigantea (25 haplotypes, 21 novel) scales. Of the novel haplotypes, 74.2% were likely from western and west-central Africa, suggesting potential resurgence of poaching and newly exploited populations in these regions. Our results illustrate the utility of extensively subsampling large seizures and outline an efficient molecular approach for rapid genetic screening that should be accessible to most forensic laboratories and enforcement agencies.
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Affiliation(s)
- Darren Yeo
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Amy H J Chan
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Kum Chew Hiong
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Jasmine Ong
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Jun Yuan Ng
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Jie Min Lim
- School of Life Sciences & Chemical Technology, Ngee Ann Polytechnic, Singapore, Singapore
| | - Wendy Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Sara R Lim
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Anna M-S Wong
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | | | - Max D Y Khoo
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | | | - Bryan T M Lim
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | | | - Maxine M Q Tan
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Wendy B G Sng
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Shaun S Adam
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Wee Foong Ang
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Choon Beng How
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Renhui Xie
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Samuel K Wasser
- Department of Biology, Center for Environmental Forensic Science, University of Washington, Seattle, Washington, USA
| | - Kristen N Finch
- Department of Biology, Center for Environmental Forensic Science, University of Washington, Seattle, Washington, USA
| | - Adrian H B Loo
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Him Hoo Yap
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | | | - Kenneth B H Er
- Centre for Wildlife Forensics, National Parks Board, Singapore
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18
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Zhang M, Tang C, Wang Z, Chen S, Zhang D, Li K, Sun K, Zhao C, Wang Y, Xu M, Dai L, Lu G, Shi H, Ren H, Chen L, Geng J. Real-time detection of 20 amino acids and discrimination of pathologically relevant peptides with functionalized nanopore. Nat Methods 2024; 21:609-618. [PMID: 38443507 PMCID: PMC11009107 DOI: 10.1038/s41592-024-02208-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
Precise identification and quantification of amino acids is crucial for many biological applications. Here we report a copper(II)-functionalized Mycobacterium smegmatis porin A (MspA) nanopore with the N91H substitution, which enables direct identification of all 20 proteinogenic amino acids when combined with a machine-learning algorithm. The validation accuracy reaches 99.1%, with 30.9% signal recovery. The feasibility of ultrasensitive quantification of amino acids was also demonstrated at the nanomolar range. Furthermore, the capability of this system for real-time analyses of two representative post-translational modifications (PTMs), one unnatural amino acid and ten synthetic peptides using exopeptidases, including clinically relevant peptides associated with Alzheimer's disease and cancer neoantigens, was demonstrated. Notably, our strategy successfully distinguishes peptides with only one amino acid difference from the hydrolysate and provides the possibility to infer the peptide sequence.
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Affiliation(s)
- Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chao Tang
- Biosafety Laboratory of West China Hospital, West China Hospital, Sichuan University, Chengdu, China
| | - Zichun Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shanchuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mengying Xu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hubing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Haiyan Ren
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China.
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu, China.
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19
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Darian JC, Kundu R, Rajaby R, Sung WK. Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly. Nat Methods 2024; 21:574-583. [PMID: 38459383 DOI: 10.1038/s41592-023-02141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/30/2023] [Indexed: 03/10/2024]
Abstract
Draft genomes generated from Oxford Nanopore Technologies (ONT) long reads are known to have a higher error rate. Although existing genome polishers can enhance their quality, the error rate (including mismatches, indels and switching errors between paternal and maternal haplotypes) can be significant. Here, we develop two polishers, hypo-short and hypo-hybrid to address this issue. Hypo-short utilizes Illumina short reads to polish an ONT-based draft assembly, resulting in a high-quality assembly with low error rates and switching errors. Expanding on this, hypo-hybrid incorporates ONT long reads to further refine the assembly into a diploid representation. Leveraging on hypo-hybrid, we have created a diploid genome assembly pipeline called hypo-assembler. Hypo-assembler automates the generation of highly accurate, contiguous and nearly complete diploid assemblies using ONT long reads, Illumina short reads and optionally Hi-C reads. Notably, our solution even allows for the production of telomere-to-telomere diploid genomes with additional manual steps. As a proof of concept, we successfully assembled a fully phased telomere-to-telomere diploid genome of HG00733, achieving a quality value exceeding 50.
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Affiliation(s)
| | - Ritu Kundu
- School of Computing, National University of Singapore, Singapore, Singapore
| | | | - Wing-Kin Sung
- School of Computing, National University of Singapore, Singapore, Singapore.
- Genome Institute of Singapore, Singapore, Singapore.
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China.
- JC STEM Laboratory of Computational Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- Hong Kong Genome Institute, Hong Kong, China.
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20
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Creating diploid assemblies from Nanopore and Illumina reads with hypo-assembler. Nat Methods 2024; 21:560-1. [PMID: 38459387 DOI: 10.1038/s41592-023-02142-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
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21
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Srivathsan A, Feng V, Suárez D, Emerson B, Meier R. ONTbarcoder 2.0: rapid species discovery and identification with real-time barcoding facilitated by Oxford Nanopore R10.4. Cladistics 2024; 40:192-203. [PMID: 38041646 DOI: 10.1111/cla.12566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 12/03/2023] Open
Abstract
Most arthropod species are undescribed and hidden in specimen-rich samples that are difficult to sort to species using morphological characters. For such samples, sorting to putative species with DNA barcodes is an attractive alternative, but needs cost-effective techniques that are suitable for use in many laboratories around the world. Barcoding using the portable and inexpensive MinION sequencer produced by Oxford Nanopore Technologies (ONT) could be useful for presorting specimen-rich samples with DNA barcodes because it requires little space and is inexpensive. However, similarly important is user-friendly and reliable software for analysis of the ONT data. It is here provided in the form of ONTbarcoder 2.0 that is suitable for all commonly used operating systems and includes a Graphical User Interface (GUI). Compared with an earlier version, ONTbarcoder 2.0 has three key improvements related to the higher read quality obtained with ONT's latest flow cells (R10.4), chemistry (V14 kits) and basecalling model (super-accuracy model). First, the improved read quality of ONT's latest flow cells (R10.4) allows for the use of primers with shorter indices than those previously needed (9 bp vs. 12-13 bp). This decreases the primer cost and can potentially improve PCR success rates. Second, ONTbarcoder now delivers real-time barcoding to complement ONT's real-time sequencing. This means that the first barcodes are obtained within minutes of starting a sequencing run; i.e. flow cell use can be optimized by terminating sequencing runs when most barcodes have already been obtained. The only input needed by ONTbarcoder 2.0 is a demultiplexing sheet and sequencing data (raw or basecalled) generated by either a Mk1B or a Mk1C. Thirdly, we demonstrate that the availability of R10.4 chemistry for the low-cost Flongle flow cell is an attractive option for users who require only 200-250 barcodes at a time.
