1
|
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 PMCID: PMC11032468 DOI: 10.1073/pnas.2400203121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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.
Collapse
Affiliation(s)
| | - S. M. Saiduzzaman
- School of Engineering, University of California, Santa Cruz, CA95064
| | - Zach J. Walker
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Tanner N. Wells
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Jesse X. Wayment
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Ephraim M. Ong
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | | | | | | | | | - Aaron R. Hawkins
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Holger Schmidt
- School of Engineering, University of California, Santa Cruz, CA95064
| |
Collapse
|
2
|
Jalboush SA, 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 PMCID: PMC11056946 DOI: 10.1021/acssensors.4c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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.
Collapse
Affiliation(s)
- Sara Abu Jalboush
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Ian D. Wadsworth
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - Komal Sethi
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - LeAnn C. Rogers
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Thomas Hollis
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Adam R. Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
- Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| |
Collapse
|
3
|
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 : THE ACS JOURNAL OF SURFACES AND COLLOIDS 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] [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.
Collapse
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
| |
Collapse
|
4
|
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] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
Collapse
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
| |
Collapse
|
5
|
Acharjee MC, Ledden B, Thomas B, He X, Messina T, Giurleo J, Talaga D, Li J. Aggregation and Oligomerization Characterization of ß-Lactoglobulin Protein Using a Solid-State Nanopore Sensor. SENSORS (BASEL, SWITZERLAND) 2023; 24:81. [PMID: 38202943 PMCID: PMC10781269 DOI: 10.3390/s24010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024]
Abstract
Protein aggregation is linked to many chronic and devastating neurodegenerative human diseases and is strongly associated with aging. This work demonstrates that protein aggregation and oligomerization can be evaluated by a solid-state nanopore method at the single molecule level. A silicon nitride nanopore sensor was used to characterize both the amyloidogenic and native-state oligomerization of a model protein ß-lactoglobulin variant A (βLGa). The findings from the nanopore measurements are validated against atomic force microscopy (AFM) and dynamic light scattering (DLS) data, comparing βLGa aggregation from the same samples at various stages. By calibrating with linear and circular dsDNA, this study estimates the amyloid fibrils' length and diameter, the quantity of the βLGa aggregates, and their distribution. The nanopore results align with the DLS and AFM data and offer additional insight at the level of individual protein molecular assemblies. As a further demonstration of the nanopore technique, βLGa self-association and aggregation at pH 4.6 as a function of temperature were measured at high (2 M KCl) and low (0.1 M KCl) ionic strength. This research highlights the advantages and limitations of using solid-state nanopore methods for analyzing protein aggregation.
Collapse
Affiliation(s)
- Mitu C. Acharjee
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Brad Ledden
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Brian Thomas
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Xianglan He
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
| | - Troy Messina
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Department of Physics, Berea College, Berea, KY 40404, USA
| | - Jason Giurleo
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - David Talaga
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Department of Chemistry, Sokol Institute, Montclair State University, Montclair, NJ 07043, USA
| | - Jiali Li
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
| |
Collapse
|
6
|
Jena MK, Mittal S, Manna SS, Pathak B. Deciphering DNA nucleotide sequences and their rotation dynamics with interpretable machine learning integrated C 3N nanopores. NANOSCALE 2023; 15:18080-18092. [PMID: 37916991 DOI: 10.1039/d3nr03771a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
A solid-state nanopore combined with the quantum transport method has garnered substantial attention and intrigue for DNA sequencing due to its potential for providing rapid and accurate sequencing results, which could have numerous applications in disease diagnosis and personalized medicine. However, the intricate and multifaceted nature of the experimental protocol poses a formidable challenge in attaining precise single nucleotide analysis. Here, we report a machine learning (ML) framework combined with the quantum transport method to accelerate high-throughput single nucleotide recognition with C3N nanopores. The optimized eXtreme Gradient Boosting Regression (XGBR) algorithm has predicted the fingerprint transmission of each unknown nucleotide and their rotation dynamics with root mean square error scores as low as 0.07. Interpretability of ML black box models with the game theory-based SHapley Additive exPlanation method has provided a quasi-explanation for the model working principle and the complex relationship between electrode-nucleotide coupling and transmission. Moreover, a comprehensive ML classification of nucleotides based on binary, ternary, and quaternary combinations shows maximum accuracy and F1 scores of 100%. The results suggest that ML in tandem with a nanopore device can potentially alleviate the experimental hurdles associated with quantum tunneling and facilitate fast and high-precision DNA sequencing.
Collapse
Affiliation(s)
- Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| | - Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| | - Surya Sekhar Manna
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| |
Collapse
|
7
|
Salehirozveh M, Kure Larsen AK, Stojmenovic M, Thei F, Dong M. In-situ PLL-g-PEG Functionalized Nanopore for Enhancing Protein Characterization. Chem Asian J 2023; 18:e202300515. [PMID: 37497831 DOI: 10.1002/asia.202300515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/03/2023] [Indexed: 07/28/2023]
Abstract
Single-molecule nanopore detection technology has revolutionized proteomics research by enabling highly sensitive and label-free detection of individual proteins. Herein, we designed a small, portable, and leak-free flowcell made of PMMA for nanopore experiments. In addition, we developed an in situ functionalizing PLL-g-PEG approach to produce non-sticky nanopores for measuring the volume of diseases-relevant biomarker, such as the Alpha-1 antitrypsin (AAT) protein. The in situ functionalization method allows continuous monitoring, ensuring adequate functionalization, which can be directly used for translocation experiments. The functionalized nanopores exhibit improved characteristics, including an increased nanopore lifetime and enhanced translocation events of the AAT proteins. Furthermore, we demonstrated the reduction in the translocation event's dwell time, along with an increase in current blockade amplitudes and translocation numbers under different voltage stimuli. The study also successfully measures the single AAT protein volume (253 nm3 ), which closely aligns with the previously reported hydrodynamic volume. The real-time in situ PLL-g-PEG functionalizing method and the developed nanopore flowcell hold great promise for various nanopores applications involving non-sticky single-molecule characterization.
Collapse
Affiliation(s)
- Mostafa Salehirozveh
- Department Of Physics And Astronomy, University of Bologna, Bologna, Italy
- Elements srl, Cesena, Italy
| | - Anne-Kathrine Kure Larsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Sino-Danish Center for Education and Research, Aarhus, Denmark
- University of the Chinese Academy of Sciences, Beijing, China
| | | | | | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Biology - Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| |
Collapse
|
8
|
Roelen Z, Tabard-Cossa V. Synthesis of length-tunable DNA carriers for nanopore sensing. PLoS One 2023; 18:e0290559. [PMID: 37611030 PMCID: PMC10446168 DOI: 10.1371/journal.pone.0290559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise hard-to-detect molecules such as small, weakly-charged proteins. However, existing carrier designs can often introduce drawbacks to nanopore experiments including higher levels of cost/complexity and carrier-pore interactions that lead to ambiguous signals and elevated clogging rates. In this work, we present a simple method of carrier production based on sticky-ended DNA molecules that emphasizes ease-of-synthesis and compatibility with nanopore sensing and analysis. In particular, our method incorporates the ability to flexibly control the length of the DNA carriers produced, enhancing the multiplexing potential of this carrier system through the separable nanopore signals they could generate for distinct targets. A proof-of-concept nanopore experiment is also presented, involving carriers produced by our method with multiple lengths and attached to DNA nanostructure targets, in order to validate the capabilities of the system. As the breadth of applications for nanopore sensors continues to expand, the availability of tools such as those presented here to help translate the outcomes of these applications into robust nanopore signals will be of major importance.
