1
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Xiao Y, Liang Z, Shyngys M, Baekova A, Cheung S, Muljadi MB, Bai Q, Zeng L, Choi CHJ. In Vivo Interactions of Nucleic Acid Nanostructures With Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2314232. [PMID: 39263835 DOI: 10.1002/adma.202314232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 07/03/2024] [Indexed: 09/13/2024]
Abstract
Nucleic acid nanostructures, derived from the assembly of nucleic acid building blocks (e.g., plasmids and oligonucleotides), are important intracellular carriers of therapeutic cargoes widely utilized in preclinical nanomedicine applications, yet their clinical translation remains scarce. In the era of "translational nucleic acid nanotechnology", a deeper mechanistic understanding of the interactions of nucleic acid nanostructures with cells in vivo will guide the development of more efficacious nanomedicines. This review showcases the recent progress in dissecting the in vivo interactions of four key types of nucleic acid nanostructures (i.e., tile-based, origami, spherical nucleic acid, and nucleic acid nanogel) with cells in rodents over the past five years. Emphasis lies on the cellular-level distribution of nucleic acid nanostructures in various organs and tissues and the cellular responses induced by their cellular entry. Next, in the spirit of preclinical translation, this review features the latest interactions of nucleic acid nanostructures with cells in large animals and humans. Finally, the review offers directions for studying the interactions of nucleic acid nanostructures with cells from both materials and biology perspectives and concludes with some regulatory updates.
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Affiliation(s)
- Yu Xiao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Zhihui Liang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Moldir Shyngys
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Aiana Baekova
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Suen Cheung
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Mathias Billy Muljadi
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Qianqian Bai
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Lula Zeng
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Chung Hang Jonathan Choi
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Shatin, New Territories, Hong Kong
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2
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Hueckel T, Woo S, Macfarlane RJ. Controlling the thermally-driven crystallization of DNA-coated nanoparticles with formamide. SOFT MATTER 2024; 20:6723-6729. [PMID: 39140263 DOI: 10.1039/d4sm00854e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
DNA-coated nanoparticles, also known as programmable atom equivalents (PAEs), facilitate the construction of materials with nanoscopic precision. Thermal annealing plays a pivotal role by controlling DNA hybridization kinetics and thermodynamics, which ensures the formation of intended structures. While various design handles such as particle size, DNA design, and salt concentration influence the stability of the DNA duplexes linking PAEs in a lattice, their influence on the system's melting temperature (Tm) often follows complicated trends that make rational tuning of self-assembly challenging. In this work, the denaturant formamide is used to precisely tune the thermal response of PAEs. Our results reveal a clear and predictable trend in the PAEs' response to formamide, enabling rational control over the Tm of a diverse set of PAE systems. Unlike adjustments made through alterations to PAE design or solution parameters such as ionic strength, formamide achieves its temperature shift without impacting the kinetics of assembly. As a result, PAEs can be rapidly crystallized at ambient temperatures, producing superlattices with similar quality to PAE crystals assembled through standard protocols that use higher temperatures. This study therefore positions formamide as a useful tool for enhancing the synthesis of complex nanostructures under mild conditions.
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Affiliation(s)
- Theodore Hueckel
- Department of Materials Science and Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
| | - Seungyeon Woo
- Department of Materials Science and Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
| | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
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3
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Ngo LT, Chaudhari P, Wang WK, Tseng YT, Kuo PL, Huang CJ, Chiang CY, Chau LK, Huang TT. Noninvasive Prenatal Genetic Screening of Cell-Free Fetal DNA for Early Prediction of β-Thalassemia Using Fiber Optic Nanogold-Linked Sorbent Assay. ACS Sens 2024; 9:4207-4215. [PMID: 39088458 DOI: 10.1021/acssensors.4c01194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
β-Thalassemia is a prevalent type of severe inherited chronic anemia, primarily identified in developing countries. The identification of single nucleotide polymorphisms (SNPs) plays a vital role in the early diagnosis of genetic diseases. Here, we reported the development of an amplification-free fiber optic nanogold-linked sorbent assay method using a fiber optic particle plasmon resonance (FOPPR) biosensor for rapid and ultrasensitive detection of SNPs. Herein, MutS protein was selected as the biorecognition capture probe and immobilized on the sensing region to capture the target mutant DNA, which was hybridized with a single-base mismatched single-stranded DNA labeled by a gold nanoparticle (AuNP). The AuNP acts as a signaling agent to be detected by the FOPPR biosensor when it is bound on the fiber core surface. The method effectively differentiates mismatched double-stranded DNA by MutS protein from perfectly matched/complementary dsDNA. It exhibits an impressively low detection limit for the detection of SNPs at approximately 10-16 M using low-cost sensor chips and devices. By determination of the ratio of mutant DNA to normal DNA in cell-free genomic DNA from blood samples, this method is promising for diagnosing β-thalassemia in fetuses without invasive testing techniques.
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Affiliation(s)
- Loan Thi Ngo
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Pallavi Chaudhari
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Wei-Kai Wang
- School of Dentistry, Institute of Oral Medicine, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
| | - Yen-Ta Tseng
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Pao-Lin Kuo
- Department of Obstetrics Gynecology, College of Medicine, National Cheng Kung University Hospital, 138 Shengli Rd., North District, Tainan City 704, Taiwan
- Department of Obstetrics & Gynecology, E-Da Hospital, 1 Yida Rd., Yanchao District, Kaohsiung City 82445, Taiwan
| | - Chun-Jen Huang
- Department of Chemical and Materials Engineering, National Central University, 300 Zhongda Rd., Zhongli District, Taoyuan City 320, Taiwan
- R&D Center for Membrane Technology, Chung Yuan Christian University, 200 Chung Pei Rd., Chung-Li City 32023, Taiwan
| | - Chang-Yue Chiang
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Lai-Kwan Chau
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
- Center for Nano Bio-Detection, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Tze-Ta Huang
- School of Dentistry, Institute of Oral Medicine, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
- Department of Stomatology, College of Medicine and Hospital, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
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4
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Lin M, Wang C, Fan R, Zhao X, Yu L, Lu M, Peng W. Multi-channel prismatic localized surface plasmon resonance biosensor for real-time competitive assay multiple COVID-19 characteristic miRNAs. Talanta 2024; 275:126142. [PMID: 38669961 DOI: 10.1016/j.talanta.2024.126142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024]
Abstract
A multi-channel prismatic localized surface plasmon resonance (LSPR) biosensor was developed for quantitative and real-time detection of multiple COVID-19 characteristic miRNAs. The well-dispersed and dense gold nanoparticles (AuNPs) arrays for LSPR biosensing were fabricated through a nano-thickness diblock copolymer template (BCPT). Both theoretical and experimental analyses were conducted to investigate the effects of particle size, interparticle spacing, and surface coverage on LSPR sensing spectrum and intensity sensitivity of varied AuNPs sizes. A competitive assay strategy was proposed and used for non-amplification miRNA detection with a low limit detection of 3.41 nM, while a four-channel prismatic LSPR system enables parallel detection of multiple miRNAs. Furthermore, this sensing strategy can effectively and specifically identify target miRNA, distinguish mismatched miRNA and interfering miRNA, and exhibit low non-specific adsorption. This BCPT-based LSPR biosensor demonstrates the practicality and potential of a multi-channel, adaptable, and integrated prismatic sensor in medical testing and diagnostic applications.
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Affiliation(s)
- Ming Lin
- Affiliated Cancer Hospital, Dalian University of Technology, Shenyang, 110042, China; School of Physics, Dalian University of Technology, Dalian, 116024, China
| | - Chen Wang
- School of Physics, Dalian University of Technology, Dalian, 116024, China
| | - Ruizhi Fan
- School of Physics, Dalian University of Technology, Dalian, 116024, China
| | - Xinya Zhao
- School of Physics, Dalian University of Technology, Dalian, 116024, China
| | - Li Yu
- School of Physics, Dalian University of Technology, Dalian, 116024, China
| | - Mengdi Lu
- Affiliated Cancer Hospital, Dalian University of Technology, Shenyang, 110042, China; School of Physics, Dalian University of Technology, Dalian, 116024, China.
| | - Wei Peng
- School of Physics, Dalian University of Technology, Dalian, 116024, China
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5
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Zhang Y, Allen A, Petrek ZJ, Cao HH, Kumar D, Goodlad MC, Martinez VG, Singh J, Zhang JZ, Ye T. Formation of Linear Plasmonic Heterotrimers Using Nanoparticle Docking to DNA Origami Cages. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2024; 128:11699-11708. [PMID: 39050926 PMCID: PMC11264316 DOI: 10.1021/acs.jpcc.4c02229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
The fabrication of complex assemblies with interesting collective properties from plasmonic nanoparticles (NPs) is often challenging. While DNA-directed self-assembly has emerged as one of the most promising approaches to forming such complex assemblies, the resulting structures tend to have large variability in gap sizes and shapes, as the DNA strands used to organize these particles are flexible, and the polydispersity of the NPs leads to variability in these critical structural features. Here, we use a new strategy termed docking to DNA origami cages (D-DOC) to organize spherical NPs into a linear heterotrimer with a precisely defined geometrical arrangement. Instead of binding NPs to the exterior of the DNA templates, D-DOC binds the NPs to either the interior or the opening of a 3D cage, which significantly reduces the variability of critical structural features by incorporating multiple diametrically arranged capture strands to tether NPs. Additionally, such a spatial arrangement of the capture strand can work synergistically with shape complementarity to achieve tighter confinement. To assemble NPs via D-DOC, we developed a multistep assembly process that first encapsulates an NP inside a cage and then binds two other NPs to the openings. Microscopic characterization shows low variability in the bond angles and gap sizes. Both UV-vis absorption and surface-enhanced Raman scattering (SERS) measurements showed strong plasmonic coupling that aligned with predictions by electrodynamic simulations, further confirming the precision of the assembly. These results suggest D-DOC could open new opportunities in biomolecular sensing, SERS and fluorescence spectroscopies, and energy harvesting through the self-assembly of NPs into more complex 3D assemblies.
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Affiliation(s)
- Yehan Zhang
- Department
of Chemistry and Biochemistry, University
of California, Merced, California 95343, United States
| | - A’Lester
C. Allen
- Department
of Chemistry and Biochemistry, University
of California, Santa Cruz, California 95064, United States
| | - Zachary J. Petrek
- Department
of Chemistry and Biochemistry, University
of California, Merced, California 95343, United States
| | - Huan H. Cao
- Department
of Chemistry and Biochemistry, University
of California, Merced, California 95343, United States
| | - Devanshu Kumar
- Department
of Chemistry and Biochemistry, University
of California, Merced, California 95343, United States
| | - Melissa C. Goodlad
- Department
of Chemistry and Biochemistry, University
of California, Merced, California 95343, United States
| | - Vianna G. Martinez
- Department
of Chemistry and Biochemistry, University
of California, Merced, California 95343, United States
| | - Jasdip Singh
- Department
of Chemistry and Biochemistry, University
of California, Merced, California 95343, United States
| | - Jin Z. Zhang
- Department
of Chemistry and Biochemistry, University
of California, Santa Cruz, California 95064, United States
| | - Tao Ye
- Department
of Chemistry and Biochemistry, University
of California, Merced, California 95343, United States
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6
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Rao A, Iglesias AS, Grzelczak M. Choreographing Oscillatory Hydrodynamics with DNA-Coated Gold Nanoparticles. J Am Chem Soc 2024; 146:18236-18240. [PMID: 38941615 PMCID: PMC11240255 DOI: 10.1021/jacs.4c06868] [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: 05/20/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 06/30/2024]
Abstract
Periodic responses to nonperiodic energy inputs, such as oscillations, are hallmarks of living systems. Nanoparticle-based systems have largely remained unexplored in the generation of oscillatory features. Here, we demonstrate a nanosystem featuring hierarchical response to light, where thermoplasmonic effects and reversible DNA-hybridization generate thermal convective forces and ultimately, oscillatory hydrodynamic flows. The slow aggregation of gold nanoparticles (AuNPs) serves as a positive feedback, while fast photothermal disassembly acts as negative feedback. These asymmetric feedback loops, combined with thermal hysteresis for time-delay, are essential ingredients for orchestrating an oscillating response.
