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Yang H, Jin Y, Qian H, Wang Y, Bao T, Wu Z, Wen W, Zhang X, Wang S. Target-driven cascade amplified assembly of covalent organic frameworks on tetrahedral DNA nanostructure with multiplex recognition domains for ultrasensitive detection of microRNA. Anal Chim Acta 2024; 1311:342743. [PMID: 38816160 DOI: 10.1016/j.aca.2024.342743] [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: 01/08/2024] [Revised: 04/13/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND MicroRNA (miRNA) emerges as important cancer biomarker, accurate detection of miRNA plays an essential role in clinical sample analysis and disease diagnosis. However, it remains challenging to realize highly sensitive detection of low-abundance miRNA. Traditional detection methods including northern blot and real-time PCR have realized quantitative miRNA detection. However, these detection methods are involved in sophisticated operation and expensive instruments. Therefore, the development of novel sensing platform with high sensitivity and specificity for miRNA detection is urgently demanded for disease diagnosis. RESULTS In this work, a novel electrochemical biosensor was constructed for miRNA detection based on target-driven cascade amplified assembly of electroactive covalent organic frameworks (COFs) on tetrahedral DNA nanostructure with multiplex recognition domains (m-TDN). COFs were employed as nanocarriers of electroactive prussian blue (PB) molecules by the "freeze-drying-reduction" method without the use of DNA as gatekeeper, which was simple, mild and efficient. The target-triggered catalytic hairpin assembly (CHA) and glutathione reduction could convert low-abundance miRNA into a large amount of Mn2+. Without the addition of exogenous Mn2+, the dynamically-generated Mn2+-powered DNAzyme cleavage process induced abundant PB-COFs probe assembled on the four recognition domains of m-TDN, resulting in significantly signal output. Using miRNA-182-5p as the model target, the proposed electrochemical biosensor achieved ultrasensitive detection of miRNA-182-5p in the range of 10 fM-100 nM with a detection limit of 2.5 fM. SIGNIFICANCE AND NOVELTY Taking advantages of PB-COFs probe as the enhanced signal labels, the integration of CHA, Mn2+-powered DNAzyme and m-TDN amplification strategy significantly improved the sensitivity and specificity of the biosensor. The designed sensing platform was capable of miRNA detection in complex samples, which provided a new idea for biomarker detection, holding promising potential in clinical diagnosis and disease screening.
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Affiliation(s)
- Hongying Yang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed By the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Yunxia Jin
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed By the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Hui Qian
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed By the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Yuqi Wang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed By the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Ting Bao
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed By the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China.
| | - Zhen Wu
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed By the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Wei Wen
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed By the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Xiuhua Zhang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed By the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Shengfu Wang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed By the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China.
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Hou J, Qian X, Xu Y, Guo Z, Thierry B, Yang CT, Zhou X, Mao C. Rapid and reliable ultrasensitive detection of pathogenic H9N2 viruses through virus-binding phage nanofibers decorated with gold nanoparticles. Biosens Bioelectron 2023; 237:115423. [PMID: 37311406 DOI: 10.1016/j.bios.2023.115423] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/19/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023]
Abstract
The rapid and sensitive detection of pathogenic viruses is important for controlling pandemics. Herein, a rapid, ultrasensitive, optical biosensing scheme was developed to detect avian influenza virus H9N2 using a genetically engineered filamentous M13 phage probe. The M13 phage was genetically engineered to bear an H9N2-binding peptide (H9N2BP) at the tip and a gold nanoparticle (AuNP)-binding peptide (AuBP) on the sidewall to form an engineered phage nanofiber, M13@H9N2BP@AuBP. Simulated modelling showed that M13@H9N2BP@AuBP enabled a 40-fold enhancement of the electric field enhancement in surface plasmon resonance (SPR) compared to conventional AuNPs. Experimentally, this signal enhancement scheme was employed for detecting H9N2 particles with a sensitivity down to 6.3 copies/mL (1.04 × 10-5 fM). The phage-based SPR scheme can detect H9N2 viruses in real allantoic samples within 10 min, even at very low concentrations beyond the detection limit of quantitative polymerase chain reaction (qPCR). Moreover, after capturing the H9N2 viruses on the sensor chip, the H9N2-binding phage nanofibers can be quantitatively converted into plaques that are visible to the naked eye for further quantification, thereby allowing us to enumerate the H9N2 virus particles through a second mode to cross-validate the SPR results. This novel phage-based biosensing strategy can be employed to detect other pathogens because the H9N2-binding peptides can be easily switched with other pathogen-binding peptides using phage display technology.
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Affiliation(s)
- Jinxiu Hou
- College of Veterinary Medicine, Institute of Comparative Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Xuejia Qian
- College of Veterinary Medicine, Institute of Comparative Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yi Xu
- School of Optoelectronic Engineering, Guilin University of Electronic Technology, Guilin, 541004, China
| | - Zhirui Guo
- The Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210011, China
| | - Benjamin Thierry
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, SA 5095, Australia
| | - Chih-Tsung Yang
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, SA 5095, Australia.
| | - Xin Zhou
- College of Veterinary Medicine, Institute of Comparative Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Chuanbin Mao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China; School of Materials Science & Engineering, Zhejiang University, Hangzhou, 310027, China.
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Miao P, Chai H, Tang Y. DNA Hairpins and Dumbbell-Wheel Transitions Amplified Walking Nanomachine for Ultrasensitive Nucleic Acid Detection. ACS NANO 2022; 16:4726-4733. [PMID: 35188755 DOI: 10.1021/acsnano.1c11582] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nucleic acids, including circulating tumor DNA (ctDNA), microRNA, and virus DNA/RNA, have been widely applied as potential disease biomarkers for early clinical diagnosis. In this study, we present a concept of DNA nanostructures transitions for the construction of DNA bipedal walking nanomachine, which integrates dual signal amplification for direct nucleic acid assay. DNA hairpins transition is developed to facilitate the generation of multiple target sequences; meanwhile, the subsequent DNA dumbbell-wheel transition is controlled to achieve the bipedal walker, which cleaves multiple tracks around electrode surface. Through combination of strand displacement reaction and digestion cycles, DNA monolayer at the electrode interface could be engineered and target-induced signal variation is realized. In addition, pH-assisted detachable intermolecular DNA triplex design is utilized for the regeneration of electrochemical biosensor. The high consistency between this work and standard quantitative polymerase chain reaction is validated. Moreover, the feasibilities of this biosensor to detect ctDNA and SARS-CoV-2 RNA in clinical samples are demonstrated with satisfactory accuracy and reliability. Therefore, the proposed approach has great potential applications for nucleic acid based clinical diagnostics.
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Affiliation(s)
- Peng Miao
- University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China
| | - Hua Chai
- University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China
| | - Yuguo Tang
- University of Science and Technology of China, Hefei 230026, China
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A High-Sensitivity Method Based on Advanced Optical Waveguide Technology to Detect HBsAg. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:8719147. [PMID: 34354809 PMCID: PMC8331295 DOI: 10.1155/2021/8719147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 11/17/2022]
Abstract
A novel method for the detection of the hepatitis B surface antigen (HBsAg) at low concentrations, using the ultrahigh-order guided mode acting as the probe excited by a symmetrical metal-cladding waveguide, is proposed. The method using the fact of the minimum value of the absorption peaks is proportional to the concentration of the sample to be detected to realize the detection of the hepatitis B virus at extremely low concentrations. It is realized that the low concentration of the HBsAg measurement relied on the principle of the minimum value of the absorption peak and the concentration having a good linear relationship. The measurement results indicate that this new method can precisely detect HBsAg at the concentrations in the lower region of the clinical gray area (i.e., below 20 ng/mL), the lower region of the current clinical gray area of HBsAg (below 20 ng/ml) can be measured, and the resolution can be reached (2 ng/mL).