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Affiliation(s)
- Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
| | - Vivian Feng
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
| | - Daniel Suárez
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain
- School of Doctoral and Postgraduate Studies, University of La Laguna, 38200 La Laguna, Tenerife, Canary Islands, 38200, Spain
| | - Brent Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
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22
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Vidal A, Wijekoon VB, Viterbo E. Concatenated Nanopore DNA Codes. IEEE Trans Nanobioscience 2024; 23:310-318. [PMID: 38546987 DOI: 10.1109/tnb.2024.3350001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
In nanopore sequencers, single-stranded DNA molecules (or k-mers) enter a small opening in a membrane called a nanopore and modulate the ionic current through the pore, producing a channel output in the form of a noisy piecewise constant signal. An important problem in DNA-based data storage is finding a set of k-mers, i.e. a DNA code, that is robust against noisy sample duplication introduced by nanopore sequencers. Good DNA codes should contain as many k-mers as possible that produce distinguishable current signals (squiggles) as measured by the sequencer. The dissimilarity between squiggles can be estimated using a bound on their pairwise error probability, which is used as a metric for code design. Unfortunately, code construction using the union bound is limited to small k's due to the difficulty of finding maximum cliques in large graphs. In this paper, we construct large codes by concatenating codewords from a base code, thereby packing more information in a single strand while retaining the storage efficiency of the base code. To facilitate decoding, we include a circumfix in the base code to reduce the effect of the nanopore channel memory. We show that the decoding complexity scales as [Formula: see text], where m is the number of concatenated k-mers. Simulations show that the base code error rate is stable as m increases.
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23
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Brinkmann A, Pape K, Uddin S, Woelk N, Förster S, Jessen H, Michel J, Kohl C, Schaade L, Nitsche A. Genome sequencing of the mpox virus 2022 outbreak with amplicon-based Oxford Nanopore MinION sequencing. J Virol Methods 2024; 325:114888. [PMID: 38246565 DOI: 10.1016/j.jviromet.2024.114888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
We present an amplicon-based assay for MinION Nanopore sequencing of mpox virus (MPXV) genomes from clinical specimens, obtaining high-quality results with an average genome coverage of 99% for Ct values of up to 25, and a genome coverage of 97.1% for Ct values from 25 to 30 which are challenging to sequence. This assay is easy to implement in PCR-based workflows and provides accurate genomic data within a short time.
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Affiliation(s)
- Annika Brinkmann
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany.
| | - Katharina Pape
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Steven Uddin
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Niklas Woelk
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Sophie Förster
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Heiko Jessen
- Praxis Jessen and Colleagues, Motzstraße 19, 10777 Berlin, Germany
| | - Janine Michel
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Claudia Kohl
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Lars Schaade
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Andreas Nitsche
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
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24
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Bloomfield M, Hutton S, Velasco C, Burton M, Benton M, Storey M. Oxford nanopore next generation sequencing in a front-line clinical microbiology laboratory without on-site bioinformaticians. Pathology 2024; 56:444-447. [PMID: 37867010 DOI: 10.1016/j.pathol.2023.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 10/24/2023]
Affiliation(s)
- Max Bloomfield
- Department of Microbiology and Molecular Pathology, Wellington Southern Community Laboratories, Wellington, New Zealand; Infection Prevention and Control Committee, Wellington Regional Hospital, Wellington, New Zealand.
| | - Samantha Hutton
- Department of Microbiology and Molecular Pathology, Wellington Southern Community Laboratories, Wellington, New Zealand
| | - Charles Velasco
- Department of Microbiology and Molecular Pathology, Wellington Southern Community Laboratories, Wellington, New Zealand
| | - Megan Burton
- Department of Microbiology and Molecular Pathology, Wellington Southern Community Laboratories, Wellington, New Zealand
| | - Miles Benton
- Genomics and Bioinformatics, Institute of Environmental Science and Research, Kenepuru Science Centre, Wellington, New Zealand
| | - Matt Storey
- Genomics and Bioinformatics, Institute of Environmental Science and Research, Kenepuru Science Centre, Wellington, New Zealand
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25
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Munro R, Wibowo S, Payne A, Loose M. Icarust, a real-time simulator for Oxford Nanopore adaptive sampling. Bioinformatics 2024; 40:btae141. [PMID: 38478392 PMCID: PMC10980563 DOI: 10.1093/bioinformatics/btae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 12/21/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
MOTIVATION Oxford Nanopore Technologies (ONT) sequencers enable real-time generation of sequence data, which allows for concurrent analysis during a run. Adaptive sampling leverages this real-time capability in extremis, rejecting or accepting reads for sequencing based on assessment of the sequence from the start of each read. This functionality is provided by ONT's software, MinKNOW (Oxford Nanopore Technologies). Designing and developing software to take advantage of adaptive sampling can be costly in terms of sequencing consumables, using precious samples and preparing sequencing libraries. MinKNOW addresses this in part by allowing the replay of previously sequenced runs for testing. However, as we show, the sequencing output only partially changes in response to adaptive sampling instructions. Here we present Icarust, a tool enabling more accurate approximations of sequencing runs. Icarust recreates all the required endpoints of MinKNOW to perform adaptive sampling and writes output compatible with current base-callers and analysis pipelines. Icarust serves nanopore signal simulating a MinION or PromethION flow cell experiment from any reference genome using either R9 or R10 pore models. We show that simulating sequencing runs with Icarust provides a realistic testing and development environment for software exploiting the real-time nature of Nanopore sequencing. AVAILABILITY AND IMPLEMENTATION All code is open source and freely available here-https://github.com/LooseLab/Icarust. Icarust is implemented in Rust, with a docker container also available. The data underlying this article will be shared on reasonable request to the corresponding author.
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Affiliation(s)
- Rory Munro
- School of Life Sciences, Medical School, Queens Medical Centre, University of Nottingham, Nottingham NG72RD, United Kingdom
| | - Satrio Wibowo
- School of Life Sciences, Medical School, Queens Medical Centre, University of Nottingham, Nottingham NG72RD, United Kingdom
| | - Alexander Payne
- School of Life Sciences, Medical School, Queens Medical Centre, University of Nottingham, Nottingham NG72RD, United Kingdom
| | - Matthew Loose
- School of Life Sciences, Medical School, Queens Medical Centre, University of Nottingham, Nottingham NG72RD, United Kingdom
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26
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Castelli F, Consolati G. Modelling Annihilation Properties of Positronium Confined in Nanoporous Materials: A Review. Int J Mol Sci 2024; 25:3692. [PMID: 38612506 PMCID: PMC11011886 DOI: 10.3390/ijms25073692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Positronium (Ps) is a valuable probe to investigate nanometric or sub-nanometric cavities in non-metallic materials, where Ps can be confined. Accessible experimental measurements concern the lifetime of trapped Ps, which is largely influenced by pick-off processes, depending on the size of the cavity as well as on the density of the electrons belonging to the surface of the host trap. Another relevant physical quantity is the contact density, that is the electron density at the positron position, which is usually found to be well below the vacuum value. Here, we review the principal models that have been formulated to account and explain for these physical properties of confined Ps. Starting with models, treating Ps as a single particle formulated essentially to study pick-off, we go on to describe more refined two-particle models because a two-body model is the simplest approach able to describe any change in the contact density, observed in many materials. Finally, we consider a theory of Ps annihilation in nanometric voids in which the exchange correlations between the electron of Ps and the outer electrons play a fundamental role. This theory is not usually taken into account in the literature, but it has to be considered for a correct theory of pick-off annihilation processes.