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Affiliation(s)
- Anish Rao
- Centro
de Física de Materiales CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 Donostia San-Sebastián, Spain
| | - Ana Sánchez Iglesias
- Centro
de Física de Materiales CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 Donostia San-Sebastián, Spain
| | - Marek Grzelczak
- Centro
de Física de Materiales CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 Donostia San-Sebastián, Spain
- Donostia
International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
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7
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Dang H, Joung Y, Yang JY, Lee SH, Lee S, Joo SW, Park SG, Choo J. Advancing COVID-19 Diagnosis: Enhancement in SERS-PCR with 30-nm Au Nanoparticle-Internalized Nanodimpled Substrates. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2403672. [PMID: 38970560 DOI: 10.1002/smll.202403672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/16/2024] [Indexed: 07/08/2024]
Abstract
Real-time polymerase chain reaction (RT-PCR) with fluorescence detection is the gold standard for diagnosing coronavirus disease 2019 (COVID-19) However, the fluorescence detection in RT-PCR requires multiple amplification steps when the initial deoxyribonucleic acid (DNA) concentration is low. Therefore, this study has developed a highly sensitive surface-enhanced Raman scattering-based PCR (SERS-PCR) assay platform using the gold nanoparticle (AuNP)-internalized gold nanodimpled substrate (AuNDS) plasmonic platform. By comparing different sizes of AuNPs, it is observed that using 30 nm AuNPs improves the detection limit by approximately ten times compared to 70 nm AuNPs. Finite-difference time-domain (FDTD) simulations show that multiple hotspots are formed between AuNPs and the cavity surface and between AuNPs when 30 nm AuNPs are internalized in the cavity, generating a strong electric field. With this 30 nm AuNPs-AuNDS SERS platform, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ribonucleic acid (RNA)-dependent RNA polymerase (RdRp) can be detected in only six amplification cycles, significantly improving over the 25 cycles required for RT-PCR. These findings pave the way for an amplification-free molecular diagnostic system based on SERS.
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Affiliation(s)
- Hajun Dang
- Department of Chemistry, Chung-Ang University, Seoul, 06974, South Korea
| | - Younju Joung
- Department of Chemistry, Chung-Ang University, Seoul, 06974, South Korea
| | - Jun-Yeong Yang
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, 51508, South Korea
| | - Soo Hyun Lee
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, 51508, South Korea
| | - Seunghun Lee
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, 51508, South Korea
| | - Sang-Woo Joo
- Department of Chemistry, Soongsil University, Seoul, 06978, South Korea
| | - Sung-Gyu Park
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, 51508, South Korea
| | - Jaebum Choo
- Department of Chemistry, Chung-Ang University, Seoul, 06974, South Korea
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8
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Siegel N, Hasebe H, Chiarelli G, Garoli D, Sugimoto H, Fujii M, Acuna GP, Kołątaj K. Universal Click-Chemistry Approach for the DNA Functionalization of Nanoparticles. J Am Chem Soc 2024; 146:17250-17260. [PMID: 38871677 DOI: 10.1021/jacs.4c03833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Nanotechnology has revolutionized the fabrication of hybrid species with tailored functionalities. A milestone in this field is the deoxyribonucleic acid (DNA) conjugation of nanoparticles, introduced almost 30 years ago, which typically exploits the affinity between thiol groups and metallic surfaces. Over the last decades, developments in colloidal research have enabled the synthesis of an assortment of nonmetallic structures, such as high-index dielectric nanoparticles, with unique properties not previously accessible with traditional metallic nanoparticles. However, to stabilize, integrate, and provide further functionality to nonmetallic nanoparticles, reliable techniques for their functionalization with DNA will be crucial. Here, we combine well-established dibenzylcyclooctyne-azide click-chemistry with a simple freeze-thaw method to achieve the functionalization of silica and silicon nanoparticles, which form exceptionally stable colloids with a high DNA surface density of ∼0.2 molecules/nm2. Furthermore, we demonstrate that these functionalized colloids can be self-assembled into high-index dielectric dimers with a yield of over 50% via the use of DNA origami. Finally, we extend this method to functionalize other important nanomaterials, including oxides, polymers, core-shell, and metal nanostructures. Our results indicate that the method presented herein serves as a crucial complement to conventional thiol functionalization chemistry and thus greatly expands the toolbox of DNA-functionalized nanoparticles currently available.
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Affiliation(s)
- Nicole Siegel
- Department of Physics, University of Fribourg, Chemin du Musée 3, Fribourg CH 1700, Switzerland
| | - Hiroaki Hasebe
- Department of Electrical and Electronic Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
| | - Germán Chiarelli
- Department of Physics, University of Fribourg, Chemin du Musée 3, Fribourg CH 1700, Switzerland
| | - Denis Garoli
- Dipartimento di Scienze e Metodi dell'Ingegneria, Università di Modena e Reggio Emilia, Via Amendola 2 Padiglione Tamburini, 42122 Reggio Emilia, Italy
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Hiroshi Sugimoto
- Department of Electrical and Electronic Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
| | - Minoru Fujii
- Department of Electrical and Electronic Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
| | - Guillermo P Acuna
- Department of Physics, University of Fribourg, Chemin du Musée 3, Fribourg CH 1700, Switzerland
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Karol Kołątaj
- Department of Physics, University of Fribourg, Chemin du Musée 3, Fribourg CH 1700, Switzerland
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
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9
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Wang G, Han S, Lu Y. From Structure to Application: The Evolutionary Trajectory of Spherical Nucleic Acids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2310026. [PMID: 38860348 DOI: 10.1002/smll.202310026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/09/2024] [Indexed: 06/12/2024]
Abstract
Since the proposal of the concept of spherical nucleic acids (SNAs) in 1996, numerous studies have focused on this topic and have achieved great advances. As a new delivery system for nucleic acids, SNAs have advantages over conventional deoxyribonucleic acid (DNA) nanostructures, including independence from transfection reagents, tolerance to nucleases, and lower immune reactions. The flexible structure of SNAs proves that various inorganic or organic materials can be used as the core, and different types of nucleic acids can be conjugated to realize diverse functions and achieve surprising and exciting outcomes. The special DNA nanostructures have been employed for immunomodulation, gene regulation, drug delivery, biosensing, and bioimaging. Despite the lack of rational design strategies, potential cytotoxicity, and structural defects of this technology, various successful examples demonstrate the bright and convincing future of SNAs in fields such as new materials, clinical practice, and pharmacy.
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Affiliation(s)
- Guijia Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
| | - Sanyang Han
- Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
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10
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Kou B, Wang Z, Mousavi S, Wang P, Ke Y. Dynamic Gold Nanostructures Based on DNA Self Assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308862. [PMID: 38143287 DOI: 10.1002/smll.202308862] [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: 10/04/2023] [Revised: 12/10/2023] [Indexed: 12/26/2023]
Abstract
The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties. Benefiting from the vast design possibilities, complete addressability, and sub-10 nm resolution, DNA duplexes, tiles, single-stranded tiles and origami structures serve as excellent platforms for constructing diverse 3D reconfigurable plasmonic nanostructures with tailored optical properties. Leveraging the responsive nature of DNA interactions, the fabrication of dynamic assemblies of NG becomes readily achievable, and environmental stimulation can be harnessed as a driving force for the nanomotors. It is envisioned that intelligent DNA-assembled NG nanodevices will assume increasingly important roles in the realms of biological, biomedical, and nanomechanical studies, opening a new avenue toward exploration and innovation.
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Affiliation(s)
- Bo Kou
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Zhichao Wang
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Shikufa Mousavi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
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11
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Ding Z, Gao H, Wang C, Li Y, Li N, Chu L, Chen H, Xie H, Su M, Liu H. Acoustic Levitation Synthesis of Ultrahigh-Density Spherical Nucleic Acid Architectures for Specific SERS Analysis. Angew Chem Int Ed Engl 2024; 63:e202317463. [PMID: 38503689 DOI: 10.1002/anie.202317463] [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: 11/16/2023] [Revised: 03/04/2024] [Accepted: 03/19/2024] [Indexed: 03/21/2024]
Abstract
Controllably regulating the electrostatic bilayer of nanogold colloids is a significant premise for synthesizing spherical nucleic acid (SNA) and building ordered plasmonic architectures. We develop a facile acoustic levitation reactor to universally synthesize SNAs with an ultra-high density of DNA strands, which is even higher than those of various state-of-the-art methods. Results reveal a new mechanism of DNA grafting via acoustic wave that can reconfigure the ligands on colloidal surfaces. The acoustic levitation reactor enables substrate-free three-dimentional (3D) spatial assembly of SNAs with controllable interparticle nanogaps through regulating DNA lengths. This kind of architecture may overcome the plasmonic enhancement limits by blocking electron tunneling and breaking electrostatic shielding in dried aggregations. Finite element simulations support the architecture with 3D spatial plasmonic hotspot matrix, and its ultrahigh surface-enhanced Raman scattering (SERS) capability is evidenced by in situ untargeted tracking of biomolecular events during photothermal stimulation (PTS)-induced cell death process. For biomarker diagnosis, the conjugation of adenosine triphosphate (ATP) aptamer onto SNAs enables in situ targeted tracking of ATP during PTS-induced cell death process. Particularly, the CD71 receptor and integrin α3β1 protein on PL45 cell membrance could be well distinguished by label-free SERS fingerprints when using specific XQ-2d and DML-7 aptamers, respectively, to synthesize SNA architectures. Our current acoustic levitation reactor offers a new method for synthesizing SNAs and enables both targeted and untargeted SERS analysis for tracking molecular events in living systems. It promises great potentials in biochemical synthesis and sensing in future.
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Affiliation(s)
- Zhongxiang Ding
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Heng Gao
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Chao Wang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230027, China
| | - Yuzhu Li
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Ning Li
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Leiming Chu
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Haijie Chen
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Haijiao Xie
- Hangzhou Yanqu Information Technology Co., Ltd., Hangzhou City, Zhejiang Province, 310003, P.R.O.C., China
| | - Mengke Su
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Honglin Liu
- Key Laboratory for Animal Food Green Manufacturing and Resource Mining of Anhui Province, China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
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12
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Lin M, Lee JU, Kim Y, Kim G, Jung Y, Jo A, Park M, Lee S, Lah JD, Park J, Noh K, Lee JH, Kwak M, Lungerich D, Cheon J. A magnetically powered nanomachine with a DNA clutch. NATURE NANOTECHNOLOGY 2024; 19:646-651. [PMID: 38326466 DOI: 10.1038/s41565-023-01599-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/22/2023] [Indexed: 02/09/2024]
Abstract
Machines found in nature and human-made machines share common components, such as an engine, and an output element, such as a rotor, linked by a clutch. This clutch, as seen in biological structures such as dynein, myosin or bacterial flagellar motors, allows for temporary disengagement of the moving parts from the running engine. However, such sophistication is still challenging to achieve in artificial nanomachines. Here we present a spherical rotary nanomotor with a reversible clutch system based on precise molecular recognition of built-in DNA strands. The clutch couples and decouples the engine from the machine's rotor in response to encoded inputs such as DNA or RNA. The nanomotor comprises a porous nanocage as a spherical rotor to confine the magnetic engine particle within the nanospace (∼0.004 μm3) of the cage. Thus, the entropically driven irreversible disintegration of the magnetic engine and the spherical rotor during the disengagement process is eliminated, and an exchange of microenvironmental inputs is possible through the nanopores. Our motor is only 200 nm in size and the clutch-mediated force transmission powered by an embedded ferromagnetic nanocrystal is high enough (∼15.5 pN at 50 mT) for the in vitro mechanical activation of Notch and integrin receptors, demonstrating its potential as nano-bio machinery.