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Liu JJ, Yan HH, Zhang Q, Gao PF, Li CM, Liang GL, Huang CZ, Wang J. High-Resolution Vertical Polarization Excited Dark-Field Microscopic Imaging of Anisotropic Gold Nanorods for the Sensitive Detection and Spatial Imaging of Intracellular microRNA-21. Anal Chem 2020; 92:13118-13125. [DOI: 10.1021/acs.analchem.0c02164] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jia Jun Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Hui Hong Yan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Qiang Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Peng Fei Gao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Chun Mei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Gao Lin Liang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu 210096, China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Jian Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
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Liu X, Zou M, Li D, Yuan R, Xiang Y. Hairpin/DNA ring ternary probes for highly sensitive detection and selective discrimination of microRNA among family members. Anal Chim Acta 2019; 1076:138-143. [DOI: 10.1016/j.aca.2019.05.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/19/2019] [Accepted: 05/13/2019] [Indexed: 12/25/2022]
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Castiello FR, Tabrizian M. Gold nanoparticle amplification strategies for multiplex SPRi-based immunosensing of human pancreatic islet hormones. Analyst 2019; 144:2541-2549. [PMID: 30864587 DOI: 10.1039/c9an00140a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this work, we demonstrate the potential use of SPRi for secretion-monitoring of pancreatic islets, small micro-organs that regulate glucose homeostasis in the body. In the islets, somatostatin works as a paracrine inhibitor of insulin and glucagon secretion. However, this inhibitory effect is lost in diabetic individuals and little is known about its contribution to the pathology of diabetes. Thus, the simultaneous detection of insulin, glucagon and somatostatin could help understand such communications. Previously, the authors introduced an SPRi biosensor to simultaneously monitor insulin, glucagon and somatostatin using an indirect competitive immunoassay. However, our sensor achieved a relatively high LOD for somatostatin detection (246 nM), the smallest of the three hormones. For this reason, the present work aimed to improve the performance of our SPRi biosensor using gold nanoparticles (GNPs) as a means of ensuring somatostatin detection from a small group of islets. Although GNP amplification is frequently reported in the literature for individual detection of analytes using SPR, studies regarding the optimal strategy in a multiplexed SPR setup are missing. Therefore, with the aim of finding the optimal GNP amplification strategies for multiplex sensing we compared three architectures: (1) GNPs immobilized on the sensor surface, (2) GNPs conjugated with primary antibodies (GNP-Ab1) and (3) GNPs conjugated with a secondary antibody (GNP-Ab2). Among these strategies an immunoassay using GNP-Ab2 conjugates was able to achieve multiplex detection of the three hormones without cross-reactivity and with 9-fold LOD improvement for insulin, 10-fold for glucagon and 200-fold for somatostatin when compared to the SPRi biosensor without GNPs. The present work denotes the first report of the simultaneous detection of such hormones with a sensitivity level comparable to ELISA assays, particularly for somatostatin.
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Affiliation(s)
- F Rafael Castiello
- Biomedical and Biological Engineering Department, McGill University, Montreal, QC, Canada.
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Jiao Y, Cui CF, He HY, He C, Duan CY. Fluorescent Recognition of 4-Amino-2,6-dinitrotoluene by a Cerium-Based Metal–Organic Tetrahedron. Inorg Chem 2019; 58:6575-6578. [DOI: 10.1021/acs.inorgchem.8b03077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang D, Loo JFC, Chen J, Yam Y, Chen SC, He H, Kong SK, Ho HP. Recent Advances in Surface Plasmon Resonance Imaging Sensors. SENSORS 2019; 19:s19061266. [PMID: 30871157 PMCID: PMC6471112 DOI: 10.3390/s19061266] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 12/12/2022]
Abstract
The surface plasmon resonance (SPR) sensor is an important tool widely used for studying binding kinetics between biomolecular species. The SPR approach offers unique advantages in light of its real-time and label-free sensing capabilities. Until now, nearly all established SPR instrumentation schemes are based on single- or several-channel configurations. With the emergence of drug screening and investigation of biomolecular interactions on a massive scale these days for finding more effective treatments of diseases, there is a growing demand for the development of high-throughput 2-D SPR sensor arrays based on imaging. The so-called SPR imaging (SPRi) approach has been explored intensively in recent years. This review aims to provide an up-to-date and concise summary of recent advances in SPRi. The specific focuses are on practical instrumentation designs and their respective biosensing applications in relation to molecular sensing, healthcare testing, and environmental screening.
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Affiliation(s)
- Dongping Wang
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Hong Kong, China.
| | - Jacky Fong Chuen Loo
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China.
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Jiajie Chen
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China.
| | - Yeung Yam
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Hong Kong, China.
| | - Shih-Chi Chen
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Hong Kong, China.
| | - Hao He
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Siu Kai Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Ho Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China.
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Yang CT, Xu Y, Pourhassan-Moghaddam M, Tran DP, Wu L, Zhou X, Thierry B. Surface Plasmon Enhanced Light Scattering Biosensing: Size Dependence on the Gold Nanoparticle Tag. SENSORS (BASEL, SWITZERLAND) 2019; 19:E323. [PMID: 30650578 PMCID: PMC6359480 DOI: 10.3390/s19020323] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 12/31/2022]
Abstract
Surface plasmon enhanced light scattering (SP-LS) is a powerful new sensing SPR modality that yields excellent sensitivity in sandwich immunoassay using spherical gold nanoparticle (AuNP) tags. Towards further improving the performance of SP-LS, we systematically investigated the AuNP size effect. Simulation results indicated an AuNP size-dependent scattered power, and predicted the optimized AuNPs sizes (i.e., 100 and 130 nm) that afford extremely high signal enhancement in SP-LS. The maximum scattered power from a 130 nm AuNP is about 1700-fold higher than that obtained from a 17 nm AuNP. Experimentally, a bio-conjugation protocol was developed by coating the AuNPs with mixture of low and high molecular weight PEG molecules. Optimal IgG antibody bioconjugation conditions were identified using physicochemical characterization and a model dot-blot assay. Aggregation prevented the use of the larger AuNPs in SP-LS experiments. As predicted by simulation, AuNPs with diameters of 50 and 64 nm yielded significantly higher SP-LS signal enhancement in comparison to the smaller particles. Finally, we demonstrated the feasibility of a two-step SP-LS protocol based on a gold enhancement step, aimed at enlarging 36 nm AuNPs tags. This study provides a blue-print for the further development of SP-LS biosensing and its translation in the bioanalytical field.
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Affiliation(s)
- Chih-Tsung Yang
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes 5095, Australia.
| | - Yi Xu
- Electronics and Photonics Department, Institute of High Performance Computing, Agency for Science, Technology, and Research (A*STAR), Singapore 138632, Singapore.
- SUTD-MIT International Design Center & Science and Math Cluster, Singapore University of Technology and Design, Singapore 487372, Singapore.
| | - Mohammad Pourhassan-Moghaddam
- School of Biomedical Engineering, University of Technology Sydney, Sydney 2007, Australia.