Collapse
Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | | |
Collapse
|
9
|
Roelen Z, Briggs K, Tabard-Cossa V. Analysis of Nanopore Data: Classification Strategies for an Unbiased Curation of Single-Molecule Events from DNA Nanostructures. ACS Sens 2023; 8:2809-2823. [PMID: 37436112 PMCID: PMC10913896 DOI: 10.1021/acssensors.3c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Nanopores are versatile single-molecule sensors that are being used to sense increasingly complex mixtures of structured molecules with applications in molecular data storage and disease biomarker detection. However, increased molecular complexity presents additional challenges to the analysis of nanopore data, including more translocation events being rejected for not matching an expected signal structure and a greater risk of selection bias entering this event curation process. To highlight these challenges, here, we present the analysis of a model molecular system consisting of a nanostructured DNA molecule attached to a linear DNA carrier. We make use of recent advances in the event segmentation capabilities of Nanolyzer, a graphical analysis tool provided for nanopore event fitting, and describe approaches to the event substructure analysis. In the process, we identify and discuss important sources of selection bias that emerge in the analysis of this molecular system and consider the complicating effects of molecular conformation and variable experimental conditions (e.g., pore diameter). We then present additional refinements to existing analysis techniques, allowing for improved separation of multiplexed samples, fewer translocation events rejected as false negatives, and a wider range of experimental conditions for which accurate molecular information can be extracted. Increasing the coverage of analyzed events within nanopore data is not only important for characterizing complex molecular samples with high fidelity but is also becoming essential to the generation of accurate, unbiased training data as machine-learning approaches to data analysis and event identification continue to increase in prevalence.
Collapse
Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | | |
Collapse
|
10
|
Gu C, Yu Z, Li X, Zhu X, Jin C, Cao Z, Dong S, Luo J, Ye Z, Liu Y. Experimental study on single biomolecule sensing using MoS 2-graphene heterostructure nanopores. NANOSCALE 2022; 15:266-274. [PMID: 36477179 DOI: 10.1039/d2nr04485d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Solid-state nanopores play an important role in sensing single-biomolecules such as DNA and proteins. However, an ultra-short translocation time hinders nanopores from acquiring more detailed information about biomolecules, and further applications such as sequencing and molecular structure analysis are limited. Related studies have shown that MoS2 has no obvious impediment to biomolecule translocation while graphene may cause obstacles to this process. By combining these two-dimensional materials, nanopores might slow the biomolecule passage. Herein, we fabricated sub-10 nm ultra-thin MoS2-graphene heterostructure nanopores with high stability and tested both dsDNA and native protein (BSA) at the single-molecule level in experiments for the first time. Some special signals with advanced order are observed, which may reflect the shape change of the BSA molecules during the slow translocation process. The results show that the translocation time of BSA is slowed down up to more than 100 ms and the signal length and form are determined by the extent of interaction between the BSA and the heterostructure nanopore. The weak interaction between the BSA and the MoS2 layer increases the translocation probability, and meanwhile, the strong interaction of the graphene layer to BSA slows down the translocation and changes its structure. Therefore, our findings indicate the possibilities of slowing down the single-biomolecule translocation and the capability of acquiring more detailed information about biomolecules using MoS2-graphene heterostructure nanopores.
Collapse
Affiliation(s)
- Chaoming Gu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Zhoubin Yu
- State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Xiaojie Li
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Xin Zhu
- Chemistry Research Laboratory, Oxford University, Oxford, OX1 3TA, UK
| | - Chuanhong Jin
- State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Zhen Cao
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Shurong Dong
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Jikui Luo
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Zhi Ye
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Yang Liu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| |
Collapse
|
11
|
Wang Y, Yuan J, Deng H, Zhang Z, Ma QDY, Wu L, Weng L. Procedural Data Processing for Single-Molecule Identification by Nanopore Sensors. BIOSENSORS 2022; 12:1152. [PMID: 36551119 PMCID: PMC9775113 DOI: 10.3390/bios12121152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Nanopores are promising single-molecule sensing devices that have been successfully used for DNA sequencing, protein identification, as well as virus/particles detection. It is important to understand and characterize the current pulses collected by nanopore sensors, which imply the associated information of the analytes, including the size, structure, and surface charge. Therefore, a signal processing program, based on the MATLAB platform, was designed to characterize the ionic current signals of nanopore measurements. In a movable data window, the selected current segment was analyzed by the adaptive thresholds and corrected by multi-functions to reduce the noise obstruction of pulse signals. Accordingly, a set of single molecular events was identified, and the abundant information of current signals with the dwell time, amplitude, and current pulse area was exported for quantitative analysis. The program contributes to the efficient and fast processing of nanopore signals with a high signal-to-noise ratio, which promotes the development of the nanopore sensing devices in various fields of diagnosis systems and precision medicine.
Collapse
Affiliation(s)
- Yupeng Wang
- School of Materials Science & Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Jianxuan Yuan
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Haofeng Deng
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Ziang Zhang
- School of Materials Science & Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Qianli D. Y. Ma
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Lingzhi Wu
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Lixing Weng
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| |
Collapse
|
12
|
Dynamics of DNA Through Solid‐state Nanopores Fabricated by Controlled Dielectric Breakdown. Chem Asian J 2022; 17:e202200888. [DOI: 10.1002/asia.202200888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/28/2022] [Indexed: 11/19/2022]
|
13
|
Lin CY, Fotis R, Xia Z, Kavetsky K, Chou YC, Niedzwiecki DJ, Biondi M, Thei F, Drndić M. Ultrafast Polymer Dynamics through a Nanopore. NANO LETTERS 2022; 22:8719-8727. [PMID: 36315497 DOI: 10.1021/acs.nanolett.2c03546] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ultrathin nanopore sensors allow single-molecule and polymer measurements at sub-microsecond time resolution enabled by high current signals (∼10-30 nA). We demonstrate for the first time the experimental probing of the ultrafast translocation and folded dynamics of double-stranded DNA (dsDNA) through a nanopore at 10 MHz bandwidth with acquisition of data points per 25 ns (150 MB/s). By introducing a rigorous algorithm, we are able to accurately identify each current level present within translocation events and elucidate the dynamic folded and unfolded behaviors. The remarkable sensitivity of this system reveals distortions of short-lived folded states at a lower bandwidth. This work revisits probing of dsDNA as a model polymer and develops broadly applicable methods. The combined improvements in sensor signals, instrumentation, and large data analysis methods uncover biomolecular dynamics at unprecedentedly small time scales.
Collapse
Affiliation(s)
- Chih-Yuan Lin
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Riley Fotis
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zehui Xia
- Goeppert LLC, Philadelphia, Pennsylvania 19146, United States
| | - Kyril Kavetsky
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Material Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yung-Chien Chou
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | | | | | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
14
|
Abrao‐Nemeir I, Bentin J, Meyer N, Janot J, Torrent J, Picaud F, Balme S. Investigation of α-Synuclein and Amyloid-β(42)-E22Δ Oligomers Using SiN Nanopore Functionalized with L-Dopa. Chem Asian J 2022; 17:e202200726. [PMID: 36038502 PMCID: PMC9826174 DOI: 10.1002/asia.202200726] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/25/2022] [Indexed: 01/11/2023]
Abstract
Solid-state nanopores are an emerging technology used as a high-throughput, label-free analytical method for the characterization of protein aggregation in an aqueous solution. In this work, we used Levodopamine to coat a silicon nitride nanopore surface that was fabricated through a dielectric breakdown in order to reduce the unspecific adsorption. The coating of inner nanopore wall by investigation of the translocation of heparin. The functionalized nanopore was used to investigate the aggregation of amyloid-β and α-synuclein, two biomarkers of degenerative diseases. In the first application, we demonstrate that the α-synuclein WT is more prone to form dimers than the variant A53T. In the second one, we show for the Aβ(42)-E22Δ (Osaka mutant) that the addition of Aβ(42)-WT monomers increases the polymorphism of oligomers, while the incubation with Aβ(42)-WT fibrils generates larger aggregates.
