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Lin Y, Wang J, Xu R, Xu Z, Wang Y, Pan S, Zhang Y, Tao Q, Zhao Y, Yan C, Cao Z, Ji K. HiFi long-read amplicon sequencing for full-spectrum variants of human mtDNA. BMC Genomics 2024; 25:538. [PMID: 38822239 PMCID: PMC11141058 DOI: 10.1186/s12864-024-10433-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/20/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND Mitochondrial diseases (MDs) can be caused by single nucleotide variants (SNVs) and structural variants (SVs) in the mitochondrial genome (mtDNA). Presently, identifying deletions in small to medium-sized fragments and accurately detecting low-percentage variants remains challenging due to the limitations of next-generation sequencing (NGS). METHODS In this study, we integrated targeted long-range polymerase chain reaction (LR-PCR) and PacBio HiFi sequencing to analyze 34 participants, including 28 patients and 6 controls. Of these, 17 samples were subjected to both targeted LR-PCR and to compare the mtDNA variant detection efficacy. RESULTS Among the 28 patients tested by long-read sequencing (LRS), 2 patients were found positive for the m.3243 A > G hotspot variant, and 20 patients exhibited single or multiple deletion variants with a proportion exceeding 4%. Comparison between the results of LRS and NGS revealed that both methods exhibited similar efficacy in detecting SNVs exceeding 5%. However, LRS outperformed NGS in detecting SNVs with a ratio below 5%. As for SVs, LRS identified single or multiple deletions in 13 out of 17 cases, whereas NGS only detected single deletions in 8 cases. Furthermore, deletions identified by LRS were validated by Sanger sequencing and quantified in single muscle fibers using real-time PCR. Notably, LRS also effectively and accurately identified secondary mtDNA deletions in idiopathic inflammatory myopathies (IIMs). CONCLUSIONS LRS outperforms NGS in detecting various types of SNVs and SVs in mtDNA, including those with low frequencies. Our research is a significant advancement in medical comprehension and will provide profound insights into genetics.
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Affiliation(s)
- Yan Lin
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Jiayin Wang
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ran Xu
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China
| | - Zhe Xu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Yifan Wang
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China
| | - Shirang Pan
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China
| | - Yan Zhang
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China
| | - Qing Tao
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China
| | - Yuying Zhao
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Chuanzhu Yan
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
- Mitochondrial Medicine Laboratory, Qilu Hospital (Qingdao), Shandong University, Qingdao, Shandong, 266035, China
- Brain Science Research Institute, Shandong University, Jinan, Shandong, 250012, China
| | - Zhenhua Cao
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China.
| | - Kunqian Ji
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
- Research Institute of Neuromuscular and Neurodegenerative Diseases, Department of Neurology, Qilu Hospital, Shandong University, No. 107 West Wenhua Road, Jinan, Shandong, 250012, China.
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Yin W, Zhuang J, Li J, Xia L, Hu K, Yin J, Mu Y. Digital Recombinase Polymerase Amplification, Digital Loop-Mediated Isothermal Amplification, and Digital CRISPR-Cas Assisted Assay: Current Status, Challenges, and Perspectives. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303398. [PMID: 37612816 DOI: 10.1002/smll.202303398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/29/2023] [Indexed: 08/25/2023]
Abstract
Digital nucleic acid detection based on microfluidics technology can quantify the initial amount of nucleic acid in the sample with low equipment requirements and simple operations, which can be widely used in clinical and in vitro diagnosis. Recently, isothermal amplification technologies such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats-CRISPR associated proteins (CRISPR-Cas) assisted technologies have become a hot spot of attention and state-of-the-art digital nucleic acid chips have provided a powerful tool for these technologies. Herein, isothermal amplification technologies including RPA, LAMP, and CRISPR-Cas assisted methods, based on digital nucleic acid microfluidics chips recently, have been reviewed. Moreover, the challenges of digital isothermal amplification and possible strategies to address them are discussed. Finally, future directions of digital isothermal amplification technology, such as microfluidic chip and device manufacturing, multiplex detection, and one-pot detection, are outlined.
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Affiliation(s)
- Weihong Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Jianjian Zhuang
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou, 310006, P. R. China
| | - Jiale Li
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Liping Xia
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Kai Hu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
- School of information and Electrical Engineering, Hangzhou City University, Hangzhou, 310015, P. R. China
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
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3
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Li C, Wang Y, Li PF, Fu Q. Construction of rolling circle amplification products-based pure nucleic acid nanostructures for biomedical applications. Acta Biomater 2023; 160:1-13. [PMID: 36764595 DOI: 10.1016/j.actbio.2023.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023]
Abstract
Nucleic acid nanomaterials with good biocompatibility, biodegradability, and programmability have important applications in biomedical field. Nucleic acid nanomaterials are usually combined with some inorganic nanomaterials to improve their biological stability. However, undefined toxic side effects of composite nanocarriers hamper their application in vivo. As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. RCA products with different functional parts can be customized by changing the sequence of the circular template, thereby generating complex multifunctional DNA nanostructures, such as DNA nanowire, nanoflower, origami, nanotube, nanoribbon, etc. More importantly, RCA products as nonnicked building blocks can enhance the biostability of DNA nanostructures, especially in vivo. These RCA products-based nucleic acid nanostructures can be used as scaffolds or nanocarriers to interact or load with metal nanoparticles, proteins, lipids, cationic polymers, therapeutic nucleic acids or drugs, etc. This paper reviews the assembly strategies of RCA based DNA nanostructures with different shape and their applications in biosensing, bioimaging and biomedicine. Finally, the development prospects of the nucleic acid nanomaterials in clinical diagnosis and treatment of diseases are described. STATEMENT OF SIGNIFICANCE: As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. This paper reviews the construction of various shapes of pure nucleic acid nanomaterials based on RCA products and their applications in biosensing, bioimaging and biomedicine. This will promote the development of biocompatible DNA nanovehicles and their further application in living systems, including bioimaging, molecular detection, disease diagnosis and drug delivery, finally producing a significant impact in the field of nanotechnology and nanomedicine.
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Affiliation(s)
- Congcong Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Qinrui Fu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
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Garafutdinov RR, Sakhabutdinova AR, Gilvanov AR, Chemeris AV. Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021; 47:1172-1189. [PMID: 34931113 PMCID: PMC8675116 DOI: 10.1134/s1068162021060078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/23/2022]
Abstract
Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.