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Affiliation(s)
- Mouhong Lin
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
| | - Jung-Uk Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
| | - Youngjoo Kim
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
| | - Gooreum Kim
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul, Republic of Korea
| | - Yunmin Jung
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
| | - Ala Jo
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
| | - Mansoo Park
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Sol Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
| | - Jungsu David Lah
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Jongseong Park
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Kunwoo Noh
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Jae-Hyun Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Minsuk Kwak
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Dominik Lungerich
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
| | - Jinwoo Cheon
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Department of Chemistry, Yonsei University, Seoul, Republic of Korea.
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
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13
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Ma KY, Perera-Gonzalez M, Langlois NI, Alzubi OM, Guimond JD, Flask CA, Clark HA. pH-responsive i-motif-conjugated nanoparticles for MRI analysis. SENSORS & DIAGNOSTICS 2024; 3:623-630. [PMID: 38646186 PMCID: PMC11025034 DOI: 10.1039/d3sd00285c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/21/2024] [Indexed: 04/23/2024]
Abstract
Gadolinium (Gd)-based contrast agents (CAs) are widely used to enhance anatomical details in magnetic resonance imaging (MRI). Significant research has expanded the field of CAs into bioresponsive CAs by modulating the signal to image and monitor biochemical processes, such as pH. In this work, we introduce the modular, dynamic actuation mechanism of DNA-based nanostructures as a new way to modulate the MRI signal based on the rotational correlation time, τR. We combined a pH-responsive oligonucleotide (i-motif) and a clinical standard CA (Gd-DOTA) to develop a pH-responsive MRI CA. The i-motif folds into a quadruplex under acidic conditions and was incorporated onto gold nanoparticles (iM-GNP) to achieve increased relaxivity, r1, compared to the unbound i-motif. In vitro, iM-GNP resulted in a significant increase in r1 over a decreasing pH range (7.5-4.5) with a calculated pKa = 5.88 ± 0.01 and a 16.7% change per 0.1 pH unit. In comparison, a control CA with a non-responsive DNA strand (T33-GNP) did not show a significant change in r1 over the same pH range. The iM-GNP was further evaluated in 20% human serum and demonstrated a 28.14 ± 11.2% increase in signal from neutral pH to acidic pH. This approach paves a path for novel programmable, dynamic DNA-based complexes for τR-modulated bioresponsive MRI CAs.
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Affiliation(s)
- Kristine Y Ma
- School of Biological and Health Systems Engineering, Arizona State University Tempe AZ USA
- Dept. of Bioengineering, Northeastern University Boston MA USA
| | | | - Nicole I Langlois
- Dept. of Chemistry and Chemical Biology, Northeastern University Boston MA USA
| | - Owen M Alzubi
- School of Biological and Health Systems Engineering, Arizona State University Tempe AZ USA
| | - Joseph D Guimond
- School of Biological and Health Systems Engineering, Arizona State University Tempe AZ USA
| | - Chris A Flask
- Depts. of Radiology, Biomedical Engineering, and Pediatrics, Case Western Reserve University Cleveland OH USA
| | - Heather A Clark
- School of Biological and Health Systems Engineering, Arizona State University Tempe AZ USA
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14
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Enea M, Nuekaew A, Franco R, Pereira E. Gold Nanoprobes for Detection of a Crucial EGFR Deletion for Early Diagnosis of Non-Small-Cell Lung Cancer. BIOSENSORS 2024; 14:162. [PMID: 38667155 PMCID: PMC11048279 DOI: 10.3390/bios14040162] [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: 03/05/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
Gold nanoparticles (AuNPs) exhibit improved optical and spectral properties compared to bulk materials, making them suitable for the detection of DNA, RNA, antigens, and antibodies. Here, we describe a simple, selective, and rapid non-cross linking detection assay, using approx. 35 nm spherical Au nanoprobes, for a common mutation occurring in exon 19 of the epidermal growth factor receptor (EGFR), associated with non-small-cell lung cancer cells. AuNPs were synthesized based on the seed-mediated growth method and functionalized with a specific 16 bp thiolated oligonucleotide using a pH-assisted method. Both AuNPs and Au nanoprobes proved to be highly stable and monodisperse through ultraviolet-visible spectrophotometry, dynamic light scattering (DLS), and electrophoretic light scattering (ELS). Our results indicate a detection limit of 1.5 µg mL-1 using a 0.15 nmol dm-3 Au nanoprobe concentration. In conclusion, this work presents an effective possibility for a straightforward, fast, and inexpensive alternative for the detection of DNA sequences related to lung cancer, leading to a potential platform for early diagnosis of lung cancer patients.
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Affiliation(s)
- Maria Enea
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 687, 4169-007 Porto, Portugal; (A.N.); (E.P.)
| | - Anupong Nuekaew
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 687, 4169-007 Porto, Portugal; (A.N.); (E.P.)
| | - Ricardo Franco
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Eulália Pereira
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 687, 4169-007 Porto, Portugal; (A.N.); (E.P.)
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15
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Yang N, Ding N, Qi S, Shang Z, Ma P, Khan IM, Wang Z, Xia Y, Zhang Y, Zhang L. High-affinity truncated aptamers for detection of Cronobacter spp with magnetic separation-assisted DNAzyme-driven 3D DNA walker. Mikrochim Acta 2024; 191:130. [PMID: 38351361 DOI: 10.1007/s00604-024-06199-2] [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: 11/01/2023] [Accepted: 01/07/2024] [Indexed: 02/16/2024]
Abstract
After optimizing the original aptamer sequence by truncation strategy, a magnetic separation-assisted DNAzyme-driven 3D DNA walker fluorescent aptasensor was developed for detecting the food-borne pathogen Cronobacter species. Iron oxide magnetic nanoparticles (MNPs) modified with a hybrid of truncated aptamer probe and DNAzyme strand (AP-E1) denoted as MNPs@AP-E1, were employed as capture probes. Simultaneously, a DNAzyme-driven 3D-DNA walker was utilized as the signal amplification element. The substrate strand (Sub) was conjugated with the gold nanoparticles (AuNPs), resulting in the formation of AuNPs@Sub, which served as a 3D walking track. In the presence of the target bacteria and Mg2+, E1-DNAzyme was activated and moved along AuNPs@Sub, continuously releasing the signal probe. Under optimized conditions, a strong linear correlation was observed for Cronobacter sakazakii (C. sakazakii) in the concentration range 101 to 106 CFU mL-1, with a low detection limit of 2 CFU mL-1. The fluorescence signal responses for different Cronobacter species exhibited insignificant differences, with a relative standard deviation of 3.6%. Moreover, the aptasensor was successfully applied to determine C. sakazakii in real samples with recoveries of 92.86%-108.33%. Therefore, the novel method could be a good candidate for ultra-sensitive and selective detection of Cronobacter species without complex manipulation.
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Affiliation(s)
- Ningru Yang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Ning Ding
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Shuo Qi
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Zixuan Shang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Pengfei Ma
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
- College of Ocean Food and Biological Engineering, Jimmie University, Jimei University, Jimei District, Xiamen City, 361021, Fujian Province, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China.
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu, 610106, China.
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China.
| | - Yu Xia
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu, 610106, China
| | - Lili Zhang
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
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16
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John-Erik Reinertsen R, Jiménez-Ángeles F, Kewalramani S, Bedzyk M, Olvera de la Cruz M. Transformations in crystals of DNA-functionalized nanoparticles by electrolytes. Faraday Discuss 2024; 249:408-423. [PMID: 37791509 DOI: 10.1039/d3fd00109a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Colloidal crystals have applications in water treatments, including water purification and desalination technologies. It is, therefore, important to understand the interactions between colloids as a function of electrolyte concentration. We study the assembly of DNA-grafted gold nanoparticles immersed in concentrated electrolyte solutions. Increasing the concentration of divalent Ca2+ ions leads to the condensation of nanoparticles into face-centered-cubic (FCC) crystals at low electrolyte concentrations. As the electrolyte concentration increases, the system undergoes a phase change to body-centered-cubic (BCC) crystals. This phase change occurs as the interparticle distance decreases. Molecular dynamics analysis suggests that the interparticle interactions change from strongly repulsive to short-range attractive as the divalent-electrolyte concentration increases. A thermodynamic analysis suggests that increasing the salt concentration leads to significant dehydration of the nanoparticle environment. We conjecture that the intercolloid attractive interactions and dehydrated states favour the BCC structure. Our results gain insight into salting out of colloids such as proteins as the concentration of salt increases in the solution.
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Affiliation(s)
- Roger John-Erik Reinertsen
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA.
| | - Felipe Jiménez-Ángeles
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA.
| | - Sumit Kewalramani
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA.
| | - Michael Bedzyk
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA.
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA.
- Department of Physics, Northwestern University, Evanston, Illinois 60208, USA
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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17
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Wang X, Yang Z, Li Y, Huang K, Cheng N. Towards rational design: Developing universal freezing routes for anchoring DNA onto gold nanoparticles. J Colloid Interface Sci 2024; 655:830-840. [PMID: 37979289 DOI: 10.1016/j.jcis.2023.11.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
DNA-functionalized gold nanoparticles (AuNPs), also known as spherical nucleic acids, are widely used in the development of biosensors, resulting in anchoring DNA onto AuNPs being a crucial preparation step and a popular research topic. The latest freeze-anchoring method is a simple and time-saving alternative to traditional salt aging; however, its universal applicability remains limited. In this study, we explored the interfacial interaction between DNA and the AuNP surface and proposed various universal routes for promoting freezing anchoring. Among them, rational design has been considered as the core idea to overcome these limitations, particularly using non-thiolated DNA anchoring, which offers significant advantages such as being unmodified, cost-effective, and easily accessible. We emphasize the importance of sequence structure and preparation process optimization, which mainly considers differences in DNA conformation and electrostatic repulsion. Additionally, the prepared DNA-functionalized AuNPs exhibited complete biological hybridization capability, and the extreme limiting conditions for non-thiolated DNA freeze anchoring were clarified. In summary, this study enhances our understanding of the interfacial relationship between DNA and AuNPs in the freeze-anchoring process and can significantly advance the applications of DNA-functionalized AuNP-based biosensors.
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Affiliation(s)
- Xin Wang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhansen Yang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunyi Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture and Rural Affairs, Beijing 100083, China.
| | - Nan Cheng
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture and Rural Affairs, Beijing 100083, China.
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18
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Liu B, Duan H, Liu Z, Liu Y, Chu H. DNA-functionalized metal or metal-containing nanoparticles for biological applications. Dalton Trans 2024; 53:839-850. [PMID: 38108230 DOI: 10.1039/d3dt03614f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The conjugation of DNA molecules with metal or metal-containing nanoparticles (M/MC NPs) has resulted in a number of new hybrid materials, enabling a diverse range of novel biological applications in nanomaterial assembly, biosensor development, and drug/gene delivery. In such materials, the molecular recognition, gene therapeutic, and structure-directing functions of DNA molecules are coupled with M/MC NPs. In turn, the M/MC NPs have optical, catalytic, pore structure, or photodynamic/photothermal properties, which are beneficial for sensing, theranostic, and drug loading applications. This review focuses on the different DNA functionalization protocols available for M/MC NPs, including gold NPs, upconversion NPs, metal-organic frameworks, metal oxide NPs and quantum dots. The biological applications of DNA-functionalized M/MC NPs in the treatment or diagnosis of cancers are discussed in detail.