Collapse
Affiliation(s)
- Imad Abrao‐Nemeir
- European Institute of Membranes, UMR5635University of Montpelier, ENCSM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France
| | - Jeremy Bentin
- Laboratory of Nanomedicin, Imagery and Therapeutics, EA4662University hospital center of BesançonUniversity of Bourgogne-Franche-Comté (UFR Sciences et Techniques)16 route de Gray25030BesançonFrance
| | - Nathan Meyer
- European Institute of Membranes, UMR5635University of Montpelier, ENCSM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France,Neurological institute of MontpellierUniversity of Montpellier, INSERM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France
| | - Jean‐Marc Janot
- European Institute of Membranes, UMR5635University of Montpelier, ENCSM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France
| | - Joan Torrent
- Neurological institute of MontpellierUniversity of Montpellier, INSERM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France
| | - Fabien Picaud
- Laboratory of Nanomedicin, Imagery and Therapeutics, EA4662University hospital center of BesançonUniversity of Bourgogne-Franche-Comté (UFR Sciences et Techniques)16 route de Gray25030BesançonFrance
| | - Sebastien Balme
- European Institute of Membranes, UMR5635University of Montpelier, ENCSM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France
| |
Collapse
|
15
|
Trivedi M, Gupta R, Nirmalkar N. Electroosmotic transport and current rectification of viscoelastic electrolyte in a conical pore nanomembrane. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.120755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
16
|
Soni N, Freundlich N, Ohayon S, Huttner D, Meller A. Single-File Translocation Dynamics of SDS-Denatured, Whole Proteins through Sub-5 nm Solid-State Nanopores. ACS NANO 2022; 16:11405-11414. [PMID: 35785960 PMCID: PMC7613183 DOI: 10.1021/acsnano.2c05391] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The ability to routinely identify and quantify the complete proteome from single cells will greatly advance medicine and basic biology research. To meet this challenge of single-cell proteomics, single-molecule technologies are being developed and improved. Most approaches, to date, rely on the analysis of polypeptides, resulting from digested proteins, either in solution or immobilized on a surface. Nanopore biosensing is an emerging single-molecule technique that circumvents surface immobilization and is optimally suited for the analysis of long biopolymers, as has already been shown for DNA sequencing. However, proteins, unlike DNA molecules, are not uniformly charged and harbor complex tertiary structures. Consequently, the ability of nanopores to analyze unfolded full-length proteins has remained elusive. Here, we evaluate the use of heat denaturation and the anionic surfactant sodium dodecyl sulfate (SDS) to facilitate electrokinetic nanopore sensing of unfolded proteins. Specifically, we characterize the voltage dependence translocation dynamics of a wide molecular weight range of proteins (from 14 to 130 kDa) through sub-5 nm solid-state nanopores, using a SDS concentration below the critical micelle concentration. Our results suggest that proteins' translocation dynamics are significantly slower than expected, presumably due to the smaller nanopore diameters used in our study and the role of the electroosmotic force opposing the translocation direction. This allows us to distinguish among the proteins of different molecular weights based on their dwell time and electrical charge deficit. Given the simplicity of the protein denaturation assay and circumvention of the tailor-made necessities for sensing protein of different folded sizes, shapes, and charges, this approach can facilitate the development of a whole proteome identification technique.
Collapse
Affiliation(s)
- Neeraj Soni
- Department
of Biomedical Engineering, Technion−IIT, Haifa, 3200003 Israel
- Russell
Berrie Nanotechnology Institute Technion−IIT, Haifa, 3200003 Israel
| | - Noam Freundlich
- Department
of Biomedical Engineering, Technion−IIT, Haifa, 3200003 Israel
| | - Shilo Ohayon
- Department
of Biomedical Engineering, Technion−IIT, Haifa, 3200003 Israel
| | - Diana Huttner
- Department
of Biomedical Engineering, Technion−IIT, Haifa, 3200003 Israel
| | - Amit Meller
- Department
of Biomedical Engineering, Technion−IIT, Haifa, 3200003 Israel
- Russell
Berrie Nanotechnology Institute Technion−IIT, Haifa, 3200003 Israel
| |
Collapse
|
17
|
Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
Collapse
Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| |
Collapse
|
18
|
Wei G, Hu R, Li Q, Lu W, Liang H, Nan H, Lu J, Li J, Zhao Q. Oligonucleotide Discrimination Enabled by Tannic Acid-Coordinated Film-Coated Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6443-6453. [PMID: 35544765 DOI: 10.1021/acs.langmuir.2c00638] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Discrimination of nucleotides serves as the basis for DNA sequencing using solid-state nanopores. However, the translocation of DNA is usually too fast to be detected, not to mention nucleotide discrimination. Here, we utilized polyphenolic TA and Fe3+, an attractive metal-organic thin film, and achieved a fast and robust surface coating for silicon nitride nanopores. The hydrophilic coating layer can greatly reduce the low-frequency noise of an original unstable nanopore, and the nanopore size can be finely tuned in situ at the nanoscale by simply adjusting the relative ratio of Fe3+ and TA monomers. Moreover, the hydrogen bonding interaction formed between the hydroxyl groups provided by TA and the phosphate groups of DNAs significantly increases the residence time of a short double-strand (100 bp) DNA. More importantly, we take advantage of the different strengths of hydrogen bonding interactions between the hydroxyl groups provided by TA and the analytes to discriminate between two oligonucleotide samples (oligodeoxycytidine and oligodeoxyadenosine) with similar sizes and lengths, of which the current signal patterns are significantly different using the coated nanopore. The results shed light on expanding the biochemical functionality of surface coatings on solid-state nanopores for future biomedical applications.
Collapse
Affiliation(s)
- Guanghao Wei
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Qiuhui Li
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Wenlong Lu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Hanyu Liang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, 310022 Hangzhou, China
| | - Hexin Nan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, 310022 Hangzhou, China
| | - Jing Lu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, 226010 Jiangsu, China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, China
| | - Juan Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, 310022 Hangzhou, China
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, 226010 Jiangsu, China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, China
| |
Collapse
|
19
|
Rivas F, Erxleben D, Smith I, Rahbar E, DeAngelis PL, Cowman MK, Hall AR. Methods for isolating and analyzing physiological hyaluronan: a review. Am J Physiol Cell Physiol 2022; 322:C674-C687. [PMID: 35196167 PMCID: PMC8977137 DOI: 10.1152/ajpcell.00019.2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 01/01/2023]
Abstract
The carbohydrate hyaluronan (or hyaluronic acid, HA) is found in all human tissues and biofluids where it has wide-ranging functions in health and disease that are dictated by both its abundance and size. Consequently, hyaluronan evaluation in physiological samples has significant translational potential. Although the analytical tools and techniques for probing other biomolecules such as proteins and nucleic acids have become standard approaches in biochemistry, those available for investigating hyaluronan are less well established. In this review, we survey methods related to the assessment of native hyaluronan in biological specimens, including protocols for separating it from biological matrices and technologies for determining its concentration and molecular weight.
Collapse
Affiliation(s)
- Felipe Rivas
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Dorothea Erxleben
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Ian Smith
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Elaheh Rahbar
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Paul L DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Mary K Cowman
- Department of Biomedical Engineering, New York University Tandon School of Engineering, New York, New York
- Department of Orthopedic Surgery, New York University Grossman School of Medicine, New York, New York
| | - Adam R Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, North Carolina
| |
Collapse
|
20
|
Rivas F, DeAngelis PL, Rahbar E, Hall AR. Optimizing the sensitivity and resolution of hyaluronan analysis with solid-state nanopores. Sci Rep 2022; 12:4469. [PMID: 35296752 PMCID: PMC8927330 DOI: 10.1038/s41598-022-08533-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
Hyaluronan (HA) is an essential carbohydrate in vertebrates that is a potentially robust bioindicator due to its critical roles in diverse physiological functions in health and disease. The intricate size-dependent function that exists for HA and its low abundance in most biological fluids have highlighted the need for sensitive technologies to provide accurate and quantitative assessments of polysaccharide molecular weight and concentration. We have demonstrated that solid state (SS-) nanopore technology can be exploited for this purpose, given its molecular sensitivity and analytical capacity, but there remains a need to further understand the impacts of experimental variables on the SS-nanopore signal for optimal interpretation of results. Here, we use model quasi-monodisperse HA polymers to determine the dependence of HA signal characteristics on a range of SS-nanopore measurement conditions, including applied voltage, pore diameter, and ionic buffer asymmetry. Our results identify important factors for improving the signal-to-noise ratio, resolution, and sensitivity of HA analysis with SS-nanopores.