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Affiliation(s)
- R. R. Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Gilvanov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. V. Chemeris
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
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5
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Hasegawa T, Hapsari D, Iwahashi H. RNase H-dependent amplification improves the accuracy of rolling circle amplification combined with loop-mediated isothermal amplification (RCA-LAMP). PeerJ 2021; 9:e11851. [PMID: 34395086 PMCID: PMC8327969 DOI: 10.7717/peerj.11851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/03/2021] [Indexed: 11/20/2022] Open
Abstract
The hybrid method upon combining rolling circle amplification and loop-mediated isothermal amplification (RCA-LAMP) was developed to quantify very small amount of different type of RNAs, such as miRNAs. RCA-LAMP can help detect short sequences through padlock probe (PLP) circularization and exhibit powerful DNA amplification. However, one of the factors that determines the detection limit of RCA-LAMP is non-specific amplification. In this study, we improved the accuracy of RCA-LAMP through applying RNase H-dependent PCR (rhPCR) technology. In this method, the non-specific amplification was suppressed by using the rh primer, which is designed through blocking the modification at the 3'end to stop DNA polymerase reaction and replacing the 6th DNA molecule from the end with RNA using RNase H2 enzyme. Traditional RCA-LAMP amplified the non-specific amplicons from linear PLP without a targeting reaction, while RCA-LAMP with rh primer and RNase H2 suppressed the non-specific amplification. Conversely, we identified the risk posed upon conducting PLP cyclization reaction using Splint R ligase in the RNA-targeting step that occurred even in the RNA-negative condition, which is another factor determining the detection limit of RCA-LAMP. Therefore, this study contributes in improving the accuracy of RNA quantification using RCA-LAMP.
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Affiliation(s)
- Takema Hasegawa
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Gifu, Japan.,Current affiliation: Research Institute for Material and Chemical Measurement, National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Diana Hapsari
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Gifu, Japan
| | - Hitoshi Iwahashi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
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6
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Zhang K, Deng R, Gao H, Teng X, Li J. Lighting up single-nucleotide variation in situ in single cells and tissues. Chem Soc Rev 2020; 49:1932-1954. [PMID: 32108196 DOI: 10.1039/c9cs00438f] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to 'see' genetic information directly in single cells can provide invaluable insights into complex biological systems. In this review, we discuss recent advances of in situ imaging technologies for visualizing the subtlest sequence alteration, single-nucleotide variation (SNV), at single-cell level. The mechanism of recently developed methods for SNV discrimination are summarized in detail. With recent developments, single-cell SNV imaging methods have opened a new door for studying the heterogenous and stochastic genetic information in individual cells. Furthermore, SNV imaging can be used on morphologically preserved tissue, which can provide information on histological context for gene expression profiling in basic research and genetic diagnosis. Moreover, the ability to visualize SNVs in situ can be further developed into in situ sequencing technology. We expect this review to inspire more research work into in situ SNV imaging technologies for investigating cellular phenotypes and gene regulation at single-nucleotide resolution, and developing new clinical and biomedical applications.
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Affiliation(s)
- Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China. and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Hua Gao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China. and Department of Pathogeny Biology, Medical College, Zhengzhou University, Zhengzhou 450001, China
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
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7
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Smith LD, Liu Y, Zahid MU, Canady TD, Wang L, Kohli M, Cunningham BT, Smith AM. High-Fidelity Single Molecule Quantification in a Flow Cytometer Using Multiparametric Optical Analysis. ACS NANO 2020; 14:2324-2335. [PMID: 31971776 PMCID: PMC7295608 DOI: 10.1021/acsnano.9b09498] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Microfluidic techniques are widely used for high-throughput quantification and discrete analysis of micron-scale objects but are difficult to apply to molecular-scale targets. Instead, single-molecule methods primarily rely on low-throughput microscopic imaging of immobilized molecules. Here we report that commercial-grade flow cytometers can detect single nucleic acid targets following enzymatic extension and dense labeling with multiple distinct fluorophores. We focus on microRNAs, short nucleic acids that can be extended by rolling circle amplification (RCA). We labeled RCA-extended microRNAs with multicolor fluorophores to generate repetitive nucleic acid products with submicron sizes and tunable multispectral profiles. By cross-correlating the multiparametric optical features, signal-to-background ratios were amplified 1600-fold to allow single-molecule detection across 4 orders of magnitude of concentration. The limit of detection was measured to be 47 fM, which is 100-fold better than gold-standard methods based on polymerase chain reaction. Furthermore, multiparametric analysis allowed discrimination of different microRNA sequences in the same solution using distinguishable optical barcodes. Barcodes can apply both ratiometric and colorimetric signatures, which could facilitate high-dimensional multiplexing. Because of the wide availability of flow cytometers, we anticipate that this technology can provide immediate access to high-throughput multiparametric single-molecule measurements and can further be adapted to the diverse range of molecular amplification methods that are continually emerging.
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Affiliation(s)
- Lucas D Smith
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yang Liu
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Mohammad U Zahid
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Taylor D Canady
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Liang Wang
- Department of Tumor Biology , H. Lee Moffitt Cancer Center , Tampa , Florida 33612 , United States
| | - Manish Kohli
- Department of Genitourinary Oncology , H. Lee Moffitt Cancer Center , Tampa , Florida 33612 United States
| | - Brian T Cunningham
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Department of Electrical and Computer Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Cancer Center at Illinois , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Andrew M Smith
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Holonyak Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Cancer Center at Illinois , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Department of Materials Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carle Illinois College of Medicine , Urbana , Illinois 61801 , United States
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Ozer T, Geiss BJ, Henry CS. Review-Chemical and Biological Sensors for Viral Detection. JOURNAL OF THE ELECTROCHEMICAL SOCIETY 2020; 167:037523. [PMID: 32287357 PMCID: PMC7106559 DOI: 10.1149/2.0232003jes] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/25/2019] [Indexed: 05/19/2023]
Abstract
Infectious diseases commonly occur in contaminated water, food, and bodily fluids and spread rapidly, resulting in death of humans and animals worldwide. Among infectious agents, viruses pose a serious threat to public health and global economy because they are often difficult to detect and their infections are hard to treat. Since it is crucial to develop rapid, accurate, cost-effective, and in-situ methods for early detection viruses, a variety of sensors have been reported so far. This review provides an overview of the recent developments in electrochemical sensors and biosensors for detecting viruses and use of these sensors on environmental, clinical and food monitoring. Electrochemical biosensors for determining viruses are divided into four main groups including nucleic acid-based, antibody-based, aptamer-based and antigen-based electrochemical biosensors. Finally, the drawbacks and advantages of each type of sensors are identified and discussed.