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia.
| | - Duy Phu Tran
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes 5095, Australia.
| | - Lin Wu
- Electronics and Photonics Department, Institute of High Performance Computing, Agency for Science, Technology, and Research (A*STAR), Singapore 138632, Singapore.
| | - Xin Zhou
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China.
| | - Benjamin Thierry
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes 5095, Australia.
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Yu T, Wei Q. Plasmonic molecular assays: Recent advances and applications for mobile health. NANO RESEARCH 2018; 11:5439-5473. [PMID: 32218913 PMCID: PMC7091255 DOI: 10.1007/s12274-018-2094-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 05/15/2023]
Abstract
Plasmonics-based biosensing assays have been extensively employed for biomedical applications. Significant advancements in use of plasmonic assays for the construction of point-of-care (POC) diagnostic methods have been made to provide effective and urgent health care of patients, especially in resourcelimited settings. This rapidly progressive research area, centered on the unique surface plasmon resonance (SPR) properties of metallic nanostructures with exceptional absorption and scattering abilities, has greatly facilitated the development of cost-effective, sensitive, and rapid strategies for disease diagnostics and improving patient healthcare in both developed and developing worlds. This review highlights the recent advances and applications of plasmonic technologies for highly sensitive protein and nucleic acid biomarker detection. In particular, we focus on the implementation and penetration of various plasmonic technologies in conventional molecular diagnostic assays, and discuss how such modification has resulted in simpler, faster, and more sensitive alternatives that are suited for point-of-use. Finally, integration of plasmonic molecular assays with various portable POC platforms for mobile health applications are highlighted.
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Affiliation(s)
- Tao Yu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Campus Box 7905, Raleigh, NC 27695 USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Campus Box 7905, Raleigh, NC 27695 USA
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Drozd M, Pietrzak MD, Malinowska E. SPRi-Based Biosensing Platforms for Detection of Specific DNA Sequences Using Thiolate and Dithiocarbamate Assemblies. Front Chem 2018; 6:173. [PMID: 29872654 PMCID: PMC5972272 DOI: 10.3389/fchem.2018.00173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/30/2018] [Indexed: 01/12/2023] Open
Abstract
The framework of presented study covers the development and examination of the analytical performance of surface plasmon resonance-based (SPR) DNA biosensors dedicated for a detection of model target oligonucleotide sequence. For this aim, various strategies of immobilization of DNA probes on gold transducers were tested. Besides the typical approaches: chemisorption of thiolated ssDNA (DNA-thiol) and physisorption of non-functionalized oligonucleotides, relatively new method based on chemisorption of dithiocarbamate-functionalized ssDNA (DNA-DTC) was applied for the first time for preparation of DNA-based SPR biosensor. The special emphasis was put on the correlation between the method of DNA immobilization and the composition of obtained receptor layer. The carried out studies focused on the examination of the capability of developed receptors layers to interact with both target DNA and DNA-functionalized AuNPs. It was found, that the detection limit of target DNA sequence (27 nb length) depends on the strategy of probe immobilization and backfilling method, and in the best case it amounted to 0.66 nM. Moreover, the application of ssDNA-functionalized gold nanoparticles (AuNPs) as plasmonic labels for secondary enhancement of SPR response is presented. The influence of spatial organization and surface density of a receptor layer on the ability to interact with DNA-functionalized AuNPs is discussed. Due to the best compatibility of receptors immobilized via DTC chemisorption: 1.47 ± 0.4 · 1012 molecules · cm-2 (with the calculated area occupied by single nanoparticle label of ~132.7 nm2), DNA chemisorption based on DTCs is pointed as especially promising for DNA biosensors utilizing indirect detection in competitive assays.
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Affiliation(s)
- Marcin Drozd
- Faculty of Chemistry, The Chair of Medical Biotechnology, Warsaw University of Technology, Warsaw, Poland
| | - Mariusz D Pietrzak
- Faculty of Chemistry, The Chair of Medical Biotechnology, Warsaw University of Technology, Warsaw, Poland
| | - Elżbieta Malinowska
- Faculty of Chemistry, The Chair of Medical Biotechnology, Warsaw University of Technology, Warsaw, Poland.,Centre for Advanced Materials and Technologies, Warsaw, Poland
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Shikha S, Zheng X, Zhang Y. Upconversion Nanoparticles-Encoded Hydrogel Microbeads-Based Multiplexed Protein Detection. NANO-MICRO LETTERS 2018; 10:31. [PMID: 30393680 PMCID: PMC6199079 DOI: 10.1007/s40820-017-0184-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/08/2017] [Indexed: 05/20/2023]
Abstract
Fluorescently encoded microbeads are in demand for multiplexed applications in different fields. Compared to organic dye-based commercially available Luminex's xMAP technology, upconversion nanoparticles (UCNPs) are better alternatives due to their large anti-Stokes shift, photostability, nil background, and single wavelength excitation. Here, we developed a new multiplexed detection system using UCNPs for encoding poly(ethylene glycol) diacrylate (PEGDA) microbeads as well as for labeling reporter antibody. However, to prepare UCNPs-encoded microbeads, currently used swelling-based encapsulation leads to non-uniformity, which is undesirable for fluorescence-based multiplexing. Hence, we utilized droplet microfluidics to obtain encoded microbeads of uniform size, shape, and UCNPs distribution inside. Additionally, PEGDA microbeads lack functionality for probe antibodies conjugation on their surface. Methods to functionalize the surface of PEGDA microbeads (acrylic acid incorporation, polydopamine coating) reported thus far quench the fluorescence of UCNPs. Here, PEGDA microbeads surface was coated with silica followed by carboxyl modification without compromising the fluorescence intensity of UCNPs. In this study, droplet microfluidics-assisted UCNPs-encoded microbeads of uniform shape, size, and fluorescence were prepared. Multiple color codes were generated by mixing UCNPs emitting red and green colors at different ratios prior to encapsulation. UCNPs emitting blue color were used to label the reporter antibody. Probe antibodies were covalently immobilized on red UCNPs-encoded microbeads for specific capture of human serum albumin (HSA) as a model protein. The system was also demonstrated for multiplexed detection of both human C-reactive protein (hCRP) and HSA protein by immobilizing anti-hCRP antibodies on green UCNPs.
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Affiliation(s)
- Swati Shikha
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore (NUS), 4 Engineering Drive 3, Block E4 #04-08, Singapore, 117583, Singapore
| | - Xiang Zheng
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore (NUS), 4 Engineering Drive 3, Block E4 #04-08, Singapore, 117583, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, Centre for Life Sciences (CeLS), 05-01 28 Medical Drive, Singapore, 117456, Singapore
| | - Yong Zhang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore (NUS), 4 Engineering Drive 3, Block E4 #04-08, Singapore, 117583, Singapore.
- NUS Graduate School for Integrative Sciences and Engineering, Centre for Life Sciences (CeLS), 05-01 28 Medical Drive, Singapore, 117456, Singapore.
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Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology. Proc Natl Acad Sci U S A 2017; 114:E7245-E7254. [PMID: 28808021 DOI: 10.1073/pnas.1704155114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Chemical modifications on histones and DNA/RNA constitute a fundamental mechanism for epigenetic regulation. These modifications often function as docking marks to recruit or stabilize cognate "reader" proteins. So far, a platform for quantitative and high-throughput profiling of the epigenetic interactome is urgently needed but still lacking. Here, we report a 3D-carbene chip-based surface plasmon resonance imaging (SPRi) technology for this purpose. The 3D-carbene chip is suitable for immobilizing versatile biomolecules (e.g., peptides, antibody, DNA/RNA) and features low nonspecific binding, random yet function-retaining immobilization, and robustness for reuses. We systematically profiled binding kinetics of 1,000 histone "reader-mark" pairs on a single 3D-carbene chip and validated two recognition events by calorimetric and structural studies. Notably, a discovery on H3K4me3 recognition by the DNA mismatch repair protein MSH6 in Capsella rubella suggests a mechanism of H3K4me3-mediated DNA damage repair in plant.