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Affiliation(s)
- Fabrizio Castelli
- Department of Physics “Aldo Pontremoli”, Università degli Studi di Milano, Via Celoria 16, 20133 Milano, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Milano, Via Celoria 16, 20133 Milano, Italy;
| | - Giovanni Consolati
- Istituto Nazionale di Fisica Nucleare, Sezione di Milano, Via Celoria 16, 20133 Milano, Italy;
- Department of Aerospace Science and Technology, Politecnico di Milano, Via La Masa 34, 20156 Milano, Italy
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27
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Zhao C, Wang Y, Chen C, Zhu Y, Miao Z, Mou X, Yuan W, Zhang Z, Li K, Chen M, Liang W, Zhang M, Miao W, Dong Y, Deng D, Wu J, Ke B, Bao R, Geng J. Direct and Continuous Monitoring of Multicomponent Antibiotic Gentamicin in Blood at Single-Molecule Resolution. ACS Nano 2024; 18:9137-9149. [PMID: 38470845 DOI: 10.1021/acsnano.4c00302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Point-of-care monitoring of small molecules in biofluids is crucial for clinical diagnosis and treatment. However, the inherent low degree of recognition of small molecules and the complex composition of biofluids present significant obstacles for current detection technologies. Although nanopore sensing excels in the analysis of small molecules, the direct detection of small molecules in complex biofluids remains a challenge. In this study, we present a method for sensing the small molecule drug gentamicin in whole blood based on the mechanosensitive channel of small conductance in Pseudomonas aeruginosa (PaMscS) nanopore. PaMscS can directly detect gentamicin and distinguish its main components with only a monomethyl difference. The 'molecular sieve' structure of PaMscS enables the direct measurement of gentamicin in human whole blood within 10 min. Furthermore, a continuous monitoring device constructed based on PaMscS achieved continuous monitoring of gentamicin in live rats for approximately 2.5 h without blood consumption, while the drug components can be analyzed in situ. This approach enables rapid and convenient drug monitoring with single-molecule level resolution, which can significantly lower the threshold for drug concentration monitoring and promote more efficient drug use. Moreover, this work also lays the foundation for the future development of continuous monitoring technology with single-molecule level resolution in the living body.
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Affiliation(s)
- Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Chen Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Yibo Zhu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhuang Miao
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xingyu Mou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Weidan Yuan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhihao Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Mutian Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Weibo Liang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wenqian Miao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuhan Dong
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Dong Deng
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, 610041 China
| | - Jianping Wu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Bowen Ke
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Rui Bao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
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28
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Oliden-Sánchez A, Sola-Llano R, Pérez-Pariente J, Gómez-Hortigüela L, Martínez-Martínez V. Confinement of a Styryl Dye into Nanoporous Aluminophosphates: Channels vs. Cavities. Int J Mol Sci 2024; 25:3577. [PMID: 38612388 PMCID: PMC11011965 DOI: 10.3390/ijms25073577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
Styryl dyes are generally poor fluorescent molecules inherited from their flexible molecular structures. However, their emissive properties can be boosted by restricting their molecular motions. A tight confinement into inorganic molecular sieves is a good strategy to yield highly fluorescent hybrid systems. In this work, we compare the confinement effect of two Mg-aluminophosphate zeotypes with distinct pore systems (the AEL framework, a one-dimensional channeled structure with elliptical pores of 6.5 Å × 4.0 Å, and the CHA framework, composed of large cavities of 6.7 Å × 10.0 Å connected by eight-ring narrower windows) for the encapsulation of 4-DASPI styryl dye (trans-4-[4-(Dimethylamino)styryl]-1-methylpyridinium iodide). The resultant hybrid systems display significantly improved photophysical features compared to 4-DASPI in solution as a result of tight confinement in both host inorganic frameworks. Molecular simulations reveal a tighter confinement of 4-DASPI in the elliptical channels of AEL, explaining its excellent photophysical properties. On the other hand, a singular arrangement of 4-DASPI dye is found when confined within the cavity-based CHA framework, where the 4-DASPI molecule spans along two adjacent cavities, with each aromatic ring sitting on these adjacent cavities and the polymethine chain residing within the narrower eight-ring window. However, despite the singularity of this host-guest arrangement, it provides less tight confinement for 4-DASPI than AEL, resulting in a slightly lower quantum yield.
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Affiliation(s)
- Ainhoa Oliden-Sánchez
- Departamento de Química Física, Universidad del País Vasco (UPV/EHU), Apartado 644, 48080 Bilbao, Spain; (A.O.-S.); (R.S.-L.)
| | - Rebeca Sola-Llano
- Departamento de Química Física, Universidad del País Vasco (UPV/EHU), Apartado 644, 48080 Bilbao, Spain; (A.O.-S.); (R.S.-L.)
| | - Joaquín Pérez-Pariente
- Instituto de Catálisis y Petroleoquímica (CSIC), c/Marie Curie 2, Cantoblanco, 28049 Madrid, Spain;
| | - Luis Gómez-Hortigüela
- Instituto de Catálisis y Petroleoquímica (CSIC), c/Marie Curie 2, Cantoblanco, 28049 Madrid, Spain;
| | - Virginia Martínez-Martínez
- Departamento de Química Física, Universidad del País Vasco (UPV/EHU), Apartado 644, 48080 Bilbao, Spain; (A.O.-S.); (R.S.-L.)
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29
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Abu Jalboush S, Wadsworth ID, Sethi K, Rogers LC, Hollis T, Hall AR. Improving the Performance of Selective Solid-State Nanopore Sensing Using a Polyhistidine-Tagged Monovalent Streptavidin. ACS Sens 2024; 9:1602-1610. [PMID: 38451864 DOI: 10.1021/acssensors.4c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Solid-state (SS-) nanopore sensing has gained tremendous attention in recent years, but it has been constrained by its intrinsic lack of selectivity. To address this, we previously established a novel SS-nanopore assay that produces translocation signals only when a target biotinylated nucleic acid fragment binds to monovalent streptavidin (MS), a protein variant with a single high-affinity biotin-binding domain. While this approach has enabled selective quantification of diverse nucleic acid biomarkers, sensitivity enhancements are needed to improve the detection of low-abundance translational targets. Because the translocation dynamics that determine assay efficacy are largely governed by constituent charge characteristics, we here incorporate a polyhistidine-tagged MS (hMS) to alter the component detectability. We investigate the effects of buffer pH, salt concentration, and SS-nanopore diameter on the performance with the alternate reagent, achieve significant improvements in measurement sensitivity and selectivity, and expand the range of device dimensions viable for the assay. We used this improvement to detect as little as 1 nM miRNA spiked into human plasma. Overall, our findings improve the potential for broader applications of SS-nanopores in the quantitative analyses of molecular biomarkers.