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Affiliation(s)
- Tugba Ozer
- Department of Chemistry, Colorado State University, USA
- Yildiz Technical University, Faculty of Chemistry-Metallurgy, Department of Bioengineering, Istanbul, Turkey
| | - Brian J Geiss
- Department of Microbiology, Immunology & Pathology, Colorado State University, USA
- School of Biomedical Engineering, Colorado State University, USA
| | - Charles S Henry
- Department of Chemistry, Colorado State University, USA
- School of Biomedical Engineering, Colorado State University, USA
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Dai S, Zhou Y, Dai P, Cheng G, He P, Fang Y. The Split Primer Ligation‐triggered 8‐17 DNAzyme Assisted Cascade Rolling Circle Amplification for High Specific Detection of Liver Cancer‐involved mRNAs: TK1 and c‐myc. ELECTROANAL 2019. [DOI: 10.1002/elan.201900539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shiyan Dai
- College of Chemistry and Molecular EngineeringEast China Normal University Shanghai 200241 P.R. China
| | - Yuting Zhou
- College of Chemistry and Molecular EngineeringEast China Normal University Shanghai 200241 P.R. China
| | - Peiqing Dai
- College of Chemistry and Molecular EngineeringEast China Normal University Shanghai 200241 P.R. China
| | - Guifang Cheng
- College of Chemistry and Molecular EngineeringEast China Normal University Shanghai 200241 P.R. China
| | - Pingang He
- College of Chemistry and Molecular EngineeringEast China Normal University Shanghai 200241 P.R. China
| | - Yuzhi Fang
- College of Chemistry and Molecular EngineeringEast China Normal University Shanghai 200241 P.R. China
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10
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Dekaliuk M, Qiu X, Troalen F, Busson P, Hildebrandt N. Discrimination of the V600E Mutation in BRAF by Rolling Circle Amplification and Förster Resonance Energy Transfer. ACS Sens 2019; 4:2786-2793. [PMID: 31577130 DOI: 10.1021/acssensors.9b01420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The quantification of very low concentrations of circulating tumor DNA (ctDNA) biomarkers from liquid biopsies has become an important requirement for clinical diagnostics and personalized medicine. In particular, the simultaneous detection of wild-type (WT) dsDNA and their cancer-related counterparts presenting single-point mutations with simple, sensitive, specific, and reproducible technologies is paramount for ctDNA assays in clinical practice. Here, we present the development and evaluation of an amplified dsDNA assay based on a combination of isothermal rolling circle amplification (RCA) and time-gated Förster resonance energy transfer (TG-FRET) between a Tb donor and two dye (Cy3.5 and Cy5.5) acceptors. The RCA-FRET assay is free of washing and separation steps and can quantify both WT and mutated (MT) (V600E) dsDNA in the BRAF gene from a single sample in the 75 fM to 4.5 pM (4.5 × 105 to 2.7 × 107 copies) concentration range. This assay includes all steps from denaturation of the dsDNA targets to the final duplexed quantification of WT and MT targets. High assay performance at different dsDNA sequence lengths and high target specificity even in the presence of a large excess of nonspecific cell-free DNA from human plasma samples demonstrated the applicability to clinical samples. The RCA-FRET single-point mutation sensor has the potential to become an important complementary technique for analyzing liquid biopsies in advanced cancer diagnostics.
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Affiliation(s)
- Mariia Dekaliuk
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
- Department of Neurochemistry, O. V. Palladin Institute of Biochemistry, Kyiv, 01030, Ukraine
| | - Xue Qiu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
| | - Frédéric Troalen
- Gustave Roussy, Université Paris-Saclay, CNRS, UMR 8126, 94805 Villejuif, France
| | - Pierre Busson
- Gustave Roussy, Université Paris-Saclay, CNRS, UMR 8126, 94805 Villejuif, France
- Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
- Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont Saint-Aignan, France
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11
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Ultrasensitive detection of T-2 toxin in food based on bio-barcode and rolling circle amplification. Anal Chim Acta 2018; 1043:98-106. [DOI: 10.1016/j.aca.2018.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/30/2018] [Accepted: 09/05/2018] [Indexed: 11/23/2022]
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12
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Chen J, Baker YR, Brown A, El-Sagheer AH, Brown T. Enzyme-free synthesis of cyclic single-stranded DNA constructs containing a single triazole, amide or phosphoramidate backbone linkage and their use as templates for rolling circle amplification and nanoflower formation. Chem Sci 2018; 9:8110-8120. [PMID: 30542561 PMCID: PMC6238721 DOI: 10.1039/c8sc02952k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Cyclic oligonucleotides are valuable targets with a broad range of potential applications spanning molecular biology and nanotechnology. Of particular importance is their role as templates in the rolling circle amplification (RCA) reaction. We describe three different chemical cyclisation methods for the preparation of single-stranded cyclic DNA constructs. These chemical cyclisation reactions are cheaper to carry out than the enzymatic reaction, and more amenable to preparative scale purification and characterisation of the cyclic product. They can also be performed under denaturing conditions and are therefore particularly valuable for cyclic DNA templates that contain secondary structures. The resulting single-stranded cyclic DNA constructs contain a single non-canonical backbone linkage at the ligation point (triazole, amide or phosphoramidate). They were compared to unmodified cyclic DNA in rolling circle amplification reactions using φ-29 and Bst 2.0 DNA polymerase enzymes. The cyclic templates containing a phosphoramidate linkage were particularly well tolerated by φ-29 polymerase, consistently performing as well in RCA as the unmodified DNA controls. Moreover, these phosphoramidate-modified cyclic constructs can be readily produced in oligonucleotide synthesis facilities from commercially available precursors. Phosphoramidate ligation therefore holds promise as a practical, scalable method for the synthesis of fully biocompatible cyclic RCA templates. The triazole-modified cyclic templates generally gave lower and more variable yields of RCA products, a significant proportion of which were double-stranded, while the performances of the templates containing an amide linkage lie in between those of the phosphoramidate- and triazole-containing templates.