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15
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Yang CT, Wu L, Liu X, Tran NT, Bai P, Liedberg B, Wang Y, Thierry B. Exploiting Surface-Plasmon-Enhanced Light Scattering for the Design of Ultrasensitive Biosensing Modality. Anal Chem 2016; 88:11924-11930. [PMID: 27934101 DOI: 10.1021/acs.analchem.6b03798] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Development of new detection methodologies and amplification schemes is indispensable for plasmonic biosensors to improve the sensitivity for the detection of trace amounts of analytes. Herein, an ultrasensitive scheme for signal enhancement based on the concept of surface-plasmon-resonance-enhanced light scattering (SP-LS) was validated experimentally and theoretically. The SP-LS of gold nanoparticles' (AuNPs) tags was employed in a sandwich assay for the detection of cardiac troponin I and provided up to 2 orders of magnitude improved sensitivity over conventional AuNPs-enhanced refractometric measurements and 3 orders of magnitude improvement over label-free SPR. Simulations were also performed to provide insights into the physical mechanisms.
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Affiliation(s)
- Chih-Tsung Yang
- Future Industries Institute, University of South Australia , Mawson Lakes Campus, Mawson Lakes, South Australia 5095, Australia
| | - Lin Wu
- Electronics and Photonics Department, Institute of High Performance Computing, Agency for Science, Technology, and Research (A*STAR) , Singapore 138632
| | - Xiaohu Liu
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University , Singapore 639798
| | - Nhung Thi Tran
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University , Singapore 639798
| | - Ping Bai
- Electronics and Photonics Department, Institute of High Performance Computing, Agency for Science, Technology, and Research (A*STAR) , Singapore 138632
| | - Bo Liedberg
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University , Singapore 639798
| | - Yi Wang
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University , Singapore 639798.,Wenzhou Institute of Biomaterials and Engineering, Chinese Academy of Sciences , Wenzhou, Zhejiang 325001, China.,Institute of Biomaterials and Engineering, Wenzhou Medical University , Wenzhou, Zhejiang 325035, China
| | - Benjamin Thierry
- Future Industries Institute, University of South Australia , Mawson Lakes Campus, Mawson Lakes, South Australia 5095, Australia
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16
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Ding X, Cheng W, Li Y, Wu J, Li X, Cheng Q, Ding S. An enzyme-free surface plasmon resonance biosensing strategy for detection of DNA and small molecule based on nonlinear hybridization chain reaction. Biosens Bioelectron 2016; 87:345-351. [PMID: 27587359 DOI: 10.1016/j.bios.2016.08.077] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023]
Abstract
A label-free and enzyme-free surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive and specific detection of target DNA by employing the nonlinear hybridization chain reaction (HCR) amplification. Nonlinear HCR is a hairpin-free system in which double-stranded DNA monomers could dendritically assemble into highly branched nanostructure upon introducing a trigger sequence. The target DNA partly hybridizes with capture probe on the gold sensing chip and the unpaired fragment of target DNA works as a trigger to initiate the nonlinear HCR, forming a chain-branching growth of DNA dendrimer by self-assembly. Real-time amplified SPR response is observed upon the introduction of nonlinear HCR system. The method is capable of detecting target DNA at the concentration down to 0.85 pM in 60min with a dynamic range from 1 pM to 1000 pM, and could discriminate target DNA from mismatched sequences. This biosensing strategy exhibits good reproducibility and precision, and has been successfully applied for detection of target DNA in complex sample matrices. In addition, the nonlinear HCR based SPR biosensing methodology is extended to the detection of adenosine triphosphate (ATP) by aptamer recognition. Thus, the versatile method might become a potential alternative tool for biomolecule detection in medical research and early clinical diagnosis.
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Affiliation(s)
- Xiaojuan Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Wei Cheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yujian Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jiangling Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xinmin Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Quan Cheng
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
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17
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Antiochia R, Bollella P, Favero G, Mazzei F. Nanotechnology-Based Surface Plasmon Resonance Affinity Biosensors for In Vitro Diagnostics. Int J Anal Chem 2016; 2016:2981931. [PMID: 27594884 PMCID: PMC4995327 DOI: 10.1155/2016/2981931] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/05/2016] [Accepted: 07/10/2016] [Indexed: 01/17/2023] Open
Abstract
In the last decades, in vitro diagnostic devices (IVDDs) became a very important tool in medicine for an early and correct diagnosis, a proper screening of targeted population, and also assessing the efficiency of a specific therapy. In this review, the most recent developments regarding different configurations of surface plasmon resonance affinity biosensors modified by using several nanostructured materials for in vitro diagnostics are critically discussed. Both assembly and performances of the IVDDs tested in biological samples are reported and compared.
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Affiliation(s)
- Riccarda Antiochia
- Department of Chemistry and Drug Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Paolo Bollella
- Department of Chemistry and Drug Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Gabriele Favero
- Department of Chemistry and Drug Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Franco Mazzei
- Department of Chemistry and Drug Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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18
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Li X, Carravetta V, Li C, Monti S, Rinkevicius Z, Ågren H. Optical Properties of Gold Nanoclusters Functionalized with a Small Organic Compound: Modeling by an Integrated Quantum-Classical Approach. J Chem Theory Comput 2016; 12:3325-39. [DOI: 10.1021/acs.jctc.6b00283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Xin Li
- Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vincenzo Carravetta
- CNR-IPCF, Institute of Chemical
and Physical Processes, via G. Moruzzi
1, I-56124 Pisa, Italy
| | - Cui Li
- CNR-IPCF, Institute of Chemical
and Physical Processes, via G. Moruzzi
1, I-56124 Pisa, Italy
| | - Susanna Monti
- Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- CNR-ICCOM, Institute of Chemistry
of Organometallic Compounds, via G.
Moruzzi 1, I-56124 Pisa, Italy
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
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19
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Energy driven cascade recognition for selective detection of nucleic acids with high discrimination factor at room temperature. Biosens Bioelectron 2016; 79:488-94. [DOI: 10.1016/j.bios.2015.12.093] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/23/2015] [Accepted: 12/25/2015] [Indexed: 01/21/2023]
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20
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Yuan R, Ding S, Yan Y, Zhang Y, Zhang Y, Cheng W. A facile and pragmatic electrochemical biosensing strategy for ultrasensitive detection of DNA in real sample based on defective T junction induced transcription amplification. Biosens Bioelectron 2016; 77:19-25. [DOI: 10.1016/j.bios.2015.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/25/2015] [Accepted: 09/04/2015] [Indexed: 11/30/2022]
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21
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Jana J, Ganguly M, Pal T. Enlightening surface plasmon resonance effect of metal nanoparticles for practical spectroscopic application. RSC Adv 2016. [DOI: 10.1039/c6ra14173k] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pictorial depiction of applications of metal nanoparticles in different fields enlightening surface plasmon resonance effect.