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Affiliation(s)
- Sara Abu Jalboush
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Ian D Wadsworth
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Komal Sethi
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - LeAnn C Rogers
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Thomas Hollis
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Adam R Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, United States
- Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
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30
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Li X, Wang Y, Zhang S, Zhang P, Huang S. Nanopore Identification of N-Acetylation by Hydroxylamine Deacetylation (NINAHD). ACS Sens 2024; 9:1359-1371. [PMID: 38449100 DOI: 10.1021/acssensors.3c02350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
N-Acetyl modification, a chemical modification commonly found on biomacromolecules, plays a crucial role in the regulation of cell activities and is related to a variety of diseases. However, due to the instability of N-acetyl modification, accurate and rapid identification of N-acetyl modification with a low measurement cost is still technically challenging. Here, based on hydroxylamine deacetylation and nanopore single molecule chemistry, a universal sensing strategy for N-acetyl modification has been developed. Acetohydroxamic acid (AHA), which is produced by the hydroxylamine deacetylation reaction and serves as a reporter for N-acetylation identification, is specifically sensed by a phenylboronic acid (PBA)-modified Mycobacterium smegmatis porin A (MspA). With this strategy, N-acetyl modifications on RNA, DNA, proteins, and glycans were identified, demonstrating its generality. Specifically, histones can be treated with hydroxylamine deacetylation, from which the generated AHA can represent the amount of N-acetyl modification detected by a nanopore sensor. The unique event features of AHA also demonstrate the robustness of sensing against other interfering analytes in the environment.
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Affiliation(s)
- Xinyue Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
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31
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Ma C, Xu W, Liu W, Xu C, Qin G, Chen D, Sha J. Confined Transport Behavior of Biomolecules within Tilted Nanopores. J Phys Chem B 2024; 128:2792-2798. [PMID: 38471969 DOI: 10.1021/acs.jpcb.3c07417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The transport behavior of biomolecules at the confined nanoscale is very different from that of the bulk state. Numerous disease diagnostics and targeted drug treatments are performed based on nanochannels in cells. The specific structure and shape of nanochannels play an important role in the behavior and efficiency of substance transport. In this paper, we fabricated nanopores with different tilt angles and the same diameters using focused ion beam. The capture frequency and the blocking current amplitude of λ-DNA within large-angle nanopores decrease obviously, suggesting an increase in the energy barrier of large-angle nanopores and the fact that they stretch biomolecules to thinness. Most importantly, large-angle nanopores slow down λ-DNA transport by 2-4 times. MD simulations find that the sloped electroosmotic flow inside the tilted nanopores is the main factor contributing to the transport phenomena. The increase in the capture time of biomolecules by nanopores assists in obtaining more biological information from the current trajectories. Our study provides a new understanding of substance transport in specially shaped nanopores, which can be instrumental in providing fresh inspiration and approaches to the biomedical field.
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Affiliation(s)
- Chaofan Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Wei Xu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Wei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Changhui Xu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Guangle Qin
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Automation Research Institute, Lianyungang, Jiangsu 222000, China
| | - Dapeng Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Automation Research Institute, Lianyungang, Jiangsu 222000, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
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32
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Chen S, He W, Li J, Xu D, Zhao R, Zhu L, Wu H, Xu F. Pulley Effect in the Capture of DNA Translocation through Solid-State Nanopores. Langmuir 2024; 40:5799-5808. [PMID: 38501264 DOI: 10.1021/acs.langmuir.3c03596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Nanopores are powerful single-molecule sensors for analyzing biomolecules such as DNA and proteins. Understanding the dynamics of DNA capture and translocation through nanopores is essential for optimizing their performance. In this study, we examine the effects of applied voltage and pore diameter on current blockage, translocation time, collision, and capture location by translocating λ-DNA through 5.7 and 16 nm solid-state nanopores. Ionic current changes are used to infer DNA conformations during translocation. We find that translocation time increases with pore diameter, which can be attributed to the decrease of the stall force. Linear and exponential decreases of collision frequency with voltage are observed in the 16 and 5.7 nm pores, respectively, indicating a free energy barrier in the small pore. Moreover, the results reveal a voltage-dependent bias in the capture location toward the DNA ends, which is explained by a "pulley effect" deforming the DNA as it approaches the pore. This study provides insights into the physics governing DNA capture and translocation, which can be useful for promoting single-file translocation to enhance nanopore sensing.
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Affiliation(s)
- Shulan Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang 330029, China
| | - Wen He
- Analysis and Testing Center, Nanchang Hangkong University, Nanchang 330063, China
| | - Jun Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Derong Xu
- Jiangxi Institute of Translational Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Rui Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Libo Zhu
- School of Medical Imageology, Wannan Medical College, Wuhu 241002, China
| | - Hongwen Wu
- Jiangxi Institute of Respiratory Disease, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Fei Xu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- Jiangxi Institute of Respiratory Disease, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- National Regional Center for Respiratory Medicine, China-Japan Friendship Jiangxi Hospital, Nanchang 330006, China
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Ulrich JU, Epping L, Pilz T, Walther B, Stingl K, Semmler T, Renard BY. Nanopore adaptive sampling effectively enriches bacterial plasmids. mSystems 2024; 9:e0094523. [PMID: 38376263 PMCID: PMC10949517 DOI: 10.1128/msystems.00945-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Bacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from the low abundance of plasmid DNA in those samples. Although sample preparation methods can enrich the proportion of plasmid DNA before sequencing, these methods are expensive and laborious, and they might introduce a bias by enriching only for specific plasmid DNA sequences. Nanopore adaptive sampling could overcome these issues by rejecting uninteresting DNA molecules during the sequencing process. In this study, we assess the application of adaptive sampling for the enrichment of low-abundant plasmids in known bacterial isolates using two different adaptive sampling tools. We show that a significant enrichment can be achieved even on expired flow cells. By applying adaptive sampling, we also improve the quality of de novo plasmid assemblies and reduce the sequencing time. However, our experiments also highlight issues with adaptive sampling if target and non-target sequences span similar regions. IMPORTANCE Antimicrobial resistance causes millions of deaths every year. Mobile genetic elements like bacterial plasmids are key drivers for the dissemination of antimicrobial resistance genes. This makes the characterization of plasmids via DNA sequencing an important tool for clinical microbiologists. Since plasmids are often underrepresented in bacterial samples, plasmid sequencing can be challenging and laborious. To accelerate the sequencing process, we evaluate nanopore adaptive sampling as an in silico method for the enrichment of low-abundant plasmids. Our results show the potential of this cost-efficient method for future plasmid research but also indicate issues that arise from using reference sequences.