Collapse
Affiliation(s)
- Felipe Rivas
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA
| | - Paul L DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK, 73104, USA
| | - Elaheh Rahbar
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA
| | - Adam R Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA. .,Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
| |
Collapse
|
21
|
Zou H, Wen S, Wu X, Wong KW, Yam C. DNA sequencing based on electronic tunneling in a gold nanogap: a first-principles study. Phys Chem Chem Phys 2022; 24:5748-5754. [PMID: 35191434 DOI: 10.1039/d1cp04910k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Deoxyribonucleic acid (DNA) sequencing has found wide applications in medicine including treatment of diseases, diagnosis and genetics studies. Rapid and cost-effective DNA sequencing has been achieved by measuring the transverse electronic conductance as a single-stranded DNA is driven through a nanojunction. With the aim of improving the accuracy and sensitivity of DNA sequencing, we investigate the electron transport properties of DNA nucleobases within gold nanogaps based on first-principles quantum transport simulations. Considering the fact that the DNA bases can rotate within the nanogap during measurements, different nucleobase orientations and their corresponding residence time within the nanogap are explicitly taken into account based on their energetics. This allows us to obtain an average current that can be compared directly to experimental measurements. Our results indicate that bare gold electrodes show low distinguishability among the four DNA nucleobases while the distinguishability can be substantially enhanced with sulfur atom decorated electrodes. We further optimized the size of the nanogap by maximizing the residence time of the desired orientation.
Collapse
Affiliation(s)
- Hao Zou
- Beijing Computational Science Research Center, Haidian District, Beijing 100193, China.
| | - Shizheng Wen
- Beijing Computational Science Research Center, Haidian District, Beijing 100193, China. .,Jiangsu Province Key Laboratory of Modern Measurement Technology and Intelligent Systems, School of Physics and Electronic Electrical Engineering, Huaiyin Normal University, Huaian 223300, China
| | - Xiaoyan Wu
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen 518109, China
| | - Ka-Wai Wong
- Genvida Technology Company Limited, Hong Kong, China.
| | - ChiYung Yam
- Beijing Computational Science Research Center, Haidian District, Beijing 100193, China. .,Shenzhen JL Computational Science and Applied Research Institute, Shenzhen 518109, China
| |
Collapse
|
22
|
Saharia J, Bandara YMNDY, Kim MJ. Investigating protein translocation in the presence of an electrolyte concentration gradient across a solid-state nanopore. Electrophoresis 2022; 43:785-792. [PMID: 35020223 DOI: 10.1002/elps.202100346] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/19/2021] [Accepted: 12/22/2021] [Indexed: 12/21/2022]
Abstract
Electrolyte chemistry plays an important role in the transport properties of analytes through nanopores. Here, we report the translocation properties of the protein human serum transferrin (hSTf) in asymmetric LiCl salt concentrations with either positive (Ctrans /Ccis < 1) or negative chemical gradients (Ctrans /Ccis > 1). The cis side concentration was fixed at 4 M for positive chemical gradients and at 0.5 M LiCl for negative chemical gradients, while the trans side concentration varied between 0.5 to 4 M which resulted in six different configurations, respectively, for both positive and negative gradient types. For positive chemical gradient conditions, translocations were observed in all six configurations for at least one voltage polarity whereas with negative gradient conditions, dead concentrations where no events at either polarity were observed. The flux of Li+ and Cl- ions and their resultant cation or anion enrichment zones, as well as the interplay of electrophoretic and electroosmotic transport directions, would determine whether hSTf can traverse across the pore.
Collapse
Affiliation(s)
- Jugal Saharia
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| | - Y M Nuwan D Y Bandara
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA.,Department of Bioengineering, University of California, Riverside, CA, USA
| | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| |
Collapse
|
23
|
Tsutsui M, Arima A, Yokota K, Baba Y, Kawai T. Ionic heat dissipation in solid-state pores. SCIENCE ADVANCES 2022; 8:eabl7002. [PMID: 35148181 PMCID: PMC8836805 DOI: 10.1126/sciadv.abl7002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Energy dissipation in solid-state nanopores is an important issue for their use as a sensor for detecting and analyzing individual objects in electrolyte solution by ionic current measurements. Here, we report on evaluations of heating via diffusive ion transport in the nanoscale conduits using thermocouple-embedded SiNx pores. We found a linear rise in the nanopore temperature with the input electrical power suggestive of steady-state ionic heat dissipation in the confined nanospace. Meanwhile, the heating efficiency was elucidated to become higher in a smaller pore due to a rapid decrease in the through-water thermal conduction for cooling the fluidic channel. The scaling law suggested nonnegligible influence of the heating to raise the temperature of single-nanometer two-dimensional nanopores by a few kelvins under the standard cross-membrane voltage and ionic strength conditions. The present findings may be useful in advancing our understanding of ion and mass transport phenomena in nanopores.
Collapse
Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Akihide Arima
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya 464-8603, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa 761-0395, Japan
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya 464-8603, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| |
Collapse
|
24
|
Xing XL, Liao QB, Ahmed SA, Wang D, Ren S, Qin X, Ding XL, Xi K, Ji LN, Wang K, Xia XH. Single Molecule DNA Analysis Based on Atomic-Controllable Nanopores in Covalent Organic Frameworks. NANO LETTERS 2022; 22:1358-1365. [PMID: 35080401 DOI: 10.1021/acs.nanolett.1c04633] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We explored the application of two-dimensional covalent organic frameworks (2D COFs) in single molecule DNA analysis. Two ultrathin COF nanosheets were exfoliated with pore sizes of 1.1 nm (COF-1.1) and 1.3 nm (COF-1.3) and covered closely on a quartz nanopipette with an orifice of 20 ± 5 nm. COF nanopores exhibited high size selectivity for fluorescent dyes and DNA molecules. The transport of long (calf thymus DNA) and short (DNA-80) DNA molecules through the COF nanopores was studied. Because of the strong interaction between DNA bases and the organic backbones of COFs, the DNA-80 was transported through the COF-1.1 nanopore at a speed of 270 μs/base, which is the slowest speed ever observed compared with 2D inorganic nanomaterials. This study shows that the COF nanosheet can work individually as a nanopore monomer with controllable pore size like its biological counterparts.
Collapse
Affiliation(s)
- Xiao-Lei Xing
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qiao-Bo Liao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Saud Asif Ahmed
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Dongni Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shibin Ren
- School of Pharmaceutical and Materials Engineering, Taizhou University, Taizhou 317000, P. R. China
| | - Xiang Qin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xin-Lei Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Kai Xi
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| |
Collapse
|
25
|
Fu J, Wu L, Hu G, Li F, Ge Q, Lu Z, Tu J. Solid-state nanopore analysis on the conformation change of DNA polymerase I induced by a DNA substrate. Analyst 2022; 147:3087-3095. [DOI: 10.1039/d2an00567k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We studied the conformational changes between a Klenow fragment and its monomer complex with a DNA substrate using a SiN nanopore and found that the monomer complex has a tighter structure and transports slower.
Collapse
Affiliation(s)
- Jiye Fu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Linlin Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Gang Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Fuyao Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| |
Collapse
|
26
|
Sampad MJN, Zhang H, Yuzvinsky TD, Stott MA, Hawkins AR, Schmidt H. Optical trapping assisted label-free and amplification-free detection of SARS-CoV-2 RNAs with an optofluidic nanopore sensor. Biosens Bioelectron 2021; 194:113588. [PMID: 34474277 PMCID: PMC8400458 DOI: 10.1016/j.bios.2021.113588] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/16/2021] [Accepted: 08/23/2021] [Indexed: 11/29/2022]
Abstract
Ultrasensitive, versatile sensors for molecular biomarkers are a critical component of disease diagnostics and personalized medicine as the COVID-19 pandemic has revealed in dramatic fashion. Integrated electrical nanopore sensors can fill this need via label-free, direct detection of individual biomolecules, but a fully functional device for clinical sample analysis has yet to be developed. Here, we report amplification-free detection of SARS-CoV-2 RNAs with single molecule sensitivity from clinical nasopharyngeal swab samples on an electro-optofluidic chip. The device relies on optically assisted delivery of target carrying microbeads to the nanopore for single RNA detection after release. A sensing rate enhancement of over 2,000x with favorable scaling towards lower concentrations is demonstrated. The combination of target specificity, chip-scale integration and rapid detection ensures the practicality of this approach for COVID-19 diagnosis over the entire clinically relevant concentration range from 104-109 copies/mL.