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Affiliation(s)
- Jinfeng Chen
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Ysobel R Baker
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Asha Brown
- ATDBio , Magdalen Centre , Oxford Science Park , Oxford , OX4 4GA , UK
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
- Chemistry Branch , Department of Science and Mathematics , Suez University , Suez 43721 , Egypt
| | - Tom Brown
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
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13
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Rasouli E, Shahnavaz Z, Basirun WJ, Rezayi M, Avan A, Ghayour-Mobarhan M, Khandanlou R, Johan MR. Advancements in electrochemical DNA sensor for detection of human papilloma virus - A review. Anal Biochem 2018; 556:136-144. [PMID: 29981317 DOI: 10.1016/j.ab.2018.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/01/2018] [Accepted: 07/03/2018] [Indexed: 12/29/2022]
Abstract
Human papillomavirus (HPV) is one of the most common sexually transmitted disease, transmitted through intimate skin contact or mucosal membrane. The HPV virus consists of a double-stranded circular DNA and the role of HPV virus in cervical cancer has been studied extensively. Thus it is critical to develop rapid identification method for early detection of the virus. A portable biosensing device could give rapid and reliable results for the identification and quantitative determination of the virus. The fabrication of electrochemical biosensors is one of the current techniques utilized to achieve this aim. In such electrochemical biosensors, a single-strand DNA is immobilized onto an electrically conducting surface and the changes in electrical parameters due to the hybridization on the electrode surface are measured. This review covers the recent developments in electrochemical DNA biosensors for the detection of HPV virus. Due to the several advantages of electrochemical DNA biosensors, their applications have witnessed an increased interest and research focus nowadays.
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Affiliation(s)
- Elisa Rasouli
- Nanotechnology & Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia; Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Zohreh Shahnavaz
- Nanotechnology & Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Wan Jefrey Basirun
- Nanotechnology & Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia; Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Majid Rezayi
- Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amir Avan
- Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majid Ghayour-Mobarhan
- Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Roshanak Khandanlou
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University, 3350, Ballarat, Australia.
| | - Mohd Rafie Johan
- Nanotechnology & Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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14
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Zingg JM, Daunert S. Trinucleotide Rolling Circle Amplification: A Novel Method for the Detection of RNA and DNA. Methods Protoc 2018. [PMCID: PMC6526412 DOI: 10.3390/mps1020015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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15
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Gu L, Yan W, Liu L, Wang S, Zhang X, Lyu M. Research Progress on Rolling Circle Amplification (RCA)-Based Biomedical Sensing. Pharmaceuticals (Basel) 2018; 11:E35. [PMID: 29690513 PMCID: PMC6027247 DOI: 10.3390/ph11020035] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 12/26/2022] Open
Abstract
Enhancing the limit of detection (LOD) is significant for crucial diseases. Cancer development could take more than 10 years, from one mutant cell to a visible tumor. Early diagnosis facilitates more effective treatment and leads to higher survival rate for cancer patients. Rolling circle amplification (RCA) is a simple and efficient isothermal enzymatic process that utilizes nuclease to generate long single stranded DNA (ssDNA) or RNA. The functional nucleic acid unit (aptamer, DNAzyme) could be replicated hundreds of times in a short period, and a lower LOD could be achieved if those units are combined with an enzymatic reaction, Surface Plasmon Resonance, electrochemical, or fluorescence detection, and other different kinds of biosensor. Multifarious RCA-based platforms have been developed to detect a variety of targets including DNA, RNA, SNP, proteins, pathogens, cytokines, micromolecules, and diseased cells. In this review, improvements in using the RCA technique for medical biosensors and biomedical applications were summarized and future trends in related research fields described.
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Affiliation(s)
- Lide Gu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Wanli Yan
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Le Liu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Shujun Wang
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
| | - Xu Zhang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
- Verschuren Centre for Sustainability in Energy & the Environment, Cape Breton University, Sydney, NS B1P 6L2, Canada.
| | - Mingsheng Lyu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
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16
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Qi H, Yue S, Bi S, Ding C, Song W. Isothermal exponential amplification techniques: From basic principles to applications in electrochemical biosensors. Biosens Bioelectron 2018; 110:207-217. [PMID: 29625328 DOI: 10.1016/j.bios.2018.03.065] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/16/2018] [Accepted: 03/28/2018] [Indexed: 12/12/2022]
Abstract
As a conventional amplification technique, polymerase chain reaction (PCR) has been widely applied to detect a variety of analytes with exponential amplification efficiency. However, the requirement of thermocycling procedures largely limits the application of PCR-based methods. Alternatively, several isothermal amplification techniques have been developed since the early 1990s. In particular, according to the reaction kinetics, isothermal exponential amplification techniques possess higher amplification efficiency and detection sensitivity. The isothermal exponential amplification techniques can be mainly divided into two categories: enzyme-based isothermal exponential amplification and enzyme-free isothermal exponential amplification. Considering the advantages of high sensitivity and selectivity, high signal-to-noise ratio, low cost and rapid response time, exponential amplification electrochemical biosensors have attracted considerable attention. In this review, we introduce the basic principles of isothermal exponential amplification techniques and summarize their applications in electrochemical biosensors during the past five years. We also highlighted the present challenges and further perspectives of isothermal exponential amplification-based electrochemical biosensors.