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Affiliation(s)
- Jens-Uwe Ulrich
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
- Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
- Phylogenomics Unit, Center for Artificial Intelligence in Public Health Research, Robert Koch Institute, Wildau, Germany
| | - Lennard Epping
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Tanja Pilz
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | - Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Bernhard Y. Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
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Kudjordjie EN, Schmidt-Høier AS, Brøndum MB, Johnsen MG, Nicolaisen M, Vestergård M. Early assessment of fungal and oomycete pathogens in greenhouse irrigation water using Oxford nanopore amplicon sequencing. PLoS One 2024; 19:e0300381. [PMID: 38489283 PMCID: PMC10942031 DOI: 10.1371/journal.pone.0300381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
Water-borne plant pathogenic fungi and oomycetes are a major threat in greenhouse production systems. Early detection and quantification of these pathogens would enable us to ascertain both economic and biological thresholds required for a timely treatment, thus improving effective disease management. Here, we used Oxford nanopore MinION amplicon sequencing to analyze microbial communities in irrigation water collected from greenhouses used for growing tomato, cucumber and Aeschynanthus sp. Fungal and oomycete communities were characterized using primers that amplify the full internal transcribed spacer (ITS) region. To assess the sensitivity of the MinION sequencing, we spiked serially diluted mock DNA into the DNA isolated from greenhouse water samples prior to library preparation. Relative abundances of fungal and oomycete reads were distinct in the greenhouse irrigation water samples and in water samples from setups with tomato that was inoculated with Fusarium oxysporum. Sequence reads derived from fungal and oomycete mock communities were proportionate in the respective serial dilution samples, thus confirming the suitability of MinION amplicon sequencing for environmental monitoring. By using spike-ins as standards to test the reliability of quantification using the MinION, we found that the detection of spike-ins was highly affected by the background quantities of fungal or oomycete DNA in the sample. We observed that spike-ins having shorter length (538bp) produced reads across most of our dilutions compared to the longer spikes (>790bp). Moreover, the sequence reads were uneven with respect to dilution series and were least retrievable in the background samples having the highest DNA concentration, suggesting a narrow dynamic range of performance. We suggest continuous benchmarking of the MinION sequencing to improve quantitative metabarcoding efforts for rapid plant disease diagnostic and monitoring in the future.
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Affiliation(s)
- Enoch Narh Kudjordjie
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | | | | | | | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Mette Vestergård
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
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Deng Q, Lin P, Gu H, Zhuang X, Wang F. Silk Protein-Based Nanoporous Microsphere for Controllable Drug Delivery through Self-Assembly in Ionic Liquid System. Biomacromolecules 2024; 25:1527-1540. [PMID: 38307005 DOI: 10.1021/acs.biomac.3c01104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
Ionic liquids (ILs) showed a promising application prospect in the field of biomedicine due to their unique recyclability, modifiability, and structure adjustability. In this study, nanoporous microsphere of silk protein and blending with poly(d,l-lactic acid) as model drug delivery was fabricated, respectively, through an IL-induced self-assembly method. Their morphology, structure, and thermal properties were comparably investigated through scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, differential scanning calorimetry, X-ray diffraction, and thermogravimetric analyses, and the interaction mechanisms were also discussed to elucidate the effect of structure on drug delivery kinetics. The pure protein exhibited a bigger nanopore size in the microsphere compared to the composite one, facilitating more effective drug loading up to 88.7%. However, drug release was over 53.5% for the composite during initial 4 h, while pure protein was only about half of the composite. Both of them exhibited sustained slow release after 24 h and anticancer efficacy. Furthermore, the favorable compatibility between drug and microsphere vehicle was found and experienced improved thermal stability upon encapsulation, which could protect the drug molecules in high temperature at 200 °C. When the protein and its composite self-assembled to microspheres in ILs due to electrostatic and hydrophobic interaction, the drug could be infiltrated into the nanoporous matrix through biophysical action, and the protein structure displayed reversible transition during delivery. The sustained slow release from pure SF was attributed to the high β-sheet block action and strong drug-protein interactions, whose strength could be tuned through blending poly(d,l-lactic acid) with protein. These findings indicated that the SF-based nanoporous microspheres formed from IL self-assembled system are an ideal and potential drug delivery vehicle which can be incorporated into various biomaterials in the future.
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Affiliation(s)
- Qianqian Deng
- Center of Analysis and Testing, Nanjing Normal University, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Ping Lin
- Center of Analysis and Testing, Nanjing Normal University, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Hanling Gu
- Center of Analysis and Testing, Nanjing Normal University, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Xincheng Zhuang
- Center of Analysis and Testing, Nanjing Normal University, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Fang Wang
- Center of Analysis and Testing, Nanjing Normal University, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
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36
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Lee D, Noh J, Moon SY, Shin TJ, Choi YK, Park J. Pectin Nanoporous Structures Prepared via Salt-Induced Phase Separation and Ambient Azeotropic Evaporation Processes. Biomacromolecules 2024; 25:1709-1723. [PMID: 38377481 DOI: 10.1021/acs.biomac.3c01230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Polysaccharide nanoporous structures are suitable for various applications, ranging from biomedical scaffolds to adsorption materials, owing to their biocompatibility and large surface areas. Pectin, in particular, can create 3D nanoporous structures in aqueous solutions by binding with calcium cations and creating nanopores by phase separation; this process involves forming hydrogen bonds between alcohols and pectin chains in water and alcohol mixtures and the resulting penetration of alcohols into calcium-bound pectin gels. However, owing to the dehydration and condensation of polysaccharide chains during drying, it has proven to be challenging to maintain the 3D nanoporous structure without using a freeze-drying process or supercritical fluid. Herein, we report a facile method for creating polysaccharide-based xerogels, involving the co-evaporation of water with a nonsolvent (e.g., a low-molecular-weight hydrophobic alcohol such as isopropyl or n-propyl alcohol) at ambient conditions. Experiments and coarse-grained molecular dynamics simulations confirmed that salt-induced phase separation and hydrogen bonding between hydrophobic alcohols and pectin chains were the dominant processes in mixtures of pectin, water, and hydrophobic alcohols. Furthermore, the azeotropic evaporation of water and alcohol mixed in approximately 1:1 molar ratios was maintained during the natural drying process under ambient conditions, preventing the hydration and aggregation of the hydrophilic pectin chains. These results introduce a simple and convenient process to produce 3D polysaccharide xerogels under ambient conditions.
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Affiliation(s)
- Dabin Lee
- Department of Chemical Engineering, Department of Intelligent Energy and Industry, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Juran Noh
- Department of Material Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Su-Young Moon
- Gas & Carbon Convergent Research Center, Chemical & Process Technology, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Tae Joo Shin
- UNIST Central Research Facilities & School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeol Kyo Choi
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Juhyun Park
- Department of Chemical Engineering, Department of Intelligent Energy and Industry, Chung-Ang University, Seoul 06974, Republic of Korea
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Zhao Y, Su Z, Zhang X, Wu D, Wu Y, Li G. Recent advances in nanopore-based analysis for carbohydrates and glycoconjugates. Anal Methods 2024; 16:1454-1467. [PMID: 38415741 DOI: 10.1039/d3ay02040a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Saccharides are not only the basic constituents and nutrients of living organisms, but also participate in various life activities, and play important roles in cell recognition, immune regulation, development, cancer, etc. The analysis of carbohydrates and glycoconjugates is a necessary means to study their transformations and physiological roles in living organisms. Existing detection techniques can hardly meet the requirements for the analysis of carbohydrates and glycoconjugates in complex matrices as they are expensive, involve complex derivatization, and are time-consuming. Nanopore sensing technology, which is amplification-free and label-free, and is a high-throughput process, provides a new solution for the identification and sequencing of carbohydrates and glycoconjugates. This review highlights recent advances in novel nanopore-based single-molecule sensing technologies for the detection of carbohydrates and glycoconjugates and discusses the advantages and challenges of nanopore sensing technologies. Finally, current issues and future perspectives are discussed with the aim of improving the performance of nanopores in complex media diagnostic applications, as well as providing a new direction for the quantification of glycan chains and the study of glycan chain properties and functions.