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Affiliation(s)
- Bei Liu
- College of Science, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China
| | - Huijuan Duan
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
| | - Zechao Liu
- College of Science, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China
| | - Yuechen Liu
- College of Science, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China
| | - Hongqian Chu
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
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19
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Pandit S, Duchow M, Chao W, Capasso A, Samanta D. DNA-Barcoded Plasmonic Nanostructures for Activity-Based Protease Sensing. Angew Chem Int Ed Engl 2024; 63:e202310964. [PMID: 37985161 DOI: 10.1002/anie.202310964] [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: 07/31/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
We report the development of a new class of protease activity sensors called DNA-barcoded plasmonic nanostructures. These probes are comprised of gold nanoparticles functionalized with peptide-DNA conjugates (GPDs), where the peptide is a substrate of the protease of interest. The DNA acts as a barcode identifying the peptide and facilitates signal amplification. Protease-mediated peptide cleavage frees the DNA from the nanoparticle surface, which is subsequently measured via a CRISPR/Cas12a-based assay as a proxy for protease activity. As proof-of-concept, we show activity-based, multiplexed detection of the SARS-CoV-2-associated protease, 3CL, and the apoptosis marker, caspase 3, with high sensitivity and selectivity. GPDs yield >25-fold turn-on signals, 100-fold improved response compared to commercial probes, and detection limits as low as 58 pM at room temperature. Moreover, nanomolar concentrations of proteases can be detected visually by leveraging the aggregation-dependent color change of the gold nanoparticles. We showcase the clinical potential of GPDs by detecting a colorectal cancer-associated protease, cathepsin B, in three different patient-derived cell lines. Taken together, GPDs detect physiologically relevant concentrations of active proteases in challenging biological samples, require minimal sample processing, and offer unmatched multiplexing capabilities (mediated by DNA), making them powerful chemical tools for biosensing and disease diagnostics.
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Affiliation(s)
- Subrata Pandit
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
| | - Mark Duchow
- Department of Oncology, Dell Medical School, The University of Texas at Austin, 1601 Trinity St., Austin, TX 78712, USA
| | - Wilson Chao
- Department of Biochemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
| | - Anna Capasso
- Department of Oncology, Dell Medical School, The University of Texas at Austin, 1601 Trinity St., Austin, TX 78712, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
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20
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García-Faustino LL, Morris SM, Elston SJ, Montelongo Y. Detection of Biomarkers through Functionalized Polymers. SMALL METHODS 2024; 8:e2301025. [PMID: 37814377 DOI: 10.1002/smtd.202301025] [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: 08/07/2023] [Indexed: 10/11/2023]
Abstract
Over the past decade, there has been a rising interest in utilizing functionalized porous polymers for sensor applications. By incorporating functional groups into nanostructured materials like hydrogels, nanosheets, and nanopores, exciting new opportunities have emerged for biomarker detection. The ability of functionalized polymers to undergo physical changes and deformations makes them perfect for modulating optical signals. This chemical mechanism enables the creation of biocompatible sensors for in situ biomarker measurement. Here a comprehensive overview of the current publication trends is provided in functionalized polymers, encompassing functional groups that can induce measurable physical deformations. It explores various materials categorized based on their detection targets, which include proteins, carbohydrates, ions, and deoxyribonucleic acid. As such, this work serves as a valuable reference for the development of functionalized polymer-based sensors.
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Affiliation(s)
- Litzy L García-Faustino
- School of Engineering and Sciences, Tecnológico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, NL, 64849, Mexico
| | - Stephen M Morris
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Steve J Elston
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Yunuen Montelongo
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
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21
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Wang ZK, Yuan ZX, Qian C, Liu XW. Plasmonic Probing of Deoxyribonucleic Acid Hybridization at the Single Base Pair Resolution. Anal Chem 2023; 95:18398-18406. [PMID: 38055795 DOI: 10.1021/acs.analchem.3c03316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Partial DNA duplex formation greatly impacts the quality of DNA hybridization and has been extensively studied due to its significance in many biological processes. However, traditional DNA sensing methods suffer from time-consuming amplification steps and hinder the acquisition of information about single-molecule behavior. In this work, we developed a plasmonic method to probe the hybridization process at a single base pair resolution and study the relationship between the complementarity of DNA analytes and DNA hybridization behaviors. We measured single-molecule hybridization events with Au NP-modified ssDNA probes in real time and found two hybridization adsorption events: stable and transient adsorption. The ratio of these two hybridization adsorption events was correlated with the length of the complementary sequences, distinguishing DNA analytes from different complementary sequences. By using dual incident angle excitation, we recognized different single-base complementary sequences. These results demonstrated that the plasmonic method can be applied to study partial DNA hybridization behavior and has the potential to be incorporated into the identification of similar DNA sequences, providing a sensitive and quantitative tool for DNA analysis.
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Affiliation(s)
- Zhao-Kun Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Zhen-Xuan Yuan
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Chen Qian
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Xian-Wei Liu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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22
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Yang S, Ding Z, Chu L, Su M, Liu H. Quantified instant conjugation of peptides on a nanogold surface for tunable ice recrystallization inhibition. NANOSCALE 2023; 15:19746-19756. [PMID: 38047706 DOI: 10.1039/d3nr05019j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The adverse effects of recrystallization limit the application of cryopreservation in many fields. Peptide-based materials play an essential role in the antifreezing area because of their excellent biocompatibility and abundant ice-binding sites. Peptide-gold nanoparticle conjugates can effectively reduce time and material costs through metal-thiol interactions, but controlled modification remains an outstanding issue, which makes it difficult to elucidate the antifreezing effects of antifreeze peptides at different densities and lengths. In this study, we developed an instant peptide capping on gold nanoparticles with butanol-assisted dehydration and provided a controllable quantitative coupling within a certain range. This chemical dehydration makes it possible to fabricate peptide-gold nanoparticle conjugates in large batches at minute levels. Based on this, the influence of the peptide density and sequence length on the antifreezing behaviors of the conjugates was investigated. The results evidenced that the antifreezing property of the flexible peptide conjugated on a rigid core is related to both the density and length of the peptide. In a certain range, the density is proportional to the antifreeze, while the length is negatively correlated with it. We proposed a rapidly controllable method for synthesizing peptide-gold nanoparticle conjugates, which may provide a universal approach for the development of subsequent recrystallization-inhibiting materials.
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Affiliation(s)
- Shixuan Yang
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Zhongxiang Ding
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Leiming Chu
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Mengke Su
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Honglin Liu
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
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23
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Gu M, Yi X, Shang Z, Nong X, Lin M, Xia F. A fuel-initiated DNA molecular machine for microRNA detection in serum via poly-adenine-mediated spherical nucleic acids. J Mater Chem B 2023; 11:11052-11063. [PMID: 37946538 DOI: 10.1039/d3tb02361c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
MicroRNAs (miRNAs) have been identified as promising disease diagnostic biomarkers. However, it is challenging to sensitively detect miRNAs, especially in complex biological environments, due to their low abundance and small size. Herein, we have developed a DNA-fueled molecular machine for sensitive detection of miRNA-22 (miR-22) in undiluted serum by combining poly-adenine-mediated spherical nucleic acids (polyA-SNAs) with a toehold mediated strand displacement reaction (TMSDR). The polyA-SNAs are constructed by the assembly of diblock DNA probes on a AuNP surface through the high binding affinity of polyA to AuNPs. The surface density of the diblock DNA probe can be controlled by tuning the length of the polyA block, and the orientation of the diblock DNA probe can adopt an upright conformation, which is beneficial to target hybridization and TMSDRs. TMSDR is an enzyme-free target recycling amplification approach. Taking advantage of polyA-mediated SNAs and TMSDR, the operation of the molecular machine based on two successive TMSDRs on polyA20-SNAs is rapid and efficient, which can significantly amplify the fluorescence response for detection of miR-22 in an undiluted complex matrix. The developed sensor can detect as low as 10 pM of target miRNA/DNA in undiluted fetal bovine serum within 30 min. The synergetic effect of polyA-mediated SNAs and TMSDR presents a potential alternative tool for the detection of biomarkers in real biological samples.
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Affiliation(s)
- Menghan Gu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Xiaoqing Yi
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Zhiwei Shang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xianliang Nong
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
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24
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Chan CKW, Szeto CC, Lee LKC, Xiao Y, Yin B, Ding X, Lee TWY, Lau JYW, Choi CHJ. A sub-10-nm, folic acid-conjugated gold nanoparticle as self-therapeutic treatment of tubulointerstitial fibrosis. Proc Natl Acad Sci U S A 2023; 120:e2305662120. [PMID: 37812696 PMCID: PMC10589645 DOI: 10.1073/pnas.2305662120] [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: 04/14/2023] [Accepted: 09/11/2023] [Indexed: 10/11/2023] Open
Abstract
Nanomedicines for treating chronic kidney disease (CKD) are on the horizon, yet their delivery to renal tubules where tubulointerstitial fibrosis occurs remains inefficient. We report a folic acid-conjugated gold nanoparticle that can transport into renal tubules and treat tubulointerstitial fibrosis in mice with unilateral ureteral obstruction. The 3-nm gold core allows for the dissection of bio-nano interactions in the fibrotic kidney, ensures the overall nanoparticle (~7 nm) to be small enough for glomerular filtration, and naturally inhibits the p38α mitogen-activated protein kinase in the absence of chemical or biological drugs. The folic acids support binding to selected tubule cells with overexpression of folate receptors and promote retention in the fibrotic kidney. Upon intravenous injection, this nanoparticle can selectively accumulate in the fibrotic kidney over the nonfibrotic contralateral kidney at ~3.6% of the injected dose. Delivery to the fibrotic kidney depends on nanoparticle size and disease stage. Notably, a single injection of this self-therapeutic nanoparticle reduces tissue degeneration, inhibits genes related to the extracellular matrix, and treats fibrosis more effectively than standard Captopril therapy. Our data underscore the importance of constructing CKD nanomedicines based on renal pathophysiology.
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Affiliation(s)
- Cecilia Ka Wing Chan
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Cheuk Chun Szeto
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Leo Kit Cheung Lee
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Yu Xiao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Bohan Yin
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Xiaofan Ding
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Thomas Wai Yip Lee
- School of Pharmacy, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - James Yun Wong Lau
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Chung Hang Jonathan Choi
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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25
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Ghoniem SM, ElZorkany HE, Hagag NM, El-Deeb AH, Shahein MA, Hussein HA. Development of multiplex gold nanoparticles biosensors for ultrasensitive detection and genotyping of equine herpes viruses. Sci Rep 2023; 13:15140. [PMID: 37704638 PMCID: PMC10500010 DOI: 10.1038/s41598-023-41918-4] [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: 06/03/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023] Open
Abstract
Gold nanoparticles (GNPs) biosensors can detect low viral loads and differentiate between viruses types, enabling early diagnosis and effective disease management. In the present study, we developed GNPs biosensors with two different capping agent, citrate-GNPs biosensors and polyvinylpyrrolidone (PVP)-GNPs biosensors for detection of EHV-1 and EHV-4 in multiplex real time PCR (rPCR). Citrate-GNPs and PVP-GNPs biosensors can detect dilution 1010 of EHV-1 with mean Cycle threshold (Ct) 11.7 and 9.6, respectively and one copy as limit of detection, while citrate-GNPs and PVP-GNPs biosensors can detect dilution 1010 of EHV-4 with mean Ct 10.5 and 9.2, respectively and one copy as limit of detection. These findings were confirmed by testing 87 different clinical samples, 4 more samples were positive with multiplex GNPs biosensors rPCR than multiplex rPCR. Multiplex citrate-GNPs and PVP-GNPs biosensors for EHV-1 and EHV-4 are a significant breakthrough in the diagnosis of these virus types. These biosensors offer high sensitivity and specificity, allowing for the accurate detection of the target viruses at very low concentrations and improve the early detection of EHV-1 and EHV-4, leading to faster control of infected animals to prevent the spread of these viruses.