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Affiliation(s)
- Hongjie Qi
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China
| | - Shuzhen Yue
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China
| | - Sai Bi
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China.
| | - Caifeng Ding
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Weiling Song
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
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17
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Veigas B, Pinto J, Vinhas R, Calmeiro T, Martins R, Fortunato E, Baptista PV. Quantitative real-time monitoring of RCA amplification of cancer biomarkers mediated by a flexible ion sensitive platform. Biosens Bioelectron 2017; 91:788-795. [DOI: 10.1016/j.bios.2017.01.052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/22/2016] [Accepted: 01/23/2017] [Indexed: 11/24/2022]
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18
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A DNAzyme sensor based on target-catalyzed hairpin assembly for enzyme-free and non-label single nucleotide polymorphism genotyping. Talanta 2017; 167:630-637. [DOI: 10.1016/j.talanta.2017.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/24/2017] [Accepted: 03/02/2017] [Indexed: 11/19/2022]
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19
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Tang Y, Zhang XL, Tang LJ, Yu RQ, Jiang JH. In Situ Imaging of Individual mRNA Mutation in Single Cells Using Ligation-Mediated Branched Hybridization Chain Reaction (Ligation-bHCR). Anal Chem 2017; 89:3445-3451. [DOI: 10.1021/acs.analchem.6b04312] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ying Tang
- State Key Laboratory of Chemeo/Bio-Sensing
and Chemometrics, Institute of Chemical Biology and Nanomedicine,
College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xiao-Li Zhang
- State Key Laboratory of Chemeo/Bio-Sensing
and Chemometrics, Institute of Chemical Biology and Nanomedicine,
College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Li-Juan Tang
- State Key Laboratory of Chemeo/Bio-Sensing
and Chemometrics, Institute of Chemical Biology and Nanomedicine,
College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemeo/Bio-Sensing
and Chemometrics, Institute of Chemical Biology and Nanomedicine,
College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemeo/Bio-Sensing
and Chemometrics, Institute of Chemical Biology and Nanomedicine,
College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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20
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Bi S, Yue S, Zhang S. Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine. Chem Soc Rev 2017; 46:4281-4298. [DOI: 10.1039/c7cs00055c] [Citation(s) in RCA: 393] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review provides a comprehensive overview of the fundamental principles, analysis techniques, and application fields of hybridization chain reaction and its development status.
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Affiliation(s)
- Sai Bi
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- Laboratory of Fiber Materials and Modern Textiles
| | - Shuzhen Yue
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- Laboratory of Fiber Materials and Modern Textiles
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Makers
- College of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- P. R. China
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21
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Affiliation(s)
- Jungho Kim
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University , Seoul 08826, Korea.,Department of Chemistry, Seoul National University , Seoul 08826, Korea
| | - Se-Jin Park
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University , Seoul 08826, Korea.,Department of Chemistry, Seoul National University , Seoul 08826, Korea
| | - Dal-Hee Min
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University , Seoul 08826, Korea.,Department of Chemistry, Seoul National University , Seoul 08826, Korea.,Institute of Nanobio Convergence Technology, Lemonex Inc., Seoul 08826, Korea
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22
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Abstract
Nucleic acid amplification is a hugely important technology for biology and medicine. While the polymerase chain reaction (PCR) has been highly useful and effective, its reliance on heating and cooling cycles places some constraints on its utility. For example, the heating step of PCR can destroy biological molecules under investigation and heat/cool cycles are not applicable in living systems. Thus, isothermal approaches to DNA and RNA amplification are under widespread study. Perhaps the simplest of these are the rolling circle approaches, including rolling circle amplification (RCA) and rolling circle transcription (RCT). In this strategy, a very small circular oligonucleotide (e.g., 25-100 nucleotides in length) acts as a template for a DNA or an RNA polymerase, producing long repeating product strands that serve as amplified copies of the circle sequence. Here we describe the early developments and studies involving circular oligonucleotides that ultimately led to the burgeoning rolling circle technologies currently under development. This Account starts with our studies on the design of circular oligonucleotides as novel DNA- and RNA-binding motifs. We describe how we developed chemical and biochemical strategies for synthesis of well-defined circular oligonucleotides having defined sequence and open (unpaired) structure, and we outline the unusual ways in which circular DNAs can interact with other nucleic acids. We proceed next to the discovery of DNA and RNA polymerase activity on these very small cyclic DNAs. DNA polymerase "rolling circle" activities were discovered concurrently in our laboratory and that of Andrew Fire. We describe the surprising efficiency of this process even on shockingly small circular DNAs, producing repeating DNAs thousands of nucleotides in length. RNA polymerase activity on circular oligonucleotides was first documented in our group in 1995; especially surprising in this case was the finding that the process occurs efficiently even without promoter sequences in the circle. We describe how one can encode cleavable sites into the product DNAs and RNAs from RCA/RCT, which can then be resolved into large quantities of almost pure oligonucleotides. Our Account then proceeds with a summary describing a broad variety of tools and methods built in many laboratories around the rolling circle concept. Among the important developments are the discovery of highly efficient DNA polymerases for RCA; the invention of exponential ("hyperbranched") RCA amplification made possible by use of a second primer; the development of the "padlock" process for detection of nucleic acids and proteins coupled with RCA; the use of circular oligonucleotides as vectors in cells to encode biologically active RNAs via RCT; and the use of small DNA circles to encode and extend human telomeres. Finally, we finish with some ideas about where the field may go in the future.
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Affiliation(s)
- Michael G Mohsen
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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23
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Zhao C, Gao F, Weng S, Liu Q, Lin L, Lin X. An electrochemical sensor based on DNA polymerase and HRP-SiO2 nanoparticles for the ultrasensitive detection of K-ras gene point mutation. RSC Adv 2016. [DOI: 10.1039/c5ra24737c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We developed a DNA sensor for the precise detection of point mutation of K-ras gene. The sensor was based on DNA replication, which employed the DNA polymerase I and the principle of base pairing, and can detect target DNA in mixture sample.