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Affiliation(s)
- Jayasmita Jana
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | | | - Tarasankar Pal
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
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22
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He Y, Shang Y, Liu Y, Zhao S, Liu H. Melting dynamics of short dsDNA chains in saline solutions. SPRINGERPLUS 2015; 4:777. [PMID: 26697287 PMCID: PMC4679706 DOI: 10.1186/s40064-015-1581-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022]
Abstract
DNA melting has attracted much attention due to its importance in understanding the life-reproduction and metabolism and in the applications of modern DNA-based technologies. While numerous works have been contributed to the determination of melting profiles in diverse environments, the understanding of DNA melting dynamics is still limited. By employing three-site-per-nucleotide (3SPN) double-stranded DNA (dsDNA) model, we here demonstrate the melting dynamics of an isolated short dsDNA under different conditions (different temperatures, ionic concentrations and DNA chain lengths) can be accessed by coarse-grained simulation studies. We particularly show that at dilute ionic concentration the dsDNA, regardless being symmetric or asymmetric, opens at both ends with roughly equal probabilities, while at high ionic concentration the asymmetric dsDNA chain opens at the A-T-rich end. The comparisons of our simulation results to available data are discussed, and overall good agreements have been found.
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Affiliation(s)
- Yichen He
- State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237 China
| | - Yazhuo Shang
- State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237 China
| | - Yu Liu
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Shuangliang Zhao
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Honglai Liu
- State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237 China
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23
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Xing X, Liu W, Li T, Xing S, Fu X, Wu D, Liu D, Wang Z. A portable optical waveguide resonance light-scattering scanner for microarray detection. Analyst 2015; 141:199-205. [PMID: 26567521 DOI: 10.1039/c5an01839k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the present work, a portable and low-cost planar waveguide based resonance light scattering (RLS) scanner (termed as: PW-RLS scanner) has been developed for microarray detection. The PW-RLS scanner employs a 2 × 4 white light emitting diode array (WLEDA) as the excitation light source, a folded optical path with a complementary metal oxide semiconductor (CMOS) as the signal/image acquisition device and stepper motors with gear drives as the mechanical drive system. The biological binding/recognizing events on the microarray can be detected with an evanescent waveguide-directed illumination and light-scattering label (e.g., nanoparticles) while the microarray slide acts as an evanescent waveguide substrate. The performance of the as-developed PW-RLS scanner has been evaluated by analyzing type 2 diabetes mellitus (T2DM) risk genes. Highly selective and sensitive (less than 1% allele frequency at the attomole-level) T2DM risk gene detection is achieved using single-stranded DNA functionalized gold nanoparticles (ssDNA-GNPs) as detection probes. Additionally, the successful simultaneous analysis of 15 T2DM patient genotypes suggests that the device has great potential for the realization of a personalized diagnostic test for a given disease or patient follow-up.
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Affiliation(s)
- Xuefeng Xing
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China.
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24
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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25
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Fasoli J, Corn RM. Surface Enzyme Chemistries for Ultrasensitive Microarray Biosensing with SPR Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:9527-9536. [PMID: 25641598 PMCID: PMC4564839 DOI: 10.1021/la504797z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/30/2015] [Indexed: 06/01/2023]
Abstract
The sensitivity and selectivity of surface plasmon resonance imaging (SPRI) biosensing with nucleic acid microarrays can be greatly enhanced by exploiting various nucleic acid ligases, nucleases, and polymerases that manipulate the surface-bound DNA and RNA. We describe here various examples from each of these different classes of surface enzyme chemistries that have been incorporated into novel detection strategies that either drastically enhance the sensitivity of or create uniquely selective methods for the SPRI biosensing of proteins and nucleic acids. A dual-element generator-detector microarray approach that couples a bioaffinity adsorption event on one microarray element to nanoparticle-enhanced SPRI measurements of nucleic acid hybridization adsorption on a different microarray element is used to quantitatively detect DNA, RNA, and proteins at femtomolar concentrations. Additionally, this dual-element format can be combined with the transcription and translation of RNA from surface-bound double-stranded DNA (dsDNA) templates for the on-chip multiplexed biosynthesis of aptamer and protein microarrays in a microfluidic format; these microarrays can be immediately used for real-time SPRI bioaffinity sensing measurements.
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26
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Leng Y, Sun K, Chen X, Li W. Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection. Chem Soc Rev 2015; 44:5552-95. [PMID: 26021602 PMCID: PMC5223091 DOI: 10.1039/c4cs00382a] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and "point of care" platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields.
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Affiliation(s)
- Yuankui Leng
- The State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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27
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Lockett MR, Smith LM. Carbon Substrates: A Stable Foundation for Biomolecular Arrays. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:263-285. [PMID: 26048550 PMCID: PMC6287745 DOI: 10.1146/annurev-anchem-071114-040146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Since their advent in the early 1990s, microarray technologies have developed into a powerful and ubiquitous platform for biomolecular analysis. Microarrays consist of three major elements: the substrate upon which they are constructed, the chemistry employed to attach biomolecules, and the biomolecules themselves. Although glass substrates and silane-based attachment chemistries are used for the vast majority of current microarray platforms, these materials suffer from severe limitations in stability, due to hydrolysis of both the substrate material itself and of the silyl ether linkages employed for attachment. These limitations in stability compromise assay performance and render impossible many potential microarray applications. We describe here a suite of alternative carbon-based substrates and associated attachment chemistries for microarray fabrication. The substrates themselves, as well as the carbon-carbon bond-based attachment chemistries, offer greatly increased chemical stability, enabling a myriad of novel applications.
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Affiliation(s)
- Matthew R Lockett
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599;
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28
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Lee M, Kang YL, Rho WY, Kyeong S, Jeong S, Jeong C, Chung WJ, Kim HM, Kang H, Lee YS, Jeong D, Jun BH. Preparation of plasmonic magnetic nanoparticles and their light scattering properties. RSC Adv 2015. [DOI: 10.1039/c5ra00513b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Fe3O4@SiO2@Au nanoparticles (NPs) that have plasmonic and magnetic properties were prepared by simple immobilization method of Au NPs to silica coated magnetic NPs.
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29
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Mariani S, Scarano S, Ermini ML, Bonini M, Minunni M. Investigating nanoparticle properties in plasmonic nanoarchitectures with DNA by surface plasmon resonance imaging. Chem Commun (Camb) 2015; 51:6587-90. [DOI: 10.1039/c4cc09889g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The optimal optical coupling conditions between SPWs and nanoparticle LSPs can be achieved by overlapping the source wavelength with the wavelength of excitation of LSPs.