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Affiliation(s)
- Shimaa M Ghoniem
- Department of Virology, Animal Health Research Institute, Agriculture Research Center, Giza, 12618, Egypt
| | - Heba E ElZorkany
- Nanotechnology and Advanced Materials Central Lab, Agriculture Research Center, Giza, 12619, Egypt
| | - Naglaa M Hagag
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Center, Giza, 12618, Egypt
| | - Ayman H El-Deeb
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, P.O. Box 12211, Giza, Egypt
- Department of Virology, Faculty of Veterinary Medicine, King Salman International University, South Sinai, Egypt
| | - Momtaz A Shahein
- Department of Virology, Animal Health Research Institute, Agriculture Research Center, Giza, 12618, Egypt
| | - Hussein A Hussein
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, P.O. Box 12211, Giza, Egypt.
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26
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Mirkin CA, Petrosko SH. Inspired Beyond Nature: Three Decades of Spherical Nucleic Acids and Colloidal Crystal Engineering with DNA. ACS NANO 2023; 17:16291-16307. [PMID: 37584399 DOI: 10.1021/acsnano.3c06564] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
The conception, synthesis, and invention of a nanostructure, now known as the spherical nucleic acid, or SNA, in 1996 marked the advent of a new field of chemistry. Over the past three decades, the SNA and its analogous anisotropic equivalents have provided an avenue for us to think about some of the most fundamental concepts in chemistry in new ways and led to technologies that are significantly impacting fields from medicine to materials science. A prime example is colloidal crystal engineering with DNA, the framework for using SNAs and related structures to synthesize programmable matter. Herein, we document the evolution of this framework, which was initially inspired by nature, and describe how it now allows researchers to chart paths to move beyond it, as programmable matter with real-world significance is envisioned and created.
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Affiliation(s)
- Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Sarah Hurst Petrosko
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
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27
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Hou TL, Zhang XL, Zhou J, Chai YQ, Yuan R. Near-Infrared-Driven Nanorocket for Rapid and Ultrasensitive Detection of MicroRNA. Anal Chem 2023; 95:13156-13162. [PMID: 37606955 DOI: 10.1021/acs.analchem.3c01962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Herein, by introducing gold nanostars (AuNSs) as fuel core, a near-infrared-driven nanorocket (NIDNR) with pretty fast walking was exploited for ultrasensitive miRNA detection. Compared with traditional nanomaterials-comprised nanomachines (NMs), the NIDNR possesses much better kinetic and thermodynamic performance owing to the extra photothermal driving force from localized surface plasmon (LSP). Impressively, the whole reaction time of NIDNR down to 15 min was realized, which is almost more than 8 times beyond those of conventional DNA-based NMs. This way, the inherent obstacle of traditional NMs, including long reaction time and low efficiency, could be easily addressed. As a proof of concept, the NIDNR was successfully applied to develop an electrochemical biosensing platform for rapid and sensitive detection of miRNA with an LOD down to 2.95 aM and achieved the real-time assay of real biological samples from human hepatocellular carcinoma cells (MHCC97L) and HeLa, thus providing an innovative insight to design more versatile DNA nanomachines for ultimate application in biosensing platform construction and clinical sample detection.
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Affiliation(s)
- Tong-Lin Hou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Jie Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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28
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Karami A, Hasani M. Methods to functionalize gold nanoparticles with tandem-phosphorothioate DNA: role of physicochemical properties of the phosphorothioate backbone in DNA adsorption to gold nanoparticles. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4104-4113. [PMID: 37551768 DOI: 10.1039/d3ay00960b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Perception of the differences in the physicochemical properties of phosphorothioate DNA (PS-DNA) and phosphodiester DNA (PO-DNA) greatly aids in understanding the AuNP-DNA binding process. Replacing one non-bridging oxygen atom of the anionic phosphodiester backbone with a sulfur atom leads to a major change in the DNA adsorption mechanism of AuNPs. In this work, we investigated and compared salt-aging, low pH-assisted, and freeze-thaw methods for conjugating phosphorothioate-modified oligonucleotides to AuNPs. The results obtained clearly demonstrate that only the pH-assisted method can successfully bind tandem phosphorothioate DNA to gold nanoparticles and sufficiently maintain the colloidal stability of AuNPs. When a phosphate group is converted to a phosphorothioate group, the negative charge of the phosphate group is located on the sulfur atom. Due to the soft nature of sulfur (a very weak H-bond acceptor), the negative charge on the sulfur atom cannot be shielded even with the gradual addition of salt to increase the ionic strength, so, the pH-assisted based method is the best for the functionalization of AuNPs with tandem-PS DNA.
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Affiliation(s)
- Abbas Karami
- Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65174, Iran.
| | - Masoumeh Hasani
- Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65174, Iran.
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29
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Calcaterra HA, Zheng CY, Seifert S, Yao Y, Jiang Y, Mirkin CA, Deng J, Lee B. Hints of Growth Mechanism Left in Supercrystals. ACS NANO 2023; 17:15999-16007. [PMID: 37552879 DOI: 10.1021/acsnano.3c04365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Supercrystals of DNA-functionalized nanoparticles are visualized in three dimensions using X-ray ptychographic tomography, and their reciprocal spaces are mapped with small-angle X-ray scattering in order to better understand their internal defect structures. X-ray ptychographic tomography reveals various types of defects in an assembly that otherwise exhibits a single crystalline diffraction pattern. On average, supercrystals composed of smaller nanoparticles are smaller in size than supercrystals composed of larger particles. Additionally, supercrystals composed of small nanoparticles are typically aggregated into larger "necklace-like" structures. Within these larger structures, some but not all pairs of connected domains are coherent in their relative orientations. In contrast, supercrystals composed of larger nanoparticles with longer DNA ligands typically form faceted crystals. The combination of these two complementary X-ray techniques reveals that the crystalline assemblies grow by aggregation of smaller assemblies followed by rearrangement of nanoparticles.
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Affiliation(s)
- Heather A Calcaterra
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Cindy Y Zheng
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Soenke Seifert
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Yudong Yao
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Yi Jiang
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Chad A Mirkin
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Junjing Deng
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
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30
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Shen P, Qu X, Ge Q, Huang T, Sun Q, Lu Z. Magnetic Bead Spherical Nucleic Acid Microstructure for Reliable DNA Preservation and Repeated DNA Reading. ACS Synth Biol 2023; 12:2393-2402. [PMID: 37470286 DOI: 10.1021/acssynbio.3c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
DNA is an attractive medium for long-term data storage because of its density, ease of copying, sustainability, and longevity. Recent advances have focused on the development of new encoding algorithms, automation, and sequencing technologies. Despite progress in these subareas, the most challenging hurdle in the deployment of DNA storage remains the reliability of preservation and the repeatability of reading. Herein, we report the construction of a magnetic bead spherical nucleic acid (MB-SNA) composite microstructure and its use as a cost-effective platform for reliable DNA preservation and repeated reading. MB-SNA has an inner core of silica@γ-Fe2O3@silica microbeads and an outer spherical shell of double-stranded DNA (dsDNA) with a density as high as 34 pmol/cm2. For MB-SNA, each strand of dsDNA stored a piece of data, and the high-density packing of dsDNA achieved high-capacity storage. MB-SNA was advantageous in terms of reliable preservation over free DNA. By accelerated aging tests, the data of MB-SNA is demonstrated to be readable after 0.23 million years of preservation at -18 °C and 50% relative humidity. Moreover, MB-SNA facilitated repeated reading by facile PCR-magnetic separation. After 10 cycles of PCR access, the retention rate of dsDNA for MB-SNA is demonstrated to be as high as 93%, and the accuracy of sequencing is more than 98%. In addition, MB-SNA makes cost-effective DNA storage feasible. By serial dilution, the physical limit for MB-SNA to achieve accurate reading is probed to be as low as two microstructures.
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Affiliation(s)
- Peng Shen
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiaojun Qu
- Laboratory Medicine Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Ting Huang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
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31
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Wang HN, Vo-Dinh T. Cascade Amplified Plasmonics Molecular Biosensor for Sensitive Detection of Disease Biomarkers. BIOSENSORS 2023; 13:774. [PMID: 37622860 PMCID: PMC10452163 DOI: 10.3390/bios13080774] [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: 06/16/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Recent advances in molecular technologies have provided various assay strategies for monitoring biomarkers, such as miRNAs for early detection of various diseases and cancers. However, there is still an urgent unmet need to develop practical and accurate miRNA analytical tools that could facilitate the incorporation of miRNA biomarkers into clinical practice and management. In this study, we demonstrate the feasibility of using a cascade amplification method, referred to as the "Cascade Amplification by Recycling Trigger Probe" (CARTP) strategy, to improve the detection sensitivity of the inverse Molecular Sentinel (iMS) nanobiosensor. The iMS nanobiosensor developed in our laboratory is a unique homogeneous multiplex bioassay technique based on surface-enhanced Raman scattering (SERS) detection, and was used to successfully detect miRNAs from clinical samples. The CARTP strategy based on the toehold-mediated strand displacement reaction is triggered by a linear DNA strand, called the "Recycling Trigger Probe" (RTP) strand, to amplify the iMS SERS signal. Herein, by using the CARTP strategy, we show a significantly improved detection sensitivity with the limit of detection (LOD) of 45 fM, which is 100-fold more sensitive than the non-amplified iMS assay used in our previous report. We envision that the further development and optimization of this strategy ultimately will allow multiplexed detection of miRNA biomarkers with ultra-high sensitivity for clinical translation and application.
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Affiliation(s)
- Hsin-Neng Wang
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC 27708, USA;
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Tuan Vo-Dinh
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC 27708, USA;
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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32
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Duan N, Chang Y, Lv W, Li C, Lu C, Wang Z, Wu S. Ratiometric SERS aptasensing for simultaneous quantitative detection of histamine and tyramine in fishes. Talanta 2023; 265:124891. [PMID: 37442002 DOI: 10.1016/j.talanta.2023.124891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023]
Abstract
Herein, a SiO2@Ag NPs core/shell nanoparticles were synthesized to fabricate a surface-enhanced Raman spectroscopy (SERS) sensor for the simultaneous determination of histamine (HIS) and tyramine (TYR) based on specific aptamer recognition and ratiometric strategy. SiO2@Ag NPs with 4-thiosaminophenol (4-ATP) and Nile blue A (NBA) molecules were used as an internal standard (IS) and labeled with aptamers corresponding to HIS and TYR, respectively. Raman reporter molecules ROX and Cy5 labeled complementary DNA (cDNA) were then hybridized with aptamers to form rigid double-stranded DNA. After the HIS and TYR were captured by their aptamers, resulting in the dissociation of cDNA and separated from the SERS substrate. Therefore, the SERS signal intensity at 1503 cm-1 of ROX and 1358 cm-1 of Cy5 tagged on the terminal of cDNA decreased with the concentration of HIS and TYR increasing, while the SERS signal intensity at 1079 cm-1 of 4-APT and 592 cm-1 of NBA on the substrate remain stable. Thus, the concentrations of HIS and TYR can be determined by the I1503/I1079 and I1358/I592 values, respectively. This sensing strategy achieves a lower detection limit of 0.2 ng/mL for HIS and 0.05 ng/mL for TYR, respectively, demonstrating promising applications in sensitive detection of BAs in animal-derived foodstuff.