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Affiliation(s)
- Chengfei Zhao
- Pharmaceutical and Medical Technology College
- Putian University
- Putian 351100
- China
| | - Feng Gao
- Department of Pathology
- The First Affiliated Hospital of Fujian Medical University
- Fuzhou 350005
- China
| | - Shaohuang Weng
- Department of Pharmaceutical Analysis
- Faculty of Pharmacy
- Fujian Medical University
- Fuzhou 350108
- China
| | - Qicai Liu
- Department of Clinical Laboratory
- The First Affiliated Hospital of Fujian Medical University
- Fuzhou 350005
- China
| | - Liqing Lin
- Department of Pharmaceutical Analysis
- Faculty of Pharmacy
- Fujian Medical University
- Fuzhou 350108
- China
| | - Xinhua Lin
- Department of Pharmaceutical Analysis
- Faculty of Pharmacy
- Fujian Medical University
- Fuzhou 350108
- China
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24
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Wan Y, Wang P, Su Y, Wang L, Pan D, Aldalbahi A, Yang S, Zuo X. Nanoprobe-Initiated Enzymatic Polymerization for Highly Sensitive Electrochemical DNA Detection. ACS APPLIED MATERIALS & INTERFACES 2015; 7:25618-25623. [PMID: 26524941 DOI: 10.1021/acsami.5b08817] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Electrochemical DNA (E-DNA) sensors have been greatly developed and play an important role in early diagnosis of different diseases. To determine the extremely low abundance of DNA biomarkers in clinical samples, scientists are making unremitting efforts toward achieving highly sensitive and selective E-DNA sensors. Here, a novel E-DNA sensor was developed taking advantage of the signal amplification efficiency of nanoprobe-initiated enzymatic polymerization (NIEP). In the NIEP based E-DNA sensor, the capture probe DNA was thiolated at its 3'-terminal to be immobilized onto gold electrode, and the nanoprobe was fabricated by 5'-thiol-terminated signal probe DNA conjugated gold nanoparticles (AuNPs). Both of the probes could simultaneously hybridize with the target DNA to form a "sandwich" structure followed by the terminal deoxynucleotidyl transferase (TdT)-catalyzed elongation of the free 3'-terminal of DNA on the nanoprobe. During the DNA elongation, biotin labels were incorporated into the NIEP-generated long single-stranded DNA (ssDNA) tentacles, leading to specific binding of avidin modified horseradish peroxidase (Av-HRP). Since there are hundreds of DNA probes on the nanoprobe, one hybridization event would generate hundreds of long ssDNA tentacles, resulting in tens of thousands of HRP catalyzed reduction of hydrogen peroxide and sharply increasing electrochemical signals. By employing nanoprobe and TdT, it is demonstrated that the NIEP amplified E-DNA sensor has a detection limit of 10 fM and excellent differentiation ability for even single-base mismatch.
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Affiliation(s)
| | | | | | - Lihua Wang
- Division of Physical Biology and Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Dun Pan
- Division of Physical Biology and Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , Riyadh 11451, Saudi Arabia
| | | | - Xiaolei Zuo
- Division of Physical Biology and Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
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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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26
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Li C, Wei G, Gu Q, Wang Q, Tao S, Xu L. Proliferation and differentiation of rat osteoporosis mesenchymal stem cells (MSCs) after telomerase reverse transcriptase (TERT) transfection. Med Sci Monit 2015; 21:845-54. [PMID: 25796354 PMCID: PMC4381855 DOI: 10.12659/msm.893144] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background The aim of this study was to determine whether MSC are excellent materials for MSCs transplantation in the treatment of osteoporosis. Material/Methods We studied normal, osteoporosis, and TERT-transfected MSC from normal and osteoporosis rats to compare the proliferation and osteogenic differentiation using RT-PCR and Western blot by constructing an ovariectomized rat model of osteoporosis (OVX). The primary MSC from model rats were extracted and cultured to evaluate the proliferation and differentiation characteristics. Results MSCs of osteoporosis rats obviously decreased in proliferation ability and osteogenic differentiation compared to that of normal rats. In contrast, in TERT-transfected MSC, the proliferation and differentiation ability, and especially the ability of osteogenic differentiation, were significantly higher than in osteoporosis MSC. Conclusions TERT-transfected MSCs can help osteoporosis patients in whom MSC proliferation and osteogenic differentiation ability are weak, with an increase in both bone mass and bone density, becoming an effective material for autologous transplantation of MSCs in further treatment of osteoporosis. However, studies are still needed to prove the in vivo effect, biological safety, and molecular mechanism of TERT-osteoporosis treatment. Additionally, because the results are from an animal model, more research is needed in generalizing rat model findings to human osteoporosis patients.
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Affiliation(s)
- Chao Li
- Department of Orthopaedics, 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China (mainland)
| | - Guojun Wei
- Department of Orthopaedics, 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China (mainland)
| | - Qun Gu
- Department of Orthopaedics, 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China (mainland)
| | - Qiang Wang
- Department of Orthopaedics, Affiliated Hospital of School of Medicine of Ningbo University, Ningbo, Zhejiang, China (mainland)
| | - Shuqin Tao
- Department of Orthopaedics, 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China (mainland)
| | - Liang Xu
- Department of Orthopaedics, 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China (mainland)
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27
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Huang H, Bai W, Dong C, Guo R, Liu Z. An ultrasensitive electrochemical DNA biosensor based on graphene/Au nanorod/polythionine for human papillomavirus DNA detection. Biosens Bioelectron 2015; 68:442-446. [PMID: 25618376 DOI: 10.1016/j.bios.2015.01.039] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/08/2015] [Accepted: 01/16/2015] [Indexed: 02/04/2023]
Abstract
An ultrasensitive electrochemical DNA biosensor for human papillomavirus (HPV) detection was developed by electrochemical impedance spectroscopy and differential pulse voltammetry. A capture probe was immobilized on a glassy carbon electrode modified with graphene/Au nanorod/polythionine (G/Au NR/PT). Two auxiliary probes were designed and used to long-range self-assemble DNA nanostructure. The target DNA can connect DNA structure to the capture probe on the electrode surface. [Ru(phen)3](2+) was selected as a redox indicator for amplifying electrochemical signal significantly. Enhanced sensitivity was obtained through combining the excellent electric conductivity of G/Au NR/PT architecture and the long-range self-assembly DNA nanostructure with the multi-signal amplification. The DNA biosensor displayed excellent performance for HPV DNA detection over the range from 1.0×10(-13) to 1.0×10(-10) mol/L with a detection limit of 4.03×10(-14) mol/L. Furthermore, the proposed method can also be used for the detection of HPV DNA in human serum samples and provides a potential application of DNA detection in clinic research.