Collapse
Affiliation(s)
| | - Han Zhang
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Thomas D Yuzvinsky
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Matthew A Stott
- ECEn Department, Brigham Young University, 450 Engineering Building, Provo, UT, 84602, USA
| | - Aaron R Hawkins
- ECEn Department, Brigham Young University, 450 Engineering Building, Provo, UT, 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.
| |
Collapse
|
27
|
Kiakojouri A, Frank I, Nadimi E. In-plane graphene/h-BN/graphene heterostructures with nanopores for electrical detection of DNA nucleotides. Phys Chem Chem Phys 2021; 23:25126-25135. [PMID: 34729571 DOI: 10.1039/d1cp03597e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The in-plane heterostructure of graphene and h-BN has unique physical and electrical characteristics, which can be exploited for single-molecule DNA sequencing. On this account, we propose a nanostructure based on a nanopore in graphene/h-BN/graphene heterostructures as a viable approach for in-plane electrical detection. The insulating h-BN layer changes the charge transport to the quantum tunneling regime, which is very sensitive to the electrostatic interactions induced by nucleotides during their translocation through the nanopore. Density functional theory (DFT) is utilized to study the membrane/nanopore interactions as well as their interactions with different nucleotides (dAMP, dGMP, dCMP, and dTMP). The results indicate that the nucleotides show stronger interactions with nanopores in h-BN rather than nanopores in pristine graphene. For the calculation of electronic transport, non-equilibrium Green's function (NEGF) formalism at the first principles level is employed. The in-plane currents at different applied voltages are calculated in the presence of different nucleotides in the nanopore. The sensitivity of the proposed nanostructure towards different nucleotides is measured based on the current modulation induced by each nucleotide. The graphene/h-BN/graphene heterostructure shows higher sensitivity toward different nucleotides compared to a similar structure consisting of pristine graphene and can be considered as a promising candidate for DNA sequencing applications.
Collapse
Affiliation(s)
- Ali Kiakojouri
- Center for Computational Micro and Nanoelectronics, Faculty of Electrical Engineering, K. N. Toosi University of Technology, 16317-14191 Tehran, Iran.
| | - Irmgard Frank
- Theoretische Chemie, Universität Hannover, Callinstr. 3A, 30167 Hannover, Germany
| | - Ebrahim Nadimi
- Center for Computational Micro and Nanoelectronics, Faculty of Electrical Engineering, K. N. Toosi University of Technology, 16317-14191 Tehran, Iran.
| |
Collapse
|
28
|
Nouri R, Jiang Y, Tang Z, Lian XL, Guan W. Detection of SARS-CoV-2 with Solid-State CRISPR-Cas12a-Assisted Nanopores. NANO LETTERS 2021; 21:8393-8400. [PMID: 34542296 PMCID: PMC8491552 DOI: 10.1021/acs.nanolett.1c02974] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/16/2021] [Indexed: 05/12/2023]
Abstract
The outbreak of the SARS-CoV-2 caused the disease COVID-19 to spread globally. Specific and sensitive detection of SARS-CoV-2 facilitates early intervention and prevents the disease from spreading. Here, we present a solid-state CRISPR-Cas12a-assisted nanopore (SCAN) sensing strategy for the specific detection of SARS-CoV-2. We introduced a nanopore-sized counting method to measure the cleavage ratio of reporters, which is used as a criterion for positive/negative classification. A kinetic cleavage model was developed and validated to predict the reporter size distributions. The model revealed the trade-offs between sensitivity, turnaround time, and false-positive rate of the SARS-CoV-2 SCAN. With preamplification and a 30 min CRISPR Cas12a assay, we achieved excellent specificity against other common human coronaviruses and a limit of detection of 13.5 copies/μL (22.5 aM) of viral RNA at a confidence level of 95%. These results suggested that the SCAN could provide a rapid, sensitive, and specific analysis of SARS-CoV-2.
Collapse
Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
| | - Yuqian Jiang
- Department of Biomedical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
- Huck Institutes of the Life Sciences,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
| | - Zifan Tang
- Department of Electrical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
| | - Xiaojun Lance Lian
- Department of Biomedical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
- Huck Institutes of the Life Sciences,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
- Department of Biology, 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
| |
Collapse
|
29
|
Szuttor K, Kreissl P, Holm C. A numerical investigation of analyte size effects in nanopore sensing systems. J Chem Phys 2021; 155:134902. [PMID: 34624966 DOI: 10.1063/5.0065085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the relative length of the translocating molecule. Our simulations show a significantly smaller ionic current for DNA molecules that are shorter than the pore at low salt concentrations. These effects can be ascribed to the polarization of the ion cloud along the DNA that leads to an opposing electric dipole field. Our results for DNA shine light on the observed discrepancy between infinite pore models and experimental data on various sized DNA complexes.
Collapse
Affiliation(s)
- Kai Szuttor
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Patrick Kreissl
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| |
Collapse
|
30
|
Rahman M, Sampad MJN, Hawkins A, Schmidt H. Recent advances in integrated solid-state nanopore sensors. LAB ON A CHIP 2021; 21:3030-3052. [PMID: 34137407 PMCID: PMC8372664 DOI: 10.1039/d1lc00294e] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.
Collapse
Affiliation(s)
- Mahmudur Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA. and Dhaka University of Engineering & Technology, Gazipur, Bangladesh
| | | | - Aaron Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA.
| |
Collapse
|
31
|
Sen P, Hoi H, Gupta M. Low Noise Hybrid Nanopore with Engineered OmpG and Bilayer MoS 2. ACS APPLIED BIO MATERIALS 2021; 4:5416-5424. [DOI: 10.1021/acsabm.1c00095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Payel Sen
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton Alberta, Canada
| | - Hiofan Hoi
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton Alberta, Canada
| | - Manisha Gupta
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton Alberta, Canada
| |
Collapse
|
32
|
Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
Collapse
Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| |
Collapse
|
33
|
Sharma RK, Agrawal I, Dai L, Doyle P, Garaj S. DNA Knot Malleability in Single-Digit Nanopores. NANO LETTERS 2021; 21:3772-3779. [PMID: 33661654 DOI: 10.1021/acs.nanolett.0c05142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Knots in long DNA molecules are prevalent in biological systems and serve as a model system for investigating static and dynamic properties of biopolymers. We explore the dynamics of knots in double-stranded DNA in a new regime of nanometer-scale confinement, large forces, and short time scales, using solid-state nanopores. We show that DNA knots undergo isomorphic translocation through a nanopore, retaining their equilibrium morphology by swiftly compressing in a lateral direction to fit the constriction. We observe no evidence of knot tightening or jamming, even for single-digit nanopores. We explain the observations as the malleability of DNA, characterized by sharp buckling of the DNA in nanopores, driven by the transient disruption of base pairing. Our molecular dynamics simulations support the model. These results are relevant not only for the understanding of DNA packing and manipulation in living cells but also for the polymer physics of DNA and the development of nanopore-based sequencing technologies.
Collapse
Affiliation(s)
- Rajesh Kumar Sharma
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, Singapore 117546, Singapore
| | - Ishita Agrawal
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, P. R. China
| | - Patrick Doyle
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Slaven Garaj
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, Singapore 117546, Singapore
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| |
Collapse
|
34
|
Tang Z, Dong M, He X, Guan W. On Stochastic Reduction in Laser-Assisted Dielectric Breakdown for Programmable Nanopore Fabrication. ACS APPLIED MATERIALS & INTERFACES 2021; 13:13383-13391. [PMID: 33705089 DOI: 10.1021/acsami.0c23106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The controlled dielectric breakdown emerged as a promising alternative toward accessible solid-state nanopore fabrication. Several prior studies have shown that laser-assisted dielectric breakdown could help control the nanopore position and reduce the possibility of forming multiple pores. Here, we developed a physical model to estimate the probability of forming a single nanopore under different combinations of the laser power and the electric field. This model relies on the material- and experiment-specific parameters: the Weibull statistical parameters and the laser-induced photothermal etching rate. Both the model and our experimental data suggest that a combination of a high laser power and a low electric field is statistically favorable for forming a single nanopore at a programmed location. While this model relies on experiment-specific parameters, we anticipate it could provide the experimental insights for nanopore fabrication by the laser-assisted dielectric breakdown method, enabling broader access to solid-state nanopores and their sensing applications.