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Affiliation(s)
- Stefano Mariani
- Dipartimento di Chimica “Ugo Schiff”
- Università di Firenze
- 50019 Sesto Fiorentino
- Italy
| | - Simona Scarano
- Dipartimento di Chimica “Ugo Schiff”
- Università di Firenze
- 50019 Sesto Fiorentino
- Italy
| | - Maria Laura Ermini
- Dipartimento di Chimica “Ugo Schiff”
- Università di Firenze
- 50019 Sesto Fiorentino
- Italy
| | - Massimo Bonini
- Dipartimento di Chimica “Ugo Schiff”
- Università di Firenze
- 50019 Sesto Fiorentino
- Italy
- Consorzio dei Sistemi a Grande Interfase (CSGI)
| | - Maria Minunni
- Dipartimento di Chimica “Ugo Schiff”
- Università di Firenze
- 50019 Sesto Fiorentino
- Italy
- Consorzio dei Sistemi a Grande Interfase (CSGI)
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30
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Spindel S, Sapsford KE. Evaluation of optical detection platforms for multiplexed detection of proteins and the need for point-of-care biosensors for clinical use. SENSORS (BASEL, SWITZERLAND) 2014; 14:22313-41. [PMID: 25429414 PMCID: PMC4299016 DOI: 10.3390/s141222313] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/12/2014] [Accepted: 11/13/2014] [Indexed: 11/16/2022]
Abstract
This review investigates optical sensor platforms for protein multiplexing, the ability to analyze multiple analytes simultaneously. Multiplexing is becoming increasingly important for clinical needs because disease and therapeutic response often involve the interplay between a variety of complex biological networks encompassing multiple, rather than single, proteins. Multiplexing is generally achieved through one of two routes, either through spatial separation on a surface (different wells or spots) or with the use of unique identifiers/labels (such as spectral separation-different colored dyes, or unique beads-size or color). The strengths and weaknesses of conventional platforms such as immunoassays and new platforms involving protein arrays and lab-on-a-chip technology, including commercially-available devices, are discussed. Three major public health concerns are identified whereby detecting medically-relevant markers using Point-of-Care (POC) multiplex assays could potentially allow for a more efficient diagnosis and treatment of diseases.
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Affiliation(s)
- Samantha Spindel
- Division of Biology, Chemistry, and Materials Science Office of Science and Engineering Laboratories; U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
| | - Kim E Sapsford
- Division of Biology, Chemistry, and Materials Science Office of Science and Engineering Laboratories; U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
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31
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Baek SH, Wark AW, Lee HJ. Dual nanoparticle amplified surface plasmon resonance detection of thrombin at subattomolar concentrations. Anal Chem 2014; 86:9824-9. [PMID: 25186782 DOI: 10.1021/ac5024183] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A novel dual nanoparticle amplification approach is introduced for the enhanced surface plasmon resonance (SPR) detection of a target protein at subattomolar concentrations. Thrombin was used as a model target protein as part of a sandwich assay involving an antithrombin (anti-Th) modified SPR chip surface and a thrombin specific DNA aptamer (Th-aptamer) whose sequence also includes a polyadenine (A30) tail. Dual nanoparticle (NP) enhancement was achieved with the controlled hybridization adsorption of first polythymine-NP conjugates (T20-NPs) followed by polyadenine-NPs (A30-NPs). Two different nanoparticle shapes (nanorod and quasi-spherical) were explored resulting in four different NP pair combinations being directly compared. It was found that both the order and NP shape were important in optimizing the assay performance. The use of real-time SPR measurements to detect target concentrations as low as 0.1 aM is a 10-fold improvement compared to single NP-enhanced SPR detection methods.
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Affiliation(s)
- Seung Hee Baek
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University , 1370 Sankyuk-dong, Buk-gu, Daegu-city, 702-701, Republic of Korea
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32
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Khodakov DA, Ellis AV. Recent developments in nucleic acid identification using solid-phase enzymatic assays. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1167-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Jang HR, Wark AW, Baek SH, Chung BH, Lee HJ. Ultrasensitive and ultrawide range detection of a cardiac biomarker on a surface plasmon resonance platform. Anal Chem 2013; 86:814-9. [PMID: 24328254 DOI: 10.1021/ac4033565] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the main challenges in the development of new analytical platforms for ultrasensitive bioaffinity detection is jointly achieving a wide dynamic range in target analyte concentration, especially for approaches that rely on multistep processes as a part of the signal amplification mechanism. In this paper, a new surface-based sandwich assay is introduced for the direct detection of B-type natriuretic peptide (BNP), an important biomarker for cardiac failure, at concentrations ranging from 1 aM to 500 nM. This was achieved using nanoparticle-enhanced surface plasmon resonance (SPR) where a DNA aptamer is immobilized on a chemically modified gold surface in conjunction with the specific adsorption of antiBNP coated gold nanocubes in the presence of the biomarker target. A concentration detection range greater than eleven orders of magnitude was achieved through dynamic control of only the secondary nanoparticle probe concentration. Furthermore, detection at low attomolar concentrations was also achieved in undiluted human serum.
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Affiliation(s)
- Hye Ri Jang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University , 1370 Sankyuk-dong, Buk-gu, Daegu-city, 702-701, Republic of Korea
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Estevez MC, Otte MA, Sepulveda B, Lechuga LM. Trends and challenges of refractometric nanoplasmonic biosensors: a review. Anal Chim Acta 2013; 806:55-73. [PMID: 24331040 DOI: 10.1016/j.aca.2013.10.048] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/22/2013] [Accepted: 10/27/2013] [Indexed: 01/28/2023]
Abstract
Motivated by potential benefits such as sensor miniaturization, multiplexing opportunities and higher sensitivities, refractometric nanoplasmonic biosensing has profiled itself in a short time span as an interesting alternative to conventional Surface Plasmon Resonance (SPR) biosensors. This latter conventional sensing concept has been subjected during the last decades to strong commercialization, thereby strongly leaning on well-developed thin-film surface chemistry protocols. Not surprisingly, the examples found in literature based on this sensing concept are generally characterized by extensive analytical studies of relevant clinical and diagnostic problems. In contrast, the more novel Localized Surface Plasmon Resonance (LSPR) alternative finds itself in a much earlier, and especially, more fundamental stage of development. Driven by new fabrication methodologies to create nanostructured substrates, published work typically focuses on the novelty of the presented material, its optical properties and its use - generally limited to a proof-of-concept - as a label-free biosensing scheme. Given the different stages of development both SPR and LSPR sensors find themselves in, it becomes apparent that providing a comparative analysis of both concepts is not a trivial task. Nevertheless, in this review we make an effort to provide an overview that illustrates the progress booked in both fields during the last five years. First, we discuss the most relevant advances in SPR biosensing, including interesting analytical applications, together with different strategies that assure improvements in performance, throughput and/or integration. Subsequently, the remaining part of this work focuses on the use of nanoplasmonic sensors for real label-free biosensing applications. First, we discuss the motivation that serves as a driving force behind this research topic, together with a brief summary that comprises the main fabrication methodologies used in this field. Next, the sensing performance of LSPR sensors is examined by analyzing different parameters that can be invoked in order to quantitatively assess their overall sensing performance. Two aspects are highlighted that turn out to be especially important when trying to maximize their sensing performance, being (1) the targeted functionalization of the electromagnetic hotspots of the nanostructures, and (2) overcoming inherent negative influence that stem from the presence of a high refractive index substrate that supports the nanostructures. Next, although few in numbers, an overview is given of the most exhaustive and diagnostically relevant LSPR sensing assays that have been recently reported in literature, followed by examples that exploit inherent LSPR characteristics in order to create highly integrated and high-throughput optical biosensors. Finally, we discuss a series of considerations that, in our opinion, should be addressed in order to bring the realization of a stand-alone LSPR biosensor with competitive levels of sensitivity, robustness and integration (when compared to a conventional SPR sensor) much closer to reality.