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Affiliation(s)
- Huayu Huang
- Shaanxi Academy of Environmental Science, Xi'an 710061, China.
| | - Wanqiao Bai
- Shaanxi Academy of Environmental Science, Xi'an 710061, China; School of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Changxun Dong
- Department of Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Rui Guo
- School of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Zhihua Liu
- Shaanxi Academy of Environmental Science, Xi'an 710061, China
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Guven B, Boyaci IH, Tamer U, Acar-Soykut E, Dogan U. Development of rolling circle amplification based surface-enhanced Raman spectroscopy method for 35S promoter gene detection. Talanta 2015; 136:68-74. [PMID: 25702987 DOI: 10.1016/j.talanta.2014.11.051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/14/2014] [Accepted: 11/22/2014] [Indexed: 02/03/2023]
Abstract
In this study, we developed the genetically modified organism detection method by using the combination of rolling circle amplification (RCA) and surface-enhanced Raman spectroscopy (SERS). An oligonucleotide probe which is specific for 35S DNA promoter target was immobilised onto the gold slide and a RCA reaction was performed. A self-assembled monolayer was formed on gold nanorods using 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) and the second probe of the 35S DNA promoter target was immobilised on the activated gold coated slide surfaces. Probes on the nanoparticles were hybridised with the target oligonucleotide. Quantification of the target concentration was performed via SERS spectra of DTNB on the nanorods. SERS spectra of target molecules were enhanced through the RCA reaction and the detection limit was found to be 6.3fM. The sensitivity of the developed RCA-SERS method was compared with another method which had been performed without using RCA reaction, and the detection limit was found to be 0.1pM. The correlation between the target concentration and the SERS signal was found to be linear, within the range of 1pM to 10nM for the traditional assay and 100fM to 100nM for the RCA assay. For the developed RCA-SERS assay, the specificity tests were performed using the 35S promoter of Bt-176 maize gene. It was found out that the developed RCA-SERS sandwich assay method is quite sensitive, selective and specific for target sequences in model and real systems.
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Affiliation(s)
- Burcu Guven
- Department of Food Engineering, Faculty of Engineering, Hacettepe University, Beytepe, Ankara 06800, Turkey
| | - Ismail Hakki Boyaci
- Department of Food Engineering, Faculty of Engineering, Hacettepe University, Beytepe, Ankara 06800, Turkey; Food Research Center, Hacettepe University, Beytepe, Ankara 06800, Turkey.
| | - Ugur Tamer
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, Ankara 06330, Turkey
| | - Esra Acar-Soykut
- Food Research Center, Hacettepe University, Beytepe, Ankara 06800, Turkey
| | - Uzeyir Dogan
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, Ankara 06330, Turkey
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Zhou H, Wang H, Liu C, Wang H, Duan X, Li Z. Ultrasensitive genotyping with target-specifically generated circular DNA templates and RNA FRET probes. Chem Commun (Camb) 2015; 51:11556-9. [DOI: 10.1039/c5cc03738g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A RNA FRET probe-based signal amplification strategy is designed for ultrasensitive detection of RCA products coupled with thermal cycle-based ligation.
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Affiliation(s)
- Haoxian Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Hui Wang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Honghong Wang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Xinrui Duan
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
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31
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Deng H, Gao Z. Bioanalytical applications of isothermal nucleic acid amplification techniques. Anal Chim Acta 2015; 853:30-45. [DOI: 10.1016/j.aca.2014.09.037] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/16/2014] [Accepted: 09/21/2014] [Indexed: 12/31/2022]
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Yan L, Zhou J, Zheng Y, Gamson AS, Roembke BT, Nakayama S, Sintim HO. Isothermal amplified detection of DNA and RNA. MOLECULAR BIOSYSTEMS 2014; 10:970-1003. [PMID: 24643211 DOI: 10.1039/c3mb70304e] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.
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Affiliation(s)
- Lei Yan
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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33
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Yang X, Yu Y, Gao Z. A highly sensitive plasmonic DNA assay based on triangular silver nanoprism etching. ACS NANO 2014; 8:4902-7. [PMID: 24766422 DOI: 10.1021/nn5008786] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Specific nucleic acid detection by using simple and low-cost assays is important in clinical diagnostics, mutation detection, and biodefense applications. Most current methods for the quantification of low concentrations of DNA require costly and sophisticated instruments. Here, we have developed a facile DNA detection platform based on a plasmonic triangular silver nanoprism etching process, in which the shape and size of the nanoprisms were altered accompanied by a substantial surface plasmon resonance shift. Through the combination of enzyme-linked hybridization chain reaction amplification and inherent sensitivity of plasmonic silver nanoprims, this assay could detect as low as 6.0 fM target DNA. Considering the high sensitivity and selectivity of this plasmonic DNA assay, it is expected to be of great interest in clinical diagnostics.
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Affiliation(s)
- Xinjian Yang
- Department of Chemistry, National University of Singapore , Singapore 117543
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34
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Yin J, Gan P, Zhou F, Wang J. Sensitive detection of transcription factors using near-infrared fluorescent solid-phase rolling circle amplification. Anal Chem 2014; 86:2572-9. [PMID: 24475783 DOI: 10.1021/ac403758p] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This study describes a method for analyzing transcription factor (TF) activity, near-infrared fluorescent solid-phase rolling circle amplification (NIRF-sRCA). This method analyzes TF activity in four steps: (i) incubate DNA with protein sample and isolate TF-bound DNA, (ii) hybridize the TF-bound DNA and rolling circle to DNA microarray, (iii) amplify the TF-bound DNA with sRCA that contains biotin-labeled dUTP, and (iv) detect sRCA products by binding of NIRF-labeled streptavidin and NIRF imaging. This method was validated by proof-of-concept detection of purified TF protein and cell nuclear extract. Detection of purified TF protein demonstrated that NIRF-sRCA could quantitatively detect NF-κB p50 protein, and as little as 6.94 ng (∼140 fmol) of this protein was detected. Detection of nuclear extract revealed that NIRF-sRCA could specifically and quantitatively detect NF-κB p50 activity in HeLa cell nuclear extracts, and the activity of this TF in as little as 0.625 μg of nuclear extracts could be detected. Detection of nuclear extract also revealed that NIRF-sRCA could detect the relative activities of multiple TFs in HeLa cell nuclear extracts and the fold induction of multiple TFs in the TNFα-induced HeLa cell nuclear extracts. Therefore, this study provides a new tool for studying TFs.