Collapse
Affiliation(s)
- Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Xiaodong He
- Department of Electrical 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
| |
Collapse
|
35
|
Yadav P, Cao Z, Barati Farimani A. DNA Detection with Single-Layer Ti 3C 2 MXene Nanopore. ACS NANO 2021; 15:4861-4869. [PMID: 33660990 DOI: 10.1021/acsnano.0c09595] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nanopore based sequencing is an exciting alternative to the conventional sequencing methods as it allows for high-throughput sequencing with lower reagent costs and time requirements. Biological nanopores, such as α-hemolysin, are subject to breakdown under thermal, electrical, and mechanical stress after being used millions of times. On the contrary, two-dimensional (2D) nanomaterials have been explored as a solid-state platform for the sequencing of DNA. Their subnanometer thickness and outstanding mechanical properties have made possible the high-resolution and high-signal-to-noise ratio detection of DNA, but such a performance is dependent on the type of nanomaterial selected. Solid-state nanopores of graphene, Si3N4, and MoS2 have been studied as potential candidates for DNA detection. However, it is important to understand the sensitivity and characterization of these solid-state materials for nanopore based detection. Recent developments in the synthesis of MXene have inspired our interest in its application as a nanopore based DNA detection membrane. Here, we simulate the metal carbide, MXene (Ti3C2), with single stranded DNA to understand its interactions and the efficiency of MXene as a putative material for the development of a nanopore based detection platform. Using molecular dynamics (MD) simulations, we present evidence that a MXene based nanopore is able to detect the different types of DNA bases. We have successfully identified features to differentiate the translocation of different types of DNA bases across the nanopore.
Collapse
|
36
|
Cai Y, Zhang B, Liang L, Wang S, Zhang L, Wang L, Cui HL, Zhou Y, Wang D. A solid-state nanopore-based single-molecule approach for label-free characterization of plant polysaccharides. PLANT COMMUNICATIONS 2021; 2:100106. [PMID: 33898974 PMCID: PMC8060702 DOI: 10.1016/j.xplc.2020.100106] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/22/2020] [Accepted: 08/28/2020] [Indexed: 05/07/2023]
Abstract
Polysaccharides are important biomacromolecules existing in all plants, most of which are integrated into a fibrillar structure called the cell wall. In the absence of an effective methodology for polysaccharide analysis that arises from compositional heterogeneity and structural flexibility, our knowledge of cell wall architecture and function is greatly constrained. Here, we develop a single-molecule approach for identifying plant polysaccharides with acetylated modification levels. We designed a solid-state nanopore sensor supported by a free-standing SiN x membrane in fluidic cells. This device was able to detect cell wall polysaccharide xylans at concentrations as low as 5 ng/μL and discriminate xylans with hyperacetylated and unacetylated modifications. We further demonstrated the capability of this method in distinguishing arabinoxylan and glucuronoxylan in monocot and dicot plants. Combining the data for categorizing polysaccharide mixtures, our study establishes a single-molecule platform for polysaccharide analysis, opening a new avenue for understanding cell wall structures, and expanding polysaccharide applications.
Collapse
Affiliation(s)
- Yao Cai
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin 130016, China
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Sen Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Liang Cui
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin 130016, China
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
37
|
Maheshwaram SK, Sreenivasa K, Soni GV. Fingerprinting branches on supercoiled plasmid DNA using quartz nanocapillaries. NANOSCALE 2021; 13:320-331. [PMID: 33346295 DOI: 10.1039/d0nr06219g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA conformation, in particular its supercoiling, plays an important structural and functional role in gene accessibility as well as in DNA condensation. Enzyme driven changes of DNA plasmids between their linear, circular and supercoiled conformations control the level of condensation and DNA distal-site interactions. Much effort has been made to quantify the branched supercoiled state of DNA to understand its ubiquitous contribution to many biological functions, such as packaging, transcription, replication etc. Nanopore technology has proven to be an excellent label-free single-molecule method to investigate the conformations of the translocating DNA in terms of the current pulse readout. In this paper, we present a comprehensive study to detect different branched-supercoils on individual plasmid DNA molecules. Using a detailed event charge deficit (ECD) analysis of the translocating molecules, we reveal, for the first time, the distributions in size and the position of the plectoneme branches on the supercoiled plasmid. Additionally, this analysis also gives an independent measure of the effective nanopore length. Finally, we use our nanopore platform for measurement of enzyme-dependent linearization of these branched-supercoiled plasmids. By simultaneous measurement of both single-molecule DNA supercoiled conformations and enzyme-dependent bulk conformational changes, we establish nanopore sensing as a promising platform for an in-depth understanding of the structural landscapes of supercoiled DNA to decipher its functional role in different biological processes.
Collapse
|
38
|
Spitzberg JD, van Kooten XF, Bercovici M, Meller A. Microfluidic device for coupling isotachophoretic sample focusing with nanopore single-molecule sensing. NANOSCALE 2020; 12:17805-17811. [PMID: 32820758 DOI: 10.1039/d0nr05000h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Solid-state nanopores (NPs) are label-free single-molecule sensors, capable of performing highly sensitive assays from a small number of biomolecule translocation events. However, single-molecule sensing is challenging at extremely low analyte concentrations due to the limited flux of analytes to the sensing volume. This leads to a low event rate and increases the overall assay time. In this work, we present a method to enhance the event rate at low analyte concentrations by using isotachophoresis (ITP) to focus and deliver analytes to a nanopore sensor. Central to this method is a device capable of performing ITP focusing directly on a solid-state NP chip, while preventing the focusing electric field from damaging the nanopore membrane. We discuss considerations and trade-offs related to the design of the focusing channel, the ITP electrolyte system and electrical decoupling between the focusing and sensing modes. Finally, we demonstrate an integrated device wherein the concentration enhancement due to ITP focusing leads to an increase in event rate of >300-fold in the ITP-NP device as compared to the NP-only case.
Collapse
Affiliation(s)
- Joshua D Spitzberg
- Department of Biomedical Engineering, The Technion - Israel Institute of Technology, Haifa, 32000 Israel.
| | | | | | | |
Collapse
|
39
|
The Influence of Electric Field Intensity and Particle Length on the Electrokinetic Transport of Cylindrical Particles Passing through Nanopore. MICROMACHINES 2020; 11:mi11080722. [PMID: 32722448 PMCID: PMC7463976 DOI: 10.3390/mi11080722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 01/08/2023]
Abstract
The electric transport of nanoparticles passing through nanopores leads to a change in the ion current, which is essential for the detection technology of DNA sequencing and protein determination. In order to further illustrate the electrokinetic transport mechanism of particles passing through nanopores, a fully coupled continuum model is constructed by using the arbitrary Lagrangian–Eulerian (ALE) method. The model consists of the electric field described by the Poisson equation, the concentration field described by Nernst–Planck equation, and the flow field described by the Navier–Stokes equation. Based on this model, the influence of imposed electric field and particle length on the electrokinetic transport of cylindrical particles is investigated. It is found firstly the translation velocities for the longer particles remain constant when they locate inside the nanopore. Both the ion current blockade effect and the ion current enhancement effect occur when cylindrical particles enter and exit the nanopore, respectively, for the experimental parameters employed in this research. Moreover, the particle translation velocity and current fluctuation amplitude are dominated by the electric field intensity, which can be used to adjust the particle transmission efficiency and the ion current detectability. In addition, the increase in particle length changes the particle position corresponding to the peak value of the ion current, which contributes to distinguishing particles with different lengths as well.