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Affiliation(s)
- Yan Zhao
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Zhuoqun Su
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Xue Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Yongning Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
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Pozo G, Albuja-Quintana M, Larreátegui L, Gutiérrez B, Fuentes N, Alfonso-Cortés F, Torres MDL. First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies. G3 (Bethesda) 2024; 14:jkae014. [PMID: 38244218 PMCID: PMC10917520 DOI: 10.1093/g3journal/jkae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered [International union for conservation of nature (IUCN)]. It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are keys for the management of endangered species, but this requires a reference genome, which until now was unavailable for A. f. fusciceps. The present study reports the first whole-genome sequence and assembly of A. f. fusciceps generated using Oxford Nanopore long reads. DNA was extracted from a subadult male, and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable with other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species.
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Affiliation(s)
- Gabriela Pozo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
| | - Martina Albuja-Quintana
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Lizbeth Larreátegui
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Bernardo Gutiérrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Nathalia Fuentes
- Proyecto Washu/Fundación Naturaleza y Arte, Quito 170521, Ecuador
| | | | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
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39
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Fan P, Zhang S, Wang Y, Li T, Zhang H, Zhang P, Huang S. Nanopore analysis of salvianolic acids in herbal medicines. Nat Commun 2024; 15:1970. [PMID: 38443335 PMCID: PMC10915175 DOI: 10.1038/s41467-024-45543-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
Natural herbs, which contain pharmacologically active compounds, have been used historically as medicines. Conventionally, the analysis of chemical components in herbal medicines requires time-consuming sample separation and state-of-the-art analytical instruments. Nanopore, a versatile single molecule sensor, might be suitable to identify bioactive compounds in natural herbs. Here, a phenylboronic acid appended Mycobacterium smegmatis porin A (MspA) nanopore is used as a sensor for herbal medicines. A variety of bioactive compounds based on salvianolic acids, including caffeic acid, protocatechuic acid, protocatechualdehyde, salvianic acid A, rosmarinic acid, lithospermic acid, salvianolic acid A and salvianolic acid B are identified. Using a custom machine learning algorithm, analyte identification is performed with an accuracy of 99.0%. This sensing principle is further used with natural herbs such as Salvia miltiorrhiza, Rosemary and Prunella vulgaris. No complex sample separation or purification is required and the sensing device is highly portable.
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Affiliation(s)
- Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
- Institute for the Environment and Health, Nanjing University Suzhou Campus, 215163, Suzhou, China
| | - Tian Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Hanhan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China.
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40
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Dong M, Kshirsagar A, Politza AJ, Guan W. High Fidelity Machine-Learning-Assisted False Positive Discrimination in Loop-Mediated Isothermal Amplification Using Nanopore-Based Sizing and Counting. ACS Nano 2024; 18:7170-7179. [PMID: 38393338 DOI: 10.1021/acsnano.3c12053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, sensitive, and cost-effective method for developing point-of-care nucleic acid testing due to its isothermal nature. Yet, LAMP can suffer from the issue of false positives, which can compromise the specificity of the results. LAMP false positives typically arise due to contamination, nonspecific amplification, and nonspecific signal reporting (intercalating dyes, colorimetric, turbidity, etc.). While dye-labeled primers or probes have been introduced for multiplexed detection and enhanced specificity in LAMP assays, they carry the risk of reaction inhibition. This inhibition can result from the labeled primers with fluorophores or quenchers and probes that do not fully dissociate during reaction. This work demonstrated a nanopore-based system for probe-free LAMP readouts by employing amplicon sizing and counting, analogous to an electronic version of gel electrophoresis. We first developed a model to explore LAMP kinetics and verified distinct patterns between true and false positives via gel electrophoresis. Subsequently, we implemented nanopore sized counting and calibrated the event charge deficit (ECD) values and frequencies to ensure a fair analysis of amplicon profiles. This sized counting method, integrated with machine learning, achieved 91.67% accuracy for false positive discrimination, enhancing LAMP's reliability for nucleic acid detection.
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Affiliation(s)
- Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Aneesh Kshirsagar
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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41
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Fan P, Cao Z, Zhang S, Wang Y, Xiao Y, Jia W, Zhang P, Huang S. Nanopore analysis of cis-diols in fruits. Nat Commun 2024; 15:1969. [PMID: 38443434 PMCID: PMC10915164 DOI: 10.1038/s41467-024-46303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
Natural fruits contain a large variety of cis-diols. However, due to the lack of a high-resolution sensor that can simultaneously identify all cis-diols without a need of complex sample pretreatment, direct and rapid analysis of fruits in a hand-held device has never been previously reported. Nanopore, a versatile single molecule sensor, can be specially engineered to perform this task. A hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore modified with a sole phenylboronic acid (PBA) adapter is prepared. This engineered MspA accurately recognizes 1,2-diphenols, alditols, α-hydroxy acids and saccharides in prune, grape, lemon, different varieties of kiwifruits and commercial juice products. Assisted with a custom machine learning program, an accuracy of 99.3% is reported and the sample pretreatment is significantly simplified. Enantiomers such as DL-malic acids can also be directly identified, enabling sensing of synthetic food additives. Though demonstrated with fruits, these results suggest wide applications of nanopore in food and drug administration uses.
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Affiliation(s)
- Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
- Institute for the Environment and Health, Nanjing University Suzhou Campus, 215163, Suzhou, China
| | - Yunqi Xiao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China.
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42
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Fu Y, Gu J, Chen LJ, Xiong M, Zhao J, Xiao X, Zhou J, Li Z, Li Y. A prospective study of nanopore-targeted sequencing in the diagnosis of central nervous system infections. Microbiol Spectr 2024; 12:e0331723. [PMID: 38294222 PMCID: PMC10913467 DOI: 10.1128/spectrum.03317-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Central nervous system (CNS) infections are a leading cause of death in patients. Nanopore-targeted sequencing (NTS) has begun to be used for pathogenic microbial detection. This study aims to evaluate the ability of NTS in the detection of pathogens in cerebrospinal fluid (CSF) through a prospective study. Fifty CSF specimens collected from 50 patients with suspected CNS infections went through three methods including NTS, metagenomic next-generation sequencing (mNGS), and microbial culture in parallel. When there was an inconsistency between NTS results and the results of the mNGS, the 16S rDNA gene was amplified followed by Sanger sequencing to further verify pathogens detected by NTS. Among 50 CSF specimens, 76% were NTS-positive, which is lower than mNGS (94.0%), yet higher than microbial culture (16.0%). The overall validation rate, diagnostic accordance rate (DAR), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of NTS were 86.7%, 50.0%, 71.0%, 15.8%, 57.9%, and 25.0%, respectively. In the CSF total nucleated cell (TNC) number ≤10 cells/µL, DAR, specificity, and PPV were 20%, 11.1%, and 11.1%, whereas in that with CSF TNC number >10 cells/µL, DAR, sensitivity, specificity, PPV, and NPV were 57.5%, 70.0%, 20.0%, 72.4%, and 18.2%, respectively. Although NTS has a higher microbial detection rate than microbial culture, it should combine CSF TNC result to evaluate the value of NTS for the diagnosis of CNS infections. IMPORTANCE This study aims to prospectively evaluate the ability of nanopore-targeted sequencing (NTS) in the detection of pathogens in cerebrospinal fluid (CSF). It was the first time combining mNGS and microbial culture to verify the NTS-positive results also using 16S rDNA amplification with Sanger sequencing. Although microbial culture was thought to be the gold standard for pathogens detection and diagnosis of infectious diseases, this study suggested that microbial culture of CSF is not the most appropriate way for diagnosing central nervous system (CNS) infection. NTS should be recommended to be used in CSF for diagnosing CNS infection. When evaluating the value of NTS for diagnosis of CNS infections, the results of CSF TNC should be combined, and NTS-positive result is observed to be more reliable in patients with CSF TNC level >10 cells/μL.