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Affiliation(s)
- M-Carmen Estevez
- Institut Català de Nanociència i Nanotecnologia (ICN2), CSIC & CIBER-BBN, ICN2 Building Campus UAB, 08193 Bellaterra, Barcelona, Spain.
| | - Marinus A Otte
- Institut Català de Nanociència i Nanotecnologia (ICN2), CSIC & CIBER-BBN, ICN2 Building Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Borja Sepulveda
- Institut Català de Nanociència i Nanotecnologia (ICN2), CSIC & CIBER-BBN, ICN2 Building Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Laura M Lechuga
- Institut Català de Nanociència i Nanotecnologia (ICN2), CSIC & CIBER-BBN, ICN2 Building Campus UAB, 08193 Bellaterra, Barcelona, Spain
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35
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Recent Advances in DNA Microarray Technology: an Overview on Production Strategies and Detection Methods. BIONANOSCIENCE 2013. [DOI: 10.1007/s12668-013-0111-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Loget G, Wood JB, Cho K, Halpern AR, Corn RM. Electrodeposition of Polydopamine Thin Films for DNA Patterning and Microarrays. Anal Chem 2013; 85:9991-5. [DOI: 10.1021/ac4022743] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriel Loget
- Department
of Chemistry, University of California-Irvine, Irvine, California 92697, United States
| | - Jennifer B. Wood
- Department
of Chemistry, University of California-Irvine, Irvine, California 92697, United States
| | - Kyunghee Cho
- Department
of Chemistry, University of California-Irvine, Irvine, California 92697, United States
| | - Aaron R. Halpern
- Department
of Chemistry, University of California-Irvine, Irvine, California 92697, United States
| | - Robert M. Corn
- Department
of Chemistry, University of California-Irvine, Irvine, California 92697, United States
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Wood JB, Szyndler MW, Halpern AR, Cho K, Corn RM. Fabrication of DNA microarrays on polydopamine-modified gold thin films for SPR imaging measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:10868-73. [PMID: 23902428 PMCID: PMC3789119 DOI: 10.1021/la402425n] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Polydopamine (PDA) films were fabricated on thin film gold substrates in a single-step polymerization-deposition process from dopamine solutions and then employed in the construction of robust DNA microarrays for the ultrasensitive detection of biomolecules with nanoparticle-enhanced surface plasmon resonance (SPR) imaging. PDA multilayers with thicknesses varying from 1 to 5 nm were characterized with a combination of scanning angle SPR and AFM experiments, and 1.3 ± 0.2 nm PDA multilayers were chosen as an optimal thickness for the SPR imaging measurements. DNA microarrays were then fabricated by the reaction of amine-functionalized single-stranded DNA (ssDNA) oligonucleotides with PDA-modified gold thin film microarray elements, and were subsequently employed in SPR imaging measurements of DNA hybridization adsorption and protein-DNA binding. Concurrent control experiments with non-complementary ssDNA sequences demonstrated that the adhesive PDA multilayer was also able to provide good resistance to the nonspecific binding of biomolecules. Finally, a series of SPR imaging measurements of the hybridization adsorption of DNA-modified gold nanoparticles onto mixed sequence DNA microarrays were used to confirm that the use of PDA multilayer films is a simple, rapid, and versatile method for fabricating DNA microarrays for ultrasensitive nanoparticle-enhanced SPR imaging biosensing.
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Affiliation(s)
- Jennifer B Wood
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, United States
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38
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Blakey I, Merican Z, Thurecht KJ. A method for controlling the aggregation of gold nanoparticles: tuning of optical and spectroscopic properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8266-74. [PMID: 23751158 DOI: 10.1021/la401361u] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Gold nanoparticles (AuNPs) have many interesting optical properties, which are derived from their surface plasmon resonance (SPR). However, the SPR of single AuNPs occurs around 520 nm, which is a limitation for biomedical imaging applications, because the maximum falls outside the tissue transparency window (∼650-1000 nm). Here the aggregation of AuNPs is mediated by balancing aggregation and steric stabilization processes. This is achieved by varying the relative amounts of hydrophobic small molecules, which act as aggregating agents, and end functional hydrophilic polymers that serve as steric stabilizing agents. This approach allows the position of the SPR shifted into the tissue transparency window, while maintaining colloidal stability. Importantly, increased depolarized scattering and surface enhanced Raman scattering (SERS) cross sections in this region are achieved compared to the single nanoparticles. By varying the structure of the aggregating agent slightly, the SERS spectra exhibit significant changes, thus demonstrating the potential to encode different aggregates. The aggregates have potential applications in biomedical imaging, as an encoding strategy for combinatorial chemistry, and for use in flow cytometry applications.
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Affiliation(s)
- Idriss Blakey
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia.
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Karhunen U, Soikkeli M, Lahdenperä S, Soukka T. Quantitative detection of well-based DNA array using switchable lanthanide luminescence. Anal Chim Acta 2013; 772:87-92. [PMID: 23540252 DOI: 10.1016/j.aca.2013.02.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/11/2013] [Accepted: 02/16/2013] [Indexed: 11/26/2022]
Abstract
In this report a novel wash-free method for multiplexed DNA detection is demonstrated employing target specific probe pairs and switchable lanthanide luminescence technology on a solid-phase array. Four oligonucleotide capture probes, conjugated at 3' to non-luminescent lanthanide ion carrier chelate, were immobilized as a small array on the bottom of a microtiter plate well onto which a mix of corresponding detection probes, conjugated at 5' to a light absorbing antenna ligand, were added. In the presence of complementary target nucleic acid both the spotted capture probe and the liquid-phase detection probe hybridize adjacently on the target. Consequently the two non-luminescent label molecules self-assemble and form a luminescent mixed lanthanide chelate complex. Lanthanide luminescence is thereafter measured without a wash step from the spots by scanning in time-resolved mode. The homogeneous solid-phase array-based method resulted in quantitative detection of synthetic target oligonucleotides with 0.32 nM and 0.60 nM detection limits in a single target and multiplexed assay, respectively, corresponding to 3× SD of the background. Also qualitative detection of PCR-amplified target from Escherichia coli is described.
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Affiliation(s)
- Ulla Karhunen
- Division of Biotechnology, University of Turku, Turku, Finland.
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40
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Chen Y, Corn RM. DNAzyme footprinting: detecting protein-aptamer complexation on surfaces by blocking DNAzyme cleavage activity. J Am Chem Soc 2013; 135:2072-5. [PMID: 23351044 DOI: 10.1021/ja311367t] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A novel method to quantitatively measure the binding of proteins to single-stranded DNA (ssDNA) aptamers that employs the inhibition of the DNAzyme hydrolysis of aptamer monolayers is described. A 28-base DNAzyme was designed to specifically bind to and cleave a 29-base ssDNA sequence that can fold into a G-quartet aptamer and bind the protein thrombin. The binding strength of the DNAzyme to the aptamer sequence was designed to be less than the binding strength of the thrombin to the aptamer (ΔG° = -43.1 and -51.8 kJ/mol, respectively). Formation of the thrombin-aptamer complex was found to block DNAzyme cleavage activity both in solution and in an ssDNA aptamer monolayer. We denote this method for detecting protein-aptamer complexation as "DNAzyme footprinting" in analogy to the process of DNase footprinting for the detection of protein-DNA interactions. By attaching a 40-base reporter sequence to the ssDNA aptamer monolayer, the detection of any protein-aptamer complexes remaining on the surface after DNAzyme activity can be greatly enhanced (down to one thrombin-aptamer complex per 10,000 ssDNA molecules corresponding to 100 fM thrombin in solution) by a subsequent surface RNA transcription amplification reaction followed by RNA detection with nanoparticle-enhanced SPR imaging. In addition to RNA transcription, DNAzyme footprinting can be coupled to a wide variety of other nucleic acid surface amplification schemes and thus is a powerful new route for the enzymatically amplified detection of proteins via protein-aptamer complex formation.