Collapse
|
40
|
Md Ibrahim NNN, Hashim AM. Fabrication of Si Micropore and Graphene Nanohole Structures by Focused Ion Beam. SENSORS (BASEL, SWITZERLAND) 2020; 20:s20061572. [PMID: 32178225 PMCID: PMC7146166 DOI: 10.3390/s20061572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
A biosensor formed by a combination of silicon (Si) micropore and graphene nanohole technology is expected to act as a promising device structure to interrogate single molecule biopolymers, such as deoxyribonucleic acid (DNA). This paper reports a novel technique of using a focused ion beam (FIB) as a tool for direct fabrication of both conical-shaped micropore in Si3N4/Si and a nanohole in graphene to act as a fluidic channel and sensing membrane, respectively. The thinning of thick Si substrate down to 50 µm has been performed prior to a multi-step milling of the conical-shaped micropore with final pore size of 3 µm. A transfer of graphene onto the fabricated conical-shaped micropore with little or no defect was successfully achieved using a newly developed all-dry transfer method. A circular shape graphene nanohole with diameter of about 30 nm was successfully obtained at beam exposure time of 0.1 s. This study opens a breakthrough in fabricating an integrated graphene nanohole and conical-shaped Si micropore structure for biosensor applications.
Collapse
|
41
|
Liang S, Xiang F, Tang Z, Nouri R, He X, Dong M, Guan W. Noise in nanopore sensors: Sources, models, reduction, and benchmarking. NANOTECHNOLOGY AND PRECISION ENGINEERING 2020. [DOI: 10.1016/j.npe.2019.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
42
|
Niedzwiecki DJ, Chou YC, Xia Z, Thei F, Drndić M. Detection of single analyte and environmental samples with silicon nitride nanopores: Antarctic dirt particulates and DNA in artificial seawater. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:031301. [PMID: 32259993 DOI: 10.1063/1.5138210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/18/2020] [Indexed: 06/11/2023]
Abstract
Nanopore sensing is a powerful tool for the detection of biomolecules. Solid-state nanopores act as single-molecule sensors that can function in harsh conditions. Their resilient nature makes them attractive candidates for taking this technology into the field to measure environmental samples for life detection in space and water quality monitoring. Here, we discuss the fabrication of silicon nitride pores from ∼1.6 to 20 nm in diameter in 20-nm-thick silicon nitride membranes suspended on glass chips and their performance. We detect pure laboratory samples containing a single analyte including DNA, BSA, microRNA, TAT, and poly-D-lys-hydrobromide. We also measured an environmental (mixed-analyte) sample, containing Antarctic dirt provided by NASA Ames. For DNA measurements, in addition to using KCl and NaCl solutions, we used the artificial (synthetic) seawater, which is a mixture of different salts mimicking the composition of natural seawater. These samples were spiked with double-stranded DNA (dsDNA) fragments at different concentrations to establish the limits of nanopore sensitivity in candidate environment conditions. Nanopore chips were cleaned and reused for successive measurements. A stand-alone, 1-MHz-bandwidth Chimera amplifier was used to determine the DNA concentration in artificial seawater that we can detect in a practical time scale of a few minutes. We also designed and developed a new compact nanopore reader, a portable read-out device with miniaturized fluidic cells, which can obtain translocation data at bandwidths up to 100 kHz. Using this new instrument, we record translocations of 400 bp, 1000 bp, and 15000 bp dsDNA fragments and show discrimination by analysis of current amplitude and event duration histograms.
Collapse
Affiliation(s)
- David J Niedzwiecki
- Goeppert LLC, Pennovation Works, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, USA
| | - Yung-Chien Chou
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 S. 33rd Street, Philadelphia, Pennsylvania 19103, USA
| | - Zehui Xia
- Goeppert LLC, Pennovation Works, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, USA
| | - Federico Thei
- Elements, SRL, Viale G. Marconi 438, Cesena 47521, Italy
| | - Marija Drndić
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 S. 33rd Street, Philadelphia, Pennsylvania 19103, USA
| |
Collapse
|
43
|
Murphy TW, Hsieh YP, Zhu B, Naler LB, Lu C. Microfluidic Platform for Next-Generation Sequencing Library Preparation with Low-Input Samples. Anal Chem 2020; 92:2519-2526. [PMID: 31894965 DOI: 10.1021/acs.analchem.9b04086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Advances in next-generation sequencing (NGS) have made available a wealth of information that had previously been inaccessible to researchers and clinicians. NGS has been applied to understand genomic, transcriptomic, and epigenomic changes and gained traction as a significant tool capable of accelerating diagnosis, prognosis, and biomarker discovery. However, these NGS assays have yet to be practical methods for patient stratification or diagnosis because of the gap between the tiny quantities of biomaterials provided by a clinical sample and the large DNA input required by most of these assays. Current library preparation methodologies typically require large input amounts of DNA and a long and complicated manual process. Here, we present a microfluidic droplet-based system for NGS library preparation, capable of reducing the number of pipetting steps significantly, reducing reagent consumption by 10×, and automating much of the process, while supporting an extremely low DNA input requirement (10 pg per library). This semiautomated technology will allow for low-input preparations of 8 libraries simultaneously while reducing batch-to-batch variation and operator hands-on time.
Collapse
Affiliation(s)
- Travis W Murphy
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Yuan-Pang Hsieh
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Bohan Zhu
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Lynette B Naler
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Chang Lu
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| |
Collapse
|
44
|
Lu ZX, Liu T, Li H. Self-supporting hybrid silica membranes with controlled porous architectures. NEW J CHEM 2020. [DOI: 10.1039/d0nj02609c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transferrable, self-supporting membranes with controlled and ordered pore architectures have been developed for potential applications in the fields of filtration, sensing, separation and catalysis.
Collapse
Affiliation(s)
- Zhe-Xue Lu
- College of Science
- Huazhong Agricultural University
- Wuhan 430070
- P. R. China
| | - Tianci Liu
- College of Science
- Huazhong Agricultural University
- Wuhan 430070
- P. R. China
| | - Huihui Li
- College of Science
- Huazhong Agricultural University
- Wuhan 430070
- P. R. China
| |
Collapse
|
45
|
Wei W, Faubel JL, Selvakumar H, Kovari DT, Tsao J, Rivas F, Mohabir AT, Krecker M, Rahbar E, Hall AR, Filler MA, Washburn JL, Weigel PH, Curtis JE. Self-regenerating giant hyaluronan polymer brushes. Nat Commun 2019; 10:5527. [PMID: 31797934 PMCID: PMC6892876 DOI: 10.1038/s41467-019-13440-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 11/08/2019] [Indexed: 12/25/2022] Open
Abstract
Tailoring interfaces with polymer brushes is a commonly used strategy to create functional materials for numerous applications. Existing methods are limited in brush thickness, the ability to generate high-density brushes of biopolymers, and the potential for regeneration. Here we introduce a scheme to synthesize ultra-thick regenerating hyaluronan polymer brushes using hyaluronan synthase. The platform provides a dynamic interface with tunable brush heights that extend up to 20 microns - two orders of magnitude thicker than standard brushes. The brushes are easily sculpted into micropatterned landscapes by photo-deactivation of the enzyme. Further, they provide a continuous source of megadalton hyaluronan or they can be covalently-stabilized to the surface. Stabilized brushes exhibit superb resistance to biofilms, yet are locally digested by fibroblasts. This brush technology provides opportunities in a range of arenas including regenerating tailorable biointerfaces for implants, wound healing or lubrication as well as fundamental studies of the glycocalyx and polymer physics.
Collapse
Affiliation(s)
- Wenbin Wei
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jessica L Faubel
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Hemaa Selvakumar
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Petit H. Parker Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Daniel T Kovari
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Physics, Emory University, Atlanta, GA, USA
| | - Joanna Tsao
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Felipe Rivas
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Amar T Mohabir
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Michelle Krecker
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Elaheh Rahbar
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Adam R Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Michael A Filler
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jennifer L Washburn
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Paul H Weigel
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jennifer E Curtis
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA.