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Affiliation(s)
- Nuo Duan
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Yuting Chang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenhui Lv
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Changxin Li
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Chunxia Lu
- Institute of Animal Husbandry and Veterinary Science, Xinjiang Academy of Agriculture and Reclamation Sciences, Shihezi, 83200, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Shijia Wu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
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33
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Park J, Ban C. Development of a one-shot dual aptamer-based fluorescence nanosensor for rapid, sensitive, and label-free detection of periostin. Sci Rep 2023; 13:10224. [PMID: 37353600 PMCID: PMC10290134 DOI: 10.1038/s41598-023-37418-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023] Open
Abstract
Periostin is associated with several diseases, including cancers. Therefore, monitoring blood periostin levels is a powerful tool for diagnosing various diseases and identifying their severity. However, conventional detection methods pose several challenges, including high costs. To address these issues, we developed a novel one-shot dual aptamer-based fluorescence nanosensor for detecting periostin. The proposed nanosensor facilitates rapid, label-free, and sensitive detection of periostin using gold nanoprobes constructed by rhodamine-b isothiocyanate, PL2trunc aptamer, and gold nanoparticles and silver nanoprobes fabricated by the PL5trunc aptamer and silver nanoparticles. The two nanoprobes form a core-satellite structure by interacting with periostin, and the nanosensor detects periostin through the fluorescence regenerated by the increased proximity between them. The nanosensor successfully detected periostin with remarkable detection limits of 106.68 pM in buffer and 463.3 pM in serum-spiked conditions within 30 min without additional washing or signal amplification processes. Considering serum periostin levels in various diseases, the proposed nanosensor provides a suitable method for identifying patients with various diseases and determining disease severity. Moreover, the platform can be helpful as a practical method for on-site medical diagnosis because it can be adapted to detect other biomarkers simply by replacing the aptamer with other detection probes.
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Affiliation(s)
- Jonghoon Park
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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Callmann CE, Vasher MK, Das A, Kusmierz CD, Mirkin CA. In Vivo Behavior of Ultrasmall Spherical Nucleic Acids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300097. [PMID: 36905236 PMCID: PMC10272074 DOI: 10.1002/smll.202300097] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/09/2023] [Indexed: 05/10/2023]
Abstract
The biological properties of spherical nucleic acids (SNAs) are largely independent of nanoparticle core identity but significantly affected by oligonucleotide surface density. Additionally, the payload-to-carrier (i.e., DNA-to-nanoparticle) mass ratio of SNAs is inversely proportional to core size. While SNAs with many core types and sizes have been developed, all in vivo analyses of SNA behavior have been limited to cores >10 nm in diameter. However, "ultrasmall" nanoparticle constructs (<10 nm diameter) can exhibit increased payload-to-carrier ratios, reduced liver accumulation, renal clearance, and enhanced tumor infiltration. Therefore, we hypothesized that SNAs with ultrasmall cores exhibit SNA-like properties, but with in vivo behavior akin to traditional ultrasmall nanoparticles. To investigate, we compared the behavior of SNAs with 1.4-nm Au102 nanocluster cores (AuNC-SNAs) and SNAs with 10-nm gold nanoparticle cores (AuNP-SNAs). Significantly, AuNC-SNAs possess SNA-like properties (e.g., high cellular uptake, low cytotoxicity) but show distinct in vivo behavior. When intravenously injected in mice, AuNC-SNAs display prolonged blood circulation, lower liver accumulation, and higher tumor accumulation than AuNP-SNAs. Thus, SNA-like properties persist at the sub-10-nm length scale and oligonucleotide arrangement and surface density are responsible for the biological properties of SNAs. This work has implications for the design of new nanocarriers for therapeutic applications.
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Affiliation(s)
- Cassandra E Callmann
- Department of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, IL, 60208, USA
| | - Matthew K Vasher
- Department of Biomedical Engineering, International Institute for Nanotechnology, Northwestern University, Evanston, IL, 60208, USA
| | - Anindita Das
- Department of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, IL, 60208, USA
| | - Caroline D Kusmierz
- Department of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, International Institute for Nanotechnology, Northwestern University, Evanston, IL, 60208, USA
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35
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Ding Q, Qiu W, Sun C, Ren H, Liu G. Comparison of DNA-Gold Nanoparticle Conjugation Methods: Application in Lateral Flow Nucleic Acid Biosensors. Molecules 2023; 28:molecules28114480. [PMID: 37298955 DOI: 10.3390/molecules28114480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Lateral flow nucleic acid biosensors (LFNABs) have attracted extensive attention due to their rapid turnaround time, low cost, and results that are visible to the naked eye. One of the key steps to develop LFNABs is to prepare DNA-gold nanoparticle (DNA-AuNP) conjugates, which affect the sensitivity of LFNABs significantly. To date, various conjugation methods-including the salt-aging method, microwave-assisted dry heating method, freeze-thaw method, low-pH method, and butanol dehydration method-have been reported to prepare DNA-AuNP conjugates. In this study, we conducted a comparative analysis of the analytical performances of LFNABs prepared with the above five conjugation methods, and we found that the butanol dehydration method gave the lowest detection limit. After systematic optimization, the LFNAB prepared with the butanol dehydration method had a detection limit of 5 pM for single-strand DNA, which is 100 times lower than that of the salt-aging method. The as-prepared LFNAB was applied to detect miRNA-21 in human serum, with satisfactory results. The butanol dehydration method thus offers a rapid conjugation approach to prepare DNA-AuNP conjugates for LFNABs, and it can also be extended to other types of DNA biosensors and biomedical applications.
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Affiliation(s)
- Qiaoling Ding
- School of Food Engineering, Anhui Science and Technology University, Fengyang 233100, China
- Yangtze Delta Drug Advanced Research Institute, No.100, Dongtinghu Road, Nantong 226133, China
- Enfin Biotech (Jiangsu) Co., Ltd., No.100, Dongtinghu Road, Nantong 226133, China
| | - Wanwei Qiu
- School of Food Engineering, Anhui Science and Technology University, Fengyang 233100, China
- School of Life and Health Science, Anhui Science and Technology University, Fengyang 233100, China
| | - Chunxue Sun
- School of Food Engineering, Anhui Science and Technology University, Fengyang 233100, China
- Yangtze Delta Drug Advanced Research Institute, No.100, Dongtinghu Road, Nantong 226133, China
- Enfin Biotech (Jiangsu) Co., Ltd., No.100, Dongtinghu Road, Nantong 226133, China
| | - Hongxin Ren
- Enfin Biotech (Jiangsu) Co., Ltd., No.100, Dongtinghu Road, Nantong 226133, China
| | - Guodong Liu
- School of Food Engineering, Anhui Science and Technology University, Fengyang 233100, China
- Enfin Biotech (Jiangsu) Co., Ltd., No.100, Dongtinghu Road, Nantong 226133, China
- School of Chemistry and Chemical Engineering, Linyi University, Shuangling Road, Linyi 276000, China
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36
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Hincapie R, Bhattacharya S, Keshavarz-Joud P, Chapman AP, Crooke SN, Finn MG. Preparation and Biological Properties of Oligonucleotide-Functionalized Virus-like Particles. Biomacromolecules 2023. [PMID: 37257068 DOI: 10.1021/acs.biomac.3c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Oligonucleotides are powerful molecules for programming function and assembly. When arrayed on nanoparticle scaffolds in high density, the resulting molecules, spherical nucleic acids (SNAs), become imbued with unique properties. We used the copper-catalyzed azide-alkyne cycloaddition to graft oligonucleotides on Qβ virus-like particles to see if such structures also gain SNA-like behavior. Copper-binding ligands were shown to promote the click reaction without degrading oligonucleotide substrates. Reactions were first optimized with a small-molecule fluorogenic reporter and were then applied to the more challenging synthesis of polyvalent protein nanoparticle-oligonucleotide conjugates. The resulting particles exhibited the enhanced cellular uptake and protection from nuclease-mediated oligonucleotide cleavage characteristic of SNAs, had similar residence time in the liver relative to unmodified particles, and were somewhat shielded from immune recognition, resulting in nearly 10-fold lower antibody titers relative to unmodified particles. Oligonucleotide-functionalized virus-like particles thus provide an interesting option for protein nanoparticle-mediated delivery of functional molecules.
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37
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Hao X, St-Pierre JP, Zou S, Cao X. Localized surface plasmon resonance biosensor chip surface modification and signal amplifications toward rapid and sensitive detection of COVID-19 infections. Biosens Bioelectron 2023; 236:115421. [PMID: 37244083 DOI: 10.1016/j.bios.2023.115421] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/01/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
We developed a multi-pronged approach to enhance the detection sensitivity of localized surface plasmon resonance (LSPR) sensor chips to detect SARS-CoV-2. To this end, poly(amidoamine) dendrimers were immobilized onto the surface of LSPR sensor chips to serve as templates to further conjugate aptamers specific for SARS-CoV-2. The immobilized dendrimers were shown to reduce surface nonspecific adsorptions and increase capturing ligand density on the sensor chips, thereby improving detection sensitivity. To characterize the detection sensitivity of the surface-modified sensor chips, SARS-CoV-2 spike protein receptor-binding domain was detected using LSPR sensor chips with different surface modifications. The results showed that the dendrimer-aptamer modified LSPR sensor chip exhibited a limit of detection (LOD) of 21.9 pM, a sensitivity that was 9 times and 152 times more sensitive than the traditional aptamer- or antibody-based LSPR sensor chips, respectively. In addition, detection sensitivity was further improved by combining rolling circle amplification product and gold nanoparticles to further amplify the detection signals by increasing both the target mass and plasmonic coupling effects. Using pseudo SARS-CoV-2 viral particles as detection targets, we demonstrated that this combined signal intensification approach further enhanced the detection sensitivity by 10 folds with a remarkable LOD of 148 vp/mL, making it one of the most sensitive SARS-CoV-2 detection assays reported to date. These results highlight the potential of a novel LSPR-based detection platform for sensitive and rapid detection of COVID-19 infections, as well as other viral infections and point-of-care applications.
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Affiliation(s)
- Xingkai Hao
- Department of Chemical and Biological Engineering, University of Ottawa, 161 Louis Pasteur, Ottawa, Ontario, K1N 6N5, Canada
| | - Jean-Philippe St-Pierre
- Department of Chemical and Biological Engineering, University of Ottawa, 161 Louis Pasteur, Ottawa, Ontario, K1N 6N5, Canada
| | - Shan Zou
- Metrology Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Xudong Cao
- Department of Chemical and Biological Engineering, University of Ottawa, 161 Louis Pasteur, Ottawa, Ontario, K1N 6N5, Canada.