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Affiliation(s)
- Yulin Chen
- Department of Chemistry, U niversity of California-Irvine, Irvine, California 92697, USA
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41
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Cheng XR, Hau BYH, Veloso AJ, Martic S, Kraatz HB, Kerman K. Surface Plasmon Resonance Imaging of Amyloid-β Aggregation Kinetics in the Presence of Epigallocatechin Gallate and Metals. Anal Chem 2013; 85:2049-55. [DOI: 10.1021/ac303181q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xin R. Cheng
- Department
of Physical and Environmental
Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
| | - Ben Y. H. Hau
- Department
of Physical and Environmental
Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
| | - Anthony J. Veloso
- Department
of Physical and Environmental
Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
| | - Sanela Martic
- Department of Chemistry and
Biochemistry, Oakland University, Rochester,
Michigan 48309, United States
| | - Heinz-Bernhard Kraatz
- Department
of Physical and Environmental
Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
| | - Kagan Kerman
- Department
of Physical and Environmental
Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
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Šípová H, Homola J. Surface plasmon resonance sensing of nucleic acids: a review. Anal Chim Acta 2013; 773:9-23. [PMID: 23561902 DOI: 10.1016/j.aca.2012.12.040] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 12/12/2022]
Abstract
Biosensors based on surface plasmon resonance (SPR) have become a central tool for the investigation and quantification of biomolecules and their interactions. Nucleic acids (NAs) play a vital role in numerous biological processes and therefore have been one of the major groups of biomolecules targeted by the SPR biosensors. This paper discusses the advances of NA SPR biosensor technology and reviews its applications both in the research of molecular interactions involving NAs (NA-NA, NA-protein, NA-small molecule), as well as for the field of bioanalytics in the areas of food safety, medical diagnosis and environmental monitoring.
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Affiliation(s)
- Hana Šípová
- Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague, Czech Republic
| | - Jiří Homola
- Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague, Czech Republic.
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Rodríguez P, Rojas H, Medina M, Arrivillaga J, Francisco Y, Dager F, Piscitelli V, Caetano M, Fernández A, Castillo J. Study of Functionalized Gold Nanoparticles with Anti-gp63 IgG Antibody for the Detection of Glycoprotein gp63 in Membrane Surface of <i>Leishmania</i> Genus Parasites. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajac.2013.47a014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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44
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Yuan W, Lu Z, Wang H, Li CM. Sacrificial polymer thin-film template with tunability to construct high-density Au nanoparticle arrays and their refractive index sensing. Phys Chem Chem Phys 2013; 15:15499-507. [DOI: 10.1039/c3cp52816b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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45
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Zhou X, Liao Y, Xing D. Sensitive monitoring of RNA transcription levels using a graphene oxide fluorescence switch. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-012-5584-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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46
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Abstract
This Perspective discusses recent advances in the field of surface plasmon resonance imaging (SPRi) for the label-free, multiplex, and sensitive study of biomolecular systems. Large efforts have been made during the past decade with the aim of developing even more sensitive and specific SPRi-based platforms. Metal nanostructures have been used to enhance SPRi sensitivity and to build a specific SPR-active surface, while special effects such as long-range SPR have been investigated to develop more effective SPRi platforms. Here, we review some of the significant work performed with SPRi for the ultrasensitive detection of biomolecular systems and provide a perspective on the challenges that need to be overcome to enable the wide use of SPRi in emerging key areas such as health diagnostics and antidoping controls.
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Affiliation(s)
- Giuseppe Spoto
- †Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
- ‡Istituto Nazionale di Biostrutture e Biosistemi, Catania, Italy
| | - Maria Minunni
- §Dipartimento di Chimica e CSGI, Università di Firenze, Via della Lastruccia, 3 50019 Sesto F.no (FI), Italy
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Lee JH, Hwang JH, Nam JM. DNA-tailored plasmonic nanoparticles for biosensing applications. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2012; 5:96-109. [DOI: 10.1002/wnan.1196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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48
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Cannon B, Campos AR, Lewitz Z, Willets KA, Russell R. Zeptomole detection of DNA nanoparticles by single-molecule fluorescence with magnetic field-directed localization. Anal Biochem 2012; 431:40-7. [PMID: 22929698 DOI: 10.1016/j.ab.2012.08.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 08/19/2012] [Accepted: 08/20/2012] [Indexed: 01/05/2023]
Abstract
Single-molecule fluorescence methods offer the promise of ultrasensitive detection of biomolecules, but the passive immobilization methods commonly employed require analyte concentrations in the picomolar range. Here, we demonstrate that superparamagnetic Fe(3)O(4) nanoparticles (NPs) can be used with an external magnetic field as a simple strategy to enhance the immobilization efficiency and thereby decrease the detection limit. Inorganic NPs functionalized with streptavidin were bound to biotinylated single-stranded DNA oligonucleotides, which were in turn annealed to complementary oligonucleotides labeled with a Cy3 fluorescent dye. Using an external magnetic field, the superparamagnetic nanoparticles were localized to a specific region within the flow chamber surface. From the single-molecule fluorescence time traces, single-step photobleaching indicated that the surface-immobilized NPs were primarily bound with a single Cy3-labeled oligonucleotide. This strategy gave a concentration detection limit for the Cy3-labeled oligonucleotide of 100aM, 3000-fold lower than that from an analogous strategy with passive immobilization. With a sample volume of 25μl, this method achieved a mole detection limit of approximately 2.5zmol (∼1500 molecules). Together, the results support that idea that single-molecule fluorescence methods could be used for biological applications such as detection and measurements of nucleic acids from biological or clinical samples without polymerase chain reaction amplification.
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Affiliation(s)
- Brian Cannon
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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49
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Hong BJ, An Z, Compton OC, Nguyen ST. Tunable biomolecular interaction and fluorescence quenching ability of graphene oxide: application to "turn-on" DNA sensing in biological media. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:2469-76. [PMID: 22696425 PMCID: PMC3639316 DOI: 10.1002/smll.201200264] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Indexed: 05/17/2023]
Abstract
As a platform for "turn-on" DNA sensing, the level of oxidation of graphene oxide strongly affects its fluorescence quenching ability and binding interactions to single-stranded oligodeoxyribonucleotides (ssODNs), leading to a broad range of sensitivity. Fine-tuning the level of oxidation of graphene oxide yields a DNA-detection platform that is highly sensitive in serum and biological media.
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50
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Escorihuela J, Bañuls MJ, García Castelló J, Toccafondo V, García-Rupérez J, Puchades R, Maquieira Á. Chemical silicon surface modification and bioreceptor attachment to develop competitive integrated photonic biosensors. Anal Bioanal Chem 2012; 404:2831-40. [PMID: 22872294 DOI: 10.1007/s00216-012-6280-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/07/2012] [Accepted: 07/17/2012] [Indexed: 11/26/2022]
Abstract
Methodology for the functionalization of silicon-based materials employed for the development of photonic label-free nanobiosensors is reported. The studied functionalization based on organosilane chemistry allowed the direct attachment of biomolecules in a single step, maintaining their bioavailability. Using this immobilization approach in probe microarrays, successful specific detection of bacterial DNA is achieved, reaching hybridization sensitivities of 10 pM. The utility of the immobilization approach for the functionalization of label-free nanobiosensors based on photonic crystals and ring resonators was demonstrated using bovine serum albumin (BSA)/anti-BSA as a model system.
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Affiliation(s)
- Jorge Escorihuela
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento de Química, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
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