- Petit H. Parker Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
| |
Collapse
|
46
|
Zeng S, Wen C, Li S, Chen X, Chen S, Zhang SL, Zhang Z. Controlled size reduction and its underlying mechanism to form solid-state nanopores via electron beam induced carbon deposition. NANOTECHNOLOGY 2019; 30:455303. [PMID: 31394513 DOI: 10.1088/1361-6528/ab39a2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Solid-state nanopores have drawn considerable attention for their potential applications in DNA sequencing and nanoparticle analysis. However, fabrication of nanopores, especially those of diameter below 30 nm, requires sophisticated techniques. Here, a versatile method to controllably reduce the diameter of prefabricated large-size pores down to sub-30 nm without greatly increasing the effective pore depth from the original membrane thickness is shown. This method exploits carbon deposition achieved via hydrocarbon evaporation, induced by an incident beam of electrons, and subsequent dissociation of hydrocarbon to solid carbon deposits. The carbon deposition employs a conventional scanning electron microscope equipped with direct visual feedback, along with a stable hydrocarbon source nearby the sample. This work systematically studies how electron beam accelerating voltage, imaging magnification, initial pore size and membrane composition affect the process of pore size reduction. Secondary electrons generated in the membrane material are confirmed to be the main cause of the dissociation of hydrocarbon. Thicker carbon deposited on one side than on the other of the membrane results in an asymmetric nanopore shape and a rectifying ionic transport. A physico-phenomenological model combined with Monte Carlo simulations is proposed to account for the observed carbon deposition behaviors.
Collapse
Affiliation(s)
- Shuangshuang Zeng
- Division of Solid-State Electronics, Department of Engineering Sciences, Uppsala University, SE-751 21 Uppsala, Sweden
| | | | | | | | | | | | | |
Collapse
|
47
|
Kumar Sharma R, Agrawal I, Dai L, Doyle PS, Garaj S. Complex DNA knots detected with a nanopore sensor. Nat Commun 2019; 10:4473. [PMID: 31578328 PMCID: PMC6775256 DOI: 10.1038/s41467-019-12358-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/27/2019] [Indexed: 01/15/2023] Open
Abstract
Equilibrium knots are common in biological polymers-their prevalence, size distribution, structure, and dynamics have been extensively studied, with implications to fundamental biological processes and DNA sequencing technologies. Nanopore microscopy is a high-throughput single-molecule technique capable of detecting the shape of biopolymers, including DNA knots. Here we demonstrate nanopore sensors that map the equilibrium structure of DNA knots, without spurious knot tightening and sliding. We show the occurrence of both tight and loose knots, reconciling previous contradictory results from different experimental techniques. We evidence the occurrence of two quantitatively different modes of knot translocation through the nanopores, involving very different tension forces. With large statistics, we explore the complex knots and, for the first time, reveal the existence of rare composite knots. We use parametrized complexity, in concert with simulations, to test the theoretical assumptions of the models, further asserting the relevance of nanopores in future investigation of knots.
Collapse
Affiliation(s)
- Rajesh Kumar Sharma
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
- Singapore-MIT Alliance for Research and Technology Centre, 1 CREATE Way, Singapore, 138602, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore
| | - Ishita Agrawal
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
| | - Liang Dai
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Patrick S Doyle
- Singapore-MIT Alliance for Research and Technology Centre, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Slaven Garaj
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore.
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore.
- Department of Physics, National University of Singapore, Singapore, Science Drive 3, Singapore, 117551, Singapore.
| |
Collapse
|
48
|
Lam MH, Briggs K, Kastritis K, Magill M, Madejski GR, McGrath JL, de Haan HW, Tabard-Cossa V. Entropic Trapping of DNA with a Nanofiltered Nanopore. ACS APPLIED NANO MATERIALS 2019; 2:4773-4781. [PMID: 32577609 PMCID: PMC7310961 DOI: 10.1021/acsanm.9b00606] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Elucidating the kinetics of DNA passage through a solid-state nanopore is a fertile field of research, and mechanisms for controlling capture, passage, and trapping of biopolymers are likely to find numerous technological applications. Here we present a nanofiltered nanopore device, which forms an entropic cage for DNA following first passage through the nanopore, trapping the translocated DNA and permitting recapture for subsequent reanalysis and investigation of kinetics of passage under confinement. We characterize the trapping properties of this nanodevice by driving individual DNA polymers into the nanoscale gap separating the nanofilter and the pore, forming an entropic cage similar to a "two pores in series" device, leaving polymers to diffuse in the cage for various time lengths, and attempting to recapture the same molecule. We show that the cage results in effectively permanent trapping when the radius of gyration of the target polymer is significantly larger than the radii of the pores in the nanofilter. We also compare translocation dynamics as a function of translocation direction in order to study the effects of confinement on DNA just prior to translocation, providing further insight into the nanopore translocation process. This nanofiltered nanopore device realizes simple fabrication of a femtoliter nanoreactor in which to study fundamental biophysics and biomolecular reactions on the single-molecule level. The device provides an electrically-permeable single-molecule trap with a higher entropic barrier to escape than previous attempts to fabricate similar structures.
Collapse
Affiliation(s)
- Michelle H. Lam
- Department of Physics, University of Ottawa, Ottawa, ON, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, ON, Canada
| | | | - Martin Magill
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
| | - Gregory R. Madejski
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - James L. McGrath
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - Hendrick W. de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
| | | |
Collapse
|
49
|
Madejski GR, Briggs K, DesOrmeaux JP, Miller JJ, Roussie JA, Tabard-Cossa V, McGrath JL. Monolithic Fabrication of NPN/SiN x Dual Membrane Cavity for Nanopore-based DNA Sensing. ADVANCED MATERIALS INTERFACES 2019; 6:1900684. [PMID: 32577337 PMCID: PMC7310959 DOI: 10.1002/admi.201900684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Indexed: 06/11/2023]
Abstract
Nanoscale preconfinement of DNA has been shown to reduce the variation of passage times through solid-state nanopores. Preconfinement has been previously achieved by forming a femtoliter-sized cavity capped with a highly porous layer of nanoporous silicon nitride (NPN). This cavity was formed by sealing a NPN nanofilter membrane against a substrate chip using water vapor delamination. Ultimately, this method of fabrication cannot keep a consistent spacing between the filter and solid-state nanopore due to thermal fluctuations and wrinkles in the membrane, nor can it be fabricated on thousands of individual devices reliably. To overcome these issues, we present a method to fabricate the femtoliter cavity monolithically, using a selective XeF2 etch to hollow out a polysilicon spacer sandwiched between silicon nitride layers. These monolithically fabricated cavities behave identically to their counterparts formed by vapor delamination, exhibiting similar translocation passage time variation reduction and folding suppression of DNA without requiring extensive manual assembly. The ability to form nanocavity sensors with nanometer-scale precision and to reliably manufacture them at scale using batch wafer processing techniques will find numerous applications, including motion control of polymers for single-molecule detection applications, filtering of dirty samples prior to nanopore detection, and simple fabrication of single-molecule nanobioreactors.
Collapse
Affiliation(s)
- Gregory R. Madejski
- Department of Biomedical Engineering, University of Rochester, Robert B. Goergen Hall Box 270168 Rochester, NY 14627, USA
| | - Kyle Briggs
- Department of Physics, University of Ottawa, 150 Louis-Pasteur Pvt, Ottawa, ON, K1N6N5, Canada
| | | | - Joshua J. Miller
- SiMPore Inc, 150 Lucius Gordon Dr, West Henrietta, NY, 14586, USA
| | - James A. Roussie
- SiMPore Inc, 150 Lucius Gordon Dr, West Henrietta, NY, 14586, USA
| | - Vincent Tabard-Cossa
- Department of Physics, University of Ottawa, 150 Louis-Pasteur Pvt, Ottawa, ON, K1N6N5, Canada
| | - James L. McGrath
- Department of Biomedical Engineering, University of Rochester, Robert B. Goergen Hall Box 270168 Rochester, NY 14627, USA
| |
Collapse
|
50
|
Albrecht T. Single-Molecule Analysis with Solid-State Nanopores. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:371-387. [PMID: 30707594 DOI: 10.1146/annurev-anchem-061417-125903] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Solid-state nanopores and nanopipettes are an exciting class of single-molecule sensors that has grown enormously over the last two decades. They offer a platform for testing fundamental concepts of stochasticity and transport at the nanoscale, for studying single-molecule biophysics and, increasingly, also for new analytical applications and in biomedical sensing. This review covers some fundamental aspects underpinning sensor operation and transport and, at the same time, it aims to put these into context as an analytical technique. It highlights new and recent developments and discusses some of the challenges lying ahead.
Collapse
Affiliation(s)
- Tim Albrecht
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, United Kingdom;
| |
Collapse
|