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Affiliation(s)
- Yu Fu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jihong Gu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liang-Jun Chen
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mengyuan Xiong
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jin Zhao
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao Xiao
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Junying Zhou
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yirong Li
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan, China
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43
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Graham KA, Gomez J, Primm TP, Houston R. Comparison of nine extraction methods for bacterial identification using the ONT MinION sequencer. Int J Legal Med 2024; 138:351-360. [PMID: 37775594 DOI: 10.1007/s00414-023-03092-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
The Anthrax mailings bioterrorism attack in 2001 revealed the need for universal and rapid microbial forensic analyses on unknown biological evidence. However, the gold standard for bacterial identification includes culturing isolates, which is laborious. Molecular approaches for bacterial identification revolve around 16S ribosomal gene sequencing using Sanger or next generation sequencing (NGS) platforms, but these techniques are laboratory-based and can also be time-consuming. The Oxford Nanopore Technologies (ONT) MinION sequencer can generate long read lengths that span the entire bacterial 16S rRNA gene and accurately identify the species level. This platform can be used in the field, allowing on-site evidence analysis. However, it requires higher quantities of pure DNA compared to other sequencing platforms; thus, the extraction method for bacterial DNA is critical for downstream analysis, which to date are tailored toward a priori knowledge of the species' taxonomic grouping. During an attack, the investigative team may not know what species they are handling; therefore, identifying an extraction method that can handle all bacterial groups and generate clean DNA for the MinION is useful for microbial forensic analysis. The purpose of this study was to identify a "universal" extraction method that can be coupled with ONT MinION sequencing for use in forensic situations for rapid identification. It also evaluated the cloud-based data analysis software provided by ONT, EPI2ME. No "universal" extraction method was identified as optimal for downstream MinION sequencing. However, the DNeasy PowerSoil Kit and Noda et al. Chelex-100 method gave comparable sequencing results and could be used as rapid extraction techniques. This study showed that the ONT 16S Barcoding Kit 1-24 coupled with the 16S FASTQ workflow might not be the best for use in forensic situations where species-level identification needs to be obtained, as most alignments were approximately 89% accurate. In all seven test organisms and nine extraction methods, accurate species identification was only obtained in 63% of the cases.
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Affiliation(s)
- Kari A Graham
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340-2525, USA
| | - Javier Gomez
- Department of Biological Sciences, College of Science and Engineering Technology, Sam Houston State University, 2000 Ave I, Huntsville, TX, 77341, USA
| | - Todd P Primm
- Department of Biological Sciences, College of Science and Engineering Technology, Sam Houston State University, 2000 Ave I, Huntsville, TX, 77341, USA
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340-2525, USA.
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44
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Dostálková A, Zdeňková K, Bartáčková J, Čermáková E, Kapisheva M, Lopez Marin MA, Kouba V, Sýkora P, Chmel M, Bartoš O, Dresler J, Demnerová K, Rumlová M, Bartáček J. Prevalence of SARS-CoV-2 variants in Prague wastewater determined by nanopore-based sequencing. Chemosphere 2024; 351:141162. [PMID: 38218235 DOI: 10.1016/j.chemosphere.2024.141162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
The early detection of upcoming disease outbreaks is essential to avoid both health and economic damage. The last four years of COVID-19 pandemic have proven wastewater-based epidemiology is a reliable system for monitoring the spread of SARS-CoV-2, a causative agent of COVID-19, in an urban population. As this monitoring enables the identification of the prevalence of spreading variants of SARS-CoV-2, it could provide a critical tool in the fight against this viral disease. In this study, we evaluated the presence of variants and subvariants of SARS-CoV-2 in Prague wastewater using nanopore-based sequencing. During August 2021, the data clearly showed that the number of identified SARS-CoV-2 RNA copies increased in the wastewater earlier than in clinical samples indicating the upcoming wave of the Delta variant. New SARS-CoV-2 variants consistently prevailed in wastewater samples around a month after they already prevailed in clinical samples. We also analyzed wastewater samples from smaller sub-sewersheds of Prague and detected significant differences in SARS-CoV-2 lineage progression dynamics among individual localities studied, e.g., suggesting faster prevalence of new variants among the sites with highest population density and mobility.
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Affiliation(s)
- Alžběta Dostálková
- Department of Biotechnology, University of Chemistry and Technology Prague, Czech Republic; National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Kamila Zdeňková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic.
| | - Jana Bartáčková
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
| | - Eliška Čermáková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Marina Kapisheva
- National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Marco A Lopez Marin
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Vojtěch Kouba
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
| | - Petr Sýkora
- PVK a.s., Prague Water Supply and Sewerage Company, Czech Republic
| | - Martin Chmel
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic; Military Health Institute, Military Medical Agency, Czech Republic
| | - Oldřich Bartoš
- Military Health Institute, Military Medical Agency, Czech Republic
| | - Jiří Dresler
- Military Health Institute, Military Medical Agency, Czech Republic
| | - Kateřina Demnerová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology Prague, Czech Republic; National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Jan Bartáček
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
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45
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Sandler SE, Weckman NE, Yorke S, Das A, Chen K, Gutierrez R, Keyser UF. Sensing the DNA-mismatch tolerance of catalytically inactive Cas9 via barcoded DNA nanostructures in solid-state nanopores. Nat Biomed Eng 2024; 8:325-334. [PMID: 37550424 DOI: 10.1038/s41551-023-01078-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/30/2023] [Indexed: 08/09/2023]
Abstract
Single-molecule quantification of the strength and sequence specificity of interactions between proteins and nucleic acids would facilitate the probing of protein-DNA binding. Here we show that binding events between the catalytically inactive Cas9 ribonucleoprotein and any pre-defined short sequence of double-stranded DNA can be identified by sensing changes in ionic current as suitably designed barcoded linear DNA nanostructures with Cas9-binding double-stranded DNA overhangs translocate through solid-state nanopores. We designed barcoded DNA nanostructures to study the relationships between DNA sequence and the DNA-binding specificity, DNA-binding efficiency and DNA-mismatch tolerance of Cas9 at the single-nucleotide level. Nanopore-based sensing of DNA-barcoded nanostructures may help to improve the design of efficient and specific ribonucleoproteins for biomedical applications, and could be developed into sensitive protein-sensing assays.