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38
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Jergens E, de Araujo Fernandes-Junior S, Cui Y, Robbins A, Castro CE, Poirier MG, Gurcan MN, Otero JJ, Winter JO. DNA-caged nanoparticles via electrostatic self-assembly. NANOSCALE 2023. [PMID: 37184508 DOI: 10.1039/d3nr01424j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
DNA-modified nanoparticles enable DNA sensing and therapeutics in nanomedicine and are also crucial for nanoparticle self-assembly with DNA-based materials. However, methods to conjugate DNA to nanoparticle surfaces are limited, inefficient, and lack control. Inspired by DNA tile nanotechnology, we demonstrate a new approach to nanoparticle modification based on electrostatic attraction between negatively charged DNA tiles and positively charged nanoparticles. This approach does not disrupt nanoparticle surfaces and leverages the programmability of DNA nanotechnology to control DNA presentation. We demonstrated this approach using a vareity of nanoparticles, including polymeric micelles, polystyrene beads, gold nanoparticles, and superparamagnetic iron oxide nanoparticles with sizes ranging from 5-20 nm in diameter. DNA cage formation was confirmed through transmission electron microscopy (TEM), neutralization of zeta potential, and a series of fluorescence experiments. DNA cages present "handle" sequences that can be used for reversible target attachment or self-assembly. Handle functionality was verified in solution, at the solid-liquid interface, and inside fixed cells, corresponding to applications in biosensing, DNA microarrays, and erasable immunocytochemistry. These experiments demonstrate the versatility of the electrostatic DNA caging approach and provide a new pathway to nanoparticle modification with DNA that will empower further applications of these materials in medicine and materials science.
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Affiliation(s)
- Elizabeth Jergens
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA.
| | - Silvio de Araujo Fernandes-Junior
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA.
- Department of Pathology and the Neurological Research Institute, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Curing Cancer Through Research in Engineering and Sciences (CCE-CURES), The Ohio State University, Columbus, OH, USA
| | - Yixiao Cui
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, USA
| | - Ariel Robbins
- Department of Physics, The Ohio State University, Columbus, OH, USA
- Biophysics Program, The Ohio State University, Columbus, OH, USA
| | - Carlos E Castro
- Biophysics Program, The Ohio State University, Columbus, OH, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, USA
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH, USA
- Biophysics Program, The Ohio State University, Columbus, OH, USA
| | - Metin N Gurcan
- Center for Biomedical Informatics, School of Medicine, Wake Forest University, Winston-Salem, NC, USA
| | - Jose J Otero
- Department of Pathology and the Neurological Research Institute, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Curing Cancer Through Research in Engineering and Sciences (CCE-CURES), The Ohio State University, Columbus, OH, USA
| | - Jessica O Winter
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA.
- Curing Cancer Through Research in Engineering and Sciences (CCE-CURES), The Ohio State University, Columbus, OH, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, USA
- Biophysics Program, The Ohio State University, Columbus, OH, USA
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39
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Abstract
ConspectusNanosynthesis is the art of creating nanostructures, with on-demand synthesis as the ultimate goal. Noble metal nanoparticles have wide applications, but the available synthetic methods are still limited, often giving nanospheres and symmetrical nanocrystals. The fundamental reason is that the conventional weak ligands are too labile to influence the materials deposition, so the equivalent facets always grow equivalently. Considering that the ligands are the main synthetic handles in colloidal synthesis, our group has been exploring strong ligands for new growth modes, giving a variety of sophisticated nanostructures. The model studies often involve metal deposition on seeds functionalized with a certain strong ligand, so that the uneven distribution of the surface ligands could guide the subsequent deposition.In this Account, we focus on the design principles underlying the new growth modes, summarizing our efforts in this area along with relevant literature works. The basics of ligand control are first revisited. Then, the four major growth modes are summarized as follows: (1) The curvature effects would divert the materials deposition away from the high-curvature tips when the ligands are insufficient. With ligands fully covering the seeds, the sparser ligand packing at the tips would then promote the initial nucleation thereon. (2) The strong ligands may get trapped under the incoming metal layer, thus modulating the interfacial energy of the core-shell interface. The evidence for embedded ligands is discussed, along with examples of Janus nanostructures arising from the synthetic control, including metal-metal, metal-semiconductor, and metal-C60 systems using a variety of ligands. (3) Active surface growth is an unusual mode with divergent growth rates, so that part of the emerging surface is inhibited, and the growth is focused onto a few active sites. With seeds attached to oxide substrates, the selective deposition at the metal-substrate interface produces ultrathin nanowires. The synthesis can be generally applied to grow Au, Ag, Pd, Pt, and hybrid nanowires, with straight, spiral, or helical structures, and even rapid alteration of segments via electrochemical methods. In contrast, active surface growth for colloidal nanoparticles has to be more carefully controlled. The rich growth phenomena are discussed, highlighting the role of strong ligands, the control of deposition rates, the chiral induction, and the evidence for the active sites. (4) An active site with sparse ligands could also be exploited in etching, where the freshly exposed surface would promote further etching. The result is an unusual sharpening etching mode, in contrast to the conventional rounding mode for minimized surface energy.Colloidal nanosynthesis holds great promise for scalable on-demand synthesis, providing the crucial nanomaterials for future explorations. The strong ligands have delivered powerful synthetic controls, which could be further enhanced with in-depth studies on growth mechanisms and synthetic strategies, as well as functions and properties.
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Affiliation(s)
- Ruixue Xiao
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jia Jia
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ruoxu Wang
- Department of Chemistry, School of Science, Westlake University, Hangzhou 310023, China
| | - Yuhua Feng
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Hongyu Chen
- Department of Chemistry, School of Science, Westlake University, Hangzhou 310023, China
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40
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Gu M, Yi X, Xiao Y, Zhang J, Lin M, Xia F. Programming the dynamic range of nanobiosensors with engineering poly-adenine-mediated spherical nucleic acid. Talanta 2023; 256:124278. [PMID: 36681039 DOI: 10.1016/j.talanta.2023.124278] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/19/2023]
Abstract
Spherical nucleic acid (SNA) conjugates consisting of gold cores functionalized with a densely packed DNA shells are of great significance in the field of medical detection and intracellular imaging. Especially, poly adenine (polyA)-mediated SNAs can improve the controllability and reproducibility of DNA assembly on the nanointerface, showing the tunable hybridization ability. However, due to the physics of single-site binding, the biosensor based on SNA usually exhibits a dynamic range spanning a fixed 81-fold change in target concentration, which limits its application in disease monitoring. To address this problem, we report a tri-block DNA-based approach to assemble SNA for nucleic acid detection based on structure-switching mechanism with programmable dynamic range. The tri-block DNA is a FAM-labeled stem-loop structure, which contains three blocks: polyA block as an anchoring block for tunable surface density, stem block with different GC base pair content for varying the structure stability, and the fixed loop block for target recognition. We find that varying the polyA block, the reaction temperature, and the GC base pair, SNA shows different target binding affinity and detection limit but with normally 81-fold dynamic range. We can extend the dynamic range to 1000-fold by using the combination of two SNAs with different affinity, and narrow the dynamic range to 5-fold by sequestration mechanism. Furthermore, the tunable SNA enables sensitive detection of mRNA in cells. Given its tunable dynamic range, such nanobiosensor based on SNA offers new possibility for various biomedical and clinical applications.
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Affiliation(s)
- Menghan Gu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China; Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Xiaoqing Yi
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Yucheng Xiao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jian Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China; Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China.
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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41
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Sun Y, Qu X, Qiu P, Mao C. A nanoparticle-based molecular beacon for directly detecting attomolar small RNA from plasma without purification. Talanta 2023; 260:124602. [PMID: 37148690 DOI: 10.1016/j.talanta.2023.124602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/08/2023]
Abstract
Molecular beacons (MBs) are DNA-based probes that detect DNA or RNA fragments and hold promise for monitoring diseases and studying protein-nucleic acid interactions. MBs usually use fluorescent molecules as fluorophores for reporting the target detection event. However, the fluorescence of the traditional fluorescent molecules can bleach and even be interfered with the background autofluorescence, reducing the detection performance. Hence, we propose to develop a nanoparticle-based MB (NPMB) that uses upconversion nanoparticles (UCNPs) as a fluorophore, which can be excited by near-infrared light to avoid background autofluorescence and thus enables us to detect small RNA from complicated clinical samples such as plasma. Specifically, we employ a DNA hairpin structure, with one segment complementary to the target RNA, to position a quencher (gold nanoparticles, Au NPs) and the UCNP fluorophore in close proximity, leading to the quenching of the fluorescence of UCNPs in the absence of a target nucleic acid. Only when the hairpin structure is complementary with the detection target, will the hairpin structure be destroyed to separate Au NPs and UCNPs, resulting in the instant recovery of the fluorescence signal of UCNPs and the consequent ultrasensitive detection of the target concentrations. The NPMB has an ultra-low background signal because UCNPs can be excited with NIR light with a wavelength longer than the emitted visible light. We demonstrate that the NPMB can successfully detect a small (22-nt) RNA (using a microRNA cancer biomarker, miR-21, as an example) and a small single-stranded DNA (complementing the cDNA of miR-21) in aqueous solutions from 1 aM to 1 pM, with the linear detection range being 10 aM to 1 pM for the former and 1 aM to 100 fM for the latter. We further show that the NPMB can be used to detect unpurified small RNA (miR-21) in clinical samples such as plasma with the same detection region. Our work suggests that the NPMB is a promising label-free and purification-free method for detecting small nucleic acid biomarkers in clinical samples with a detection limit as low as the aM level.
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Affiliation(s)
- Yueyi Sun
- Department of Chemistry and Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, Norman, OK, 73019, USA
| | - Xuewei Qu
- Department of Chemistry and Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, Norman, OK, 73019, USA
| | - Penghe Qiu
- Department of Chemistry and Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, Norman, OK, 73019, USA
| | - Chuanbin Mao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, PR China.
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42
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Wang X, Mu X, Li J, Liu G, Zhao S, Tian J. A novel nanoparticle surface-constrained CRISPR-Cas12a 3D DNA walker-like nanomachines for sensitive and stable miRNAs detection. Anal Chim Acta 2023; 1251:340950. [PMID: 36925314 DOI: 10.1016/j.aca.2023.340950] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 02/01/2023] [Accepted: 02/05/2023] [Indexed: 02/10/2023]
Abstract
The CRISPR-Cas system has broad prospects as a new type of nucleic acid signal amplification technology based on the trans-cleavage activity of Cas12a to single-stranded DNA, but the trans-cleavage reaction efficiency is relatively low in solution. In order to overcome this negative factor, a new 3D DNA nanomachine whose CRISPR-Cas12a is limited to the surface of nanoparticles is used for sensitive and stable detection of miRNA. By loading Cas12a activator onto spherical nucleic acid (SNA), the CRISPR-Cas12a activator system on the surface of Au nanoparticles (AuNPs) acts as a walker to carry out continuous recognition-walking-cutting reaction on the surface of AuNPs, which enhances the trans-cleavage activity of Cas12a to SNAs. Benefiting from the confinement effect of spherical nucleic acids surface, a 3D DNA nanomachine has been developed for the detection of miRNA-21, which has achieved high sensitivity and accuracy, and the detection limit is able to reach 8.0 pM. This new 3D DNA walker-like nanomachine provided another insight for future bioanalysis and early clinical diagnoses of disease and liquid biopsy.
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Affiliation(s)
- Xin Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Xiaomei Mu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Jinshen Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Guang Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Shulin Zhao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Jianniao Tian
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China.