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Affiliation(s)
- Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Nicole E Weckman
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Institute for Studies in Transdisciplinary Engineering Education & Practice, Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Canada
| | - Sarah Yorke
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, Cambridge, UK
| | - Akashaditya Das
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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46
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Dorey A, Howorka S. Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics. Nat Chem 2024; 16:314-334. [PMID: 38448507 DOI: 10.1038/s41557-023-01322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 07/14/2023] [Indexed: 03/08/2024]
Abstract
Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.
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Affiliation(s)
- Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
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47
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Li Z, Yi Y, Liu L, Wu H. One step forward for nanopore protein sequencing. Clin Transl Med 2024; 14:e1615. [PMID: 38468491 PMCID: PMC10928323 DOI: 10.1002/ctm2.1615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Affiliation(s)
- Ziyi Li
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Analytical Chemistry for Living BiosystemsInstitute of Chemistry Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yakun Yi
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Analytical Chemistry for Living BiosystemsInstitute of Chemistry Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyInstitute of High Energy Physics Chinese Academy of SciencesBeijingChina
| | - Hai‐Chen Wu
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Analytical Chemistry for Living BiosystemsInstitute of Chemistry Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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48
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Devriese M, Rouquie J, Da Silva S, Benassaya N, Maillard L, Dewez M, Caillat-Zucman S, Werner G, Taupin JL. Single locus HLA sequencing with the nanopore technology for HLA disease association diagnosis. HLA 2024; 103:e15424. [PMID: 38516926 DOI: 10.1111/tan.15424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/09/2024] [Accepted: 02/19/2024] [Indexed: 03/23/2024]
Abstract
Associations between HLA genotype and disease susceptibility encompass almost all the classic HLA loci. The level of typing resolution enabling a correct identification of an HLA disease susceptibility gene depends on the disease itself and/or on the accumulated knowledge about the molecular involvement of the HLA allele(s) engaged. Therefore, the application of Next Generation Sequencing technologies to HLA disease association, which would improve typing resolution, could prove useful to better understand disease severity. In the present study, we tested a nanopore sequencing approach developed by Omixon Biocomputing Ltd, dedicated to on-demand locus typing for HLA and disease, as an alternative to the conventional widely used sequence specific oligoprobe (SSO) approach. A total of 145 DNA samples used in routine diagnosis by SSO were retrospectively analyzed with nanopore technology, for HLA-A*02 immunotherapy decision for A*29, B*27, B*51, B*57 identification in class I, and DRB1, DQA1, and DQB1 for bullous dermatosis, rheumatoid arthritis, diabetes, and celiac disease requests in class II. Each locus was typed in a separate experiment, except for DQB1 and DQA1, which were analyzed together. Concordance between typings reached 100% for all the loci tested. Ambiguities by nanopore were only found for missing exon coverage. This approach was found to be very well adapted to the routine flow imposed by the SSO technique. This study illustrates the use of the new NanoTYPE MONO kit for single locus HLA sequencing for HLA and disease association diagnosis.
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Affiliation(s)
- Magali Devriese
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
- INSERM UMR976, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Julien Rouquie
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
| | - Sephora Da Silva
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
| | - Nadine Benassaya
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
| | - Lucie Maillard
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
| | - Mathieu Dewez
- Omixon Biocomputing Ltd. H-1117 Budapest, Kaposvár, Hungary
| | - Sophie Caillat-Zucman
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
- INSERM UMR976, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Gregory Werner
- Omixon Biocomputing Ltd. H-1117 Budapest, Kaposvár, Hungary
| | - Jean-Luc Taupin
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint Louis, Paris, France
- INSERM UMR976, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
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49
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Ma K, Cheung YH, Kirlikovali KO, Xie H, Idrees KB, Wang X, Islamoglu T, Xin JH, Farha OK. Fibrous Zr-MOF Nanozyme Aerogels with Macro-Nanoporous Structure for Enhanced Catalytic Hydrolysis of Organophosphate Toxins. Adv Mater 2024; 36:e2300951. [PMID: 37310697 DOI: 10.1002/adma.202300951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/07/2023] [Indexed: 06/14/2023]
Abstract
Metal-organic frameworks (MOFs) with Lewis acid catalytic sites, such as zirconium-based MOFs (Zr-MOFs), comprise a growing class of phosphatase-like nanozymes that can degrade toxic organophosphate pesticides and nerve agents. Rationally engineering and shaping MOFs from as-synthesized powders into hierarchically porous monoliths is essential for their use in emerging applications, such as filters for air and water purification and personal protection gear. However, several challenges still limit the production of practical MOF composites, including the need for sophisticated reaction conditions, low MOF catalyst loadings in the resulting composites, and poor accessibility to MOF-based active sites. To overcome these limitations, a rapid synthesis method is developed to introduce Zr-MOF nanozyme coating into cellulose nanofibers, resulting in the formation of processable monolithic aerogel composites with high MOF loadings. These composites contain Zr-MOF nanozymes embedded in the structure, and hierarchical macro-micro porosity enables excellent accessibility to catalytic active sites. This multifaceted rational design strategy, including the selection of a MOF with many catalytic sites, fine-tuning the coating morphology, and the fabrication of a hierarchically structured monolithic aerogel, renders synergistic effects toward the efficient continuous hydrolytic detoxification of organophosphorus-based nerve agent simulants and pesticides from contaminated water.
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Affiliation(s)
- Kaikai Ma
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
- School of Fashion and Textiles, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, SAR, China
| | - Yuk Ha Cheung
- School of Fashion and Textiles, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, SAR, China
| | - Kent O Kirlikovali
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Haomiao Xie
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Karam B Idrees
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Xiaoliang Wang
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Timur Islamoglu
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - John H Xin
- School of Fashion and Textiles, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, SAR, China
| | - Omar K Farha
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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Shi X, Pumm AK, Maffeo C, Kohler F, Feigl E, Zhao W, Verschueren D, Golestanian R, Aksimentiev A, Dietz H, Dekker C. A DNA turbine powered by a transmembrane potential across a nanopore. Nat Nanotechnol 2024; 19:338-344. [PMID: 37884658 PMCID: PMC10950783 DOI: 10.1038/s41565-023-01527-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023]
Abstract
Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines at many scales, developing functional synthetic turbines at the nanoscale has remained challenging. Here, we experimentally demonstrate rationally designed nanoscale DNA origami turbines with three chiral blades. These DNA nanoturbines are 24-27 nm in height and diameter and can utilize transmembrane electrochemical potentials across nanopores to drive DNA bundles into sustained unidirectional rotations of up to 10 revolutions s-1. The rotation direction is set by the designed chirality of the turbine. All-atom molecular dynamics simulations show how hydrodynamic flows drive this turbine. At high salt concentrations, the rotation direction of turbines with the same chirality is reversed, which is explained by a change in the anisotropy of the electrophoretic mobility. Our artificial turbines operate autonomously in physiological conditions, converting energy from naturally abundant electrochemical potentials into mechanical work. The results open new possibilities for engineering active robotics at the nanoscale.
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Affiliation(s)
- Xin Shi
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
- Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Anna-Katharina Pumm
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching, Germany
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Fabian Kohler
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Elija Feigl
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Wenxuan Zhao
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Daniel Verschueren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
- The SW7 Group, London, UK
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, UK
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Hendrik Dietz
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
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