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43
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Jiang K, Wu J, Kim JE, An S, Nam JM, Peng YK, Lee JH. Plasmonic Cross-Linking Colorimetric PCR for Simple and Sensitive Nucleic Acid Detection. NANO LETTERS 2023; 23:3897-3903. [PMID: 37083438 DOI: 10.1021/acs.nanolett.3c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Simple, low-cost, and accurate nucleic acid assay platforms hold great promise for point-of-care (POC) pathogen detection, disease surveillance, and control. Plasmonic photothermal polymerase chain reaction (PPT-PCR) is a powerful and efficient nucleic acid amplification technique, but it lacks a simple and convenient analysis method for POC applications. Herein, we propose a novel plasmonic cross-linking colorimetric PCR (PPT-ccPCR) assay by integrating plasmonic magnetic nanoparticle (PMN)-based PPT-PCR with gold nanoparticle (AuNP)-based cross-linking colorimetry. AuNPs form assembled structures with the PMNs in the presence of amplicons and collect in a magnetic field, resulting in color changes to the supernatant. Target DNA with concentrations as low as 5 copies/μL can be visually detected within 40 min. The achieved limit of detection was 1.8 copies/μL based on the absorption signals. This simple and sensitive strategy needs no expensive instrumentation and demonstrates high potential for POC detection while enabling further applications in clinical diagnostics.
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Affiliation(s)
- Kunlun Jiang
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jingrui Wu
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Ji-Eun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sujin An
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Yung-Kang Peng
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jung-Hoon Lee
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
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44
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Rehn SM, Gerrard-Anderson TM, Chen Y, Wang P, Robertson T, Senftle TP, Jones MR. Surface Ligands Dictate the Mechanical Properties of Inorganic Nanomaterials. ACS NANO 2023; 17:6698-6707. [PMID: 36971281 DOI: 10.1021/acsnano.2c12497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The ability for organic surface chemistry to influence the properties of inorganic nanomaterials is appreciated in some instances but is poorly understood in terms of mechanical behavior. Here we demonstrate that the global mechanical strength of a silver nanoplate can be modulated according to the local binding enthalpy of its surface ligands. A continuum-based core-shell model for nanoplate deformation shows that the interior of a particle retains bulk-like properties while the surface shell has yield strength values that depend on surface chemistry. Electron diffraction experiments reveal that, relative to the core, atoms at the nanoplate surface undergo lattice expansion and disordering directly related to the coordinating strength of the surface ligand. As a result, plastic deformation of the shell is more difficult, leading to an enhancement of the global mechanical strength of the plate. These results demonstrate a size-dependent coupling between chemistry and mechanics at the nanoscale.
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45
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Xu Z, Ma T, Han X, Liu G, Luo T, Yu M, Han L, Chen K, Chen G. Study on the detection of anthrax by ICP-MS based on gold nanoparticle labeling. Technol Health Care 2023; 31:283-292. [PMID: 37066929 DOI: 10.3233/thc-236024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
BACKGROUND In recent years, inductively coupled plasma mass spectrometry (ICP-MS) has been widely used in the field of molecular biology because of its unique advantages. Anthrax is a widespread and long-standing infectious disease, which affects and restricts people's work and life seriously. OBJECTIVE The study goal is to develop a new method for the detection of anthrax. METHODS A rapid, sensitive and accurate method for the detection of anthrax characteristic DNA was proposed by combing gold nanoparticles (AuNPs) and inductively coupled plasma mass spectrometry. RESULTS The linear range of this method is 100-2500 pmol/L and the limit of detection of 16.61 pmol/L. CONCLUSION The proposed method has numerous advantages, including simplicity of operation, high sensitivity, and specificity, which provides a new idea for the detection of anthrax. Importantly, this methodology has good potential for the detection of other biological substances such as bacteria and viruses by changing the modification sequence on the nanoparticle probe.
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Dimitrov E, Toncheva-Moncheva N, Doumanov JA, Mladenova K, Petrova S, Pispas S, Rangelov S. Three-Dimensional Nucleic Acid Nanostructures Based on Self-Assembled Polymer-Oligonucleotide Conjugates of Comblike and Coil-Comb Chain Architectures. Biomacromolecules 2023; 24:2213-2224. [PMID: 37014992 DOI: 10.1021/acs.biomac.3c00126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Spherical nucleic acids have emerged as a class of nanostructures, exhibiting a wide variety of properties, distinctly different from those of linear nucleic acids, and a plethora of applications in therapeutics and diagnostics. Herein, we report on preparation of 3D nucleic acid nanostructures, prepared by self-assembly of polymer-oligonucleotide conjugates. The latter are obtained by grafting multiple alkyne-functionalized oligonucleotide strands onto azide-modified homo-, block, and random (co)polymers of chloromethylstyrene via initiator-free click coupling chemistry to form conjugates of comblike and coil-comb chain architectures. The resulting conjugates are amphiphilic and form stable nanosized supramolecular structures in aqueous solution. The nanoconstructs are thoroughly investigated and a number of physical characteristics, in particular, molar mass, size, aggregation number, zeta potential, material density, number of oligonucleotide strands per particle, grafting density, and their relation to hallmark properties of spherical nucleic acids - biocompatibility, resistance against DNase I, cellular uptake without the need for transfection agents - are determined.
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Affiliation(s)
- Erik Dimitrov
- Institute of Polymers, Bulgarian Academy of Sciences, Akad. G. Bonchev St. 103A, 1113 Sofia, Bulgaria
| | - Natalia Toncheva-Moncheva
- Institute of Polymers, Bulgarian Academy of Sciences, Akad. G. Bonchev St. 103A, 1113 Sofia, Bulgaria
| | - Jordan A Doumanov
- Department of Biochemistry, Faculty of Biology, Sofia University ″St. Kliment Ohridski″ 8, Dragan Tsankov Blvd., 1164 Sofia, Bulgaria
| | - Kirilka Mladenova
- Department of Biochemistry, Faculty of Biology, Sofia University ″St. Kliment Ohridski″ 8, Dragan Tsankov Blvd., 1164 Sofia, Bulgaria
| | - Svetla Petrova
- Department of Biochemistry, Faculty of Biology, Sofia University ″St. Kliment Ohridski″ 8, Dragan Tsankov Blvd., 1164 Sofia, Bulgaria
| | - Stergios Pispas
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vass. Constantinou Ave., 116 35 Athens, Greece
| | - Stanislav Rangelov
- Institute of Polymers, Bulgarian Academy of Sciences, Akad. G. Bonchev St. 103A, 1113 Sofia, Bulgaria
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Fitzgerald G, Low D, Morgan L, Hilt C, Benford M, Akers C, Hornback S, Hilt JZ, Scott D. Controlled Release of DNA Binding Anticancer Drugs from Gold Nanoparticles with Near-Infrared Radiation. J Pharm Sci 2023; 112:1064-1071. [PMID: 36493881 PMCID: PMC10033344 DOI: 10.1016/j.xphs.2022.12.001] [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: 08/20/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Traditional chemotherapies target rapidly developing cells in the human body resulting in harsh side effects including fatigue, immune system suppression, and nausea, among others. Delivery systems to focus the active pharmaceutical ingredients (APIs) to the diseased tissue can diminish the negative side effects while improving treatment outcomes. Gold nanoparticles (AuNP) offer many unique advantages as drug delivery vehicles, including being biologically inert, easily adaptable to various shapes and sizes, able to create a strong Au-thiol bond, and able to generate heat upon the absorption of near-infrared light. To this end, a AuNP delivery vehicle was engineered to load and release two DNA binding anti-cancer drugs, mithramycin and doxorubicin, in a controlled fashion. The drugs were loaded onto the surface of the AuNP with temperature sensitive linkages. The amount of heat generated, and subsequent release of the drugs was controlled by the irradiation time with a near-infrared laser. By modulating the linkage used to load the drugs three different release profiles were able to be achieved, indicating the feasibility of such a system for combinational therapy requiring sequential release of APIs.
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Affiliation(s)
- Gracie Fitzgerald
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Daniel Low
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Luc Morgan
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Cole Hilt
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Micai Benford
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Caleb Akers
- Department of Chemistry and Biochemistry, DePauw University, Greencastle, IN 46135, United States
| | - Skyler Hornback
- Department of Chemical Engineering, University of Kentucky, Lexington, KY 40506, United States
| | - J Zach Hilt
- Department of Chemical Engineering, University of Kentucky, Lexington, KY 40506, United States
| | - Daniel Scott
- Department of Chemistry, Centre College, Danville, KY 40422, United States.
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Bohlin J, Turberfield AJ, Louis AA, Šulc P. Designing the Self-Assembly of Arbitrary Shapes Using Minimal Complexity Building Blocks. ACS NANO 2023; 17:5387-5398. [PMID: 36763807 DOI: 10.1021/acsnano.2c09677] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The design space for self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. We develop a pipeline to explore the design spaces for a set of structures of various sizes and complexities. To understand the implications of the different solutions, we analyze their assembly dynamics using patchy particle simulations and study the influence of the number of distinct building blocks, and the angular and spatial tolerances on their interactions, on the kinetics and yield of the target assembly. We show that the resource-saving solution with a minimum number of distinct blocks can often assemble just as well (or faster) than designs where each building block is unique. We further use our methods to design multifarious structures, where building blocks are shared between different target structures. Finally, we use coarse-grained DNA simulations to investigate the realization of multicomponent shapes using DNA nanostructures as building blocks.
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Affiliation(s)
- Joakim Bohlin
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, U.K
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
| | - Andrew J Turberfield
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, U.K
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Keble Road, Oxford OX1 3NP, U.K
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
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Kemper U, Ye J, Poppitz D, Gläser R, Seidel R. DNA Mold-Based Fabrication of Palladium Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2206438. [PMID: 36960479 DOI: 10.1002/smll.202206438] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/03/2023] [Indexed: 06/18/2023]
Abstract
DNA origami molds allow a shape-controlled growth of metallic nanoparticles. So far, this approach is limited to gold and silver. Here, the fabrication of linear palladium nanostructures with controlled lengths and patterns is demonstrated. To obtain nucleation centers for a seeded growth, a synthesis procedure of palladium nanoparticles (PdNPs) using Bis(p-sulfonatophenyl)phenylphosphine (BSPP) both as reductant and stabilizer is developed to establish an efficient functionalization protocol of the particles with single-stranded DNA. Attaching the functionalized particles to complementary DNA strands inside DNA mold cavities supports subsequently a highly specific seeded palladium deposition. This provides rod-like PdNPs with diameters of 20-35 nm of grainy morphology. Using an annealing procedure and a post-reduction step with hydrogen, homogeneous palladium nanostructures can be obtained. With the adaptation of the procedure to palladium the capabilities of the mold-based tool-box are expanded. In the future, this may allow a facile adaptation of the mold approach to less noble metals including magnetic materials such as Ni and Co.
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Affiliation(s)
- Ulrich Kemper
- Molecular Biophysics group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Jingjing Ye
- Molecular Biophysics group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - David Poppitz
- Heterogeneous Catalysis, Institute of Chemical Technology, Universität Leipzig, 04103, Leipzig, Germany
| | - Roger Gläser
- Heterogeneous Catalysis, Institute of Chemical Technology, Universität Leipzig, 04103, Leipzig, Germany
| | - Ralf Seidel
- Molecular Biophysics group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
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50
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Wu H, Zhang C, Zhu F, Zhu Y, Lu X, Wan Y, Su S, Chao J, Wang L, Zhu D. programmably engineered FRET-nanoflare for ratiometric live-cell ATP imaging with anti-interference capability. Chem Commun (Camb) 2023; 59:4047-4050. [PMID: 36928909 DOI: 10.1039/d3cc00690e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Herein, we present a poly-adenine (polyA)-mediated programmably engineered FRET-nanoflare for ratiometric intracellular ATP imaging with anti-interference capability. The programmable polyA attachment is advantageous in enhancing the signal response for ATP. Moreover, the FRET-based nanoflare is capable of avoiding false-positive signals due to probe degradation in a complex environment, which has great potential for clinical diagnosis.
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Affiliation(s)
- Hongyu Wu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Chengwen Zhang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Fulin Zhu
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yu Zhu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Xinhui Lu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Ying Wan
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Shao Su
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Dan Zhu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
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