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Affiliation(s)
- Junhuan Yin
- State Key Laboratory of Bioelectronics, Southeast University , Nanjing 210096, China
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35
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Ali MM, Li F, Zhang Z, Zhang K, Kang DK, Ankrum JA, Le XC, Zhao W. Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine. Chem Soc Rev 2014; 43:3324-41. [DOI: 10.1039/c3cs60439j] [Citation(s) in RCA: 650] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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36
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Li H, Ren J, Liu Y, Wang E. Application of DNA machine in amplified DNA detection. Chem Commun (Camb) 2014; 50:704-6. [DOI: 10.1039/c3cc47147k] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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37
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Yaroslavsky AI, Smolina IV. Fluorescence imaging of single-copy DNA sequences within the human genome using PNA-directed padlock probe assembly. ACTA ACUST UNITED AC 2013; 20:445-53. [PMID: 23521801 DOI: 10.1016/j.chembiol.2013.02.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 12/24/2012] [Accepted: 02/07/2013] [Indexed: 01/07/2023]
Abstract
We present an approach for fluorescent in situ detection of short, single-copy sequences within genomic DNA in human cells. The single-copy sensitivity and single-base specificity of our method is achieved due to the combination of three components. First, a peptide nucleic acid (PNA) probe locally opens a chosen target site, which allows a padlock DNA probe to access the site and become ligated. Second, rolling circle amplification (RCA) generates thousands of single-stranded copies of the target sequence. Finally, fluorescent in situ hybridization (FISH) is used to visualize the amplified DNA. We validate this technique by successfully detecting six single-copy target sites on human mitochondrial and autosomal DNA. We also demonstrate the high selectivity of this method by detecting X- and Y-specific sequences on human sex chromosomes and by simultaneously detecting three sequence-specific target sites. Finally, we discriminate two target sites that differ by 2 nt. The PNA-RCA-FISH approach is a distinctive in situ hybridization method capable of multitarget visualization within human chromosomes and nuclei that does not require DNA denaturation and is extremely sequence specific.
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38
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39
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Wan Y, Xu H, Su Y, Zhu X, Song S, Fan C. A surface-initiated enzymatic polymerization strategy for electrochemical DNA sensors. Biosens Bioelectron 2013; 41:526-31. [DOI: 10.1016/j.bios.2012.09.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 09/11/2012] [Accepted: 09/12/2012] [Indexed: 11/29/2022]
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40
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Chen X, Hong CY, Lin YH, Chen JH, Chen GN, Yang HH. Enzyme-Free and Label-Free Ultrasensitive Electrochemical Detection of Human Immunodeficiency Virus DNA in Biological Samples Based on Long-Range Self-Assembled DNA Nanostructures. Anal Chem 2012; 84:8277-83. [DOI: 10.1021/ac3017828] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Xian Chen
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Cheng-Yi Hong
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Ya-Hui Lin
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Jing-Hua Chen
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350004, China
| | - Guo-Nan Chen
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Huang-Hao Yang
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
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41
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Ding C, Liu H, Wang N, Wang Z. Cascade signal amplification strategy for the detection of cancer cells by rolling circle amplification and nanoparticles tagging. Chem Commun (Camb) 2012; 48:5019-21. [PMID: 22511176 DOI: 10.1039/c2cc31390a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A cascade signal amplification strategy was proposed for detection of cancer cells at ultralow concentration by combining the rolling circle amplification (RCA) technique with oligonucleotide functionalized nanoparticles (NPs), and anodic stripping voltammetric detection. This flexible biosensing system exhibited high sensitivity and specificity with the detection limits of 10 Ramos cells mL(-1).
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Affiliation(s)
- Caifeng Ding
- State Key Laboratory Base of Eco-chemical Engineering, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, China.
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42
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Ju E, Yang X, Lin Y, Pu F, Ren J, Qu X. Exonuclease-aided amplification for label-free and fluorescence turn-on DNA detection based on aggregation-induced quenching. Chem Commun (Camb) 2012; 48:11662-4. [DOI: 10.1039/c2cc37039e] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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43
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Wang G, He X, Wang B, Zhang X, Wang L. Electrochemical amplified detection of Hg2+ based on the supersandwich DNA structure. Analyst 2012; 137:2036-8. [DOI: 10.1039/c2an35048c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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44
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Lu Z, Duan D, Cao R, Zhang L, Zheng K, Li J. A reverse transcription-free real-time PCR assay for rapid miRNAs quantification based on effects of base stacking. Chem Commun (Camb) 2011; 47:7452-4. [PMID: 21597629 DOI: 10.1039/c1cc10442j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A rapid and reverse transcription-free real-time PCR microRNA assay was developed based on effects of base stacking. This microRNA assay has been shown to be highly specific to homogenous miRNAs, and the procedure can be completed within 30 min starting from total RNA.
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Affiliation(s)
- Zhuoxuan Lu
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, 398 Ruoshui Road, Dushu Lake Higher Education Town, Suzhou Industrial Park, Suzhou 215123, P. R. China
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45
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Abstract
Isothermal DNA amplification is an alternative to PCR-based amplification for point-of-care diagnosis. Since the early 1990s, the approach has been refined into a simple, rapid and cost-effective tool by means of several distinct strategies. Input signals have been diversified from DNA to RNA, protein or small organic molecules by translating these signals into input DNA before amplification, thus allowing assays on various classes of biomolecules. In situ detection of single biomolecules has been achieved using an isothermal method, leveraging localized signal amplification in an intact specimen. A few pioneering studies to develop a homogenous isothermal protein assay have successfully translated structure-switching of a probe upon target binding into input DNA for isothermal amplification. In addition to the detection of specific targets, isothermal methods have made whole-genome amplification of single cells possible owing to the unbiased, linear nature of the amplification process as well as the large size of amplified products given by ϕ29 DNA polymerase. These applications have been devised with the four isothermal amplification strategies covered in this review: strand-displacement amplification, rolling circle amplification, helicase-dependent amplification and recombinase polymerase amplification.
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46
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Chen X, Lin YH, Li J, Lin LS, Chen GN, Yang HH. A simple and ultrasensitive electrochemical DNA biosensor based on DNA concatamers. Chem Commun (Camb) 2011; 47:12116-8. [DOI: 10.1039/c1cc15695k] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Stougaard M, Juul S, Andersen FF, Knudsen BR. Strategies for highly sensitive biomarker detection by Rolling Circle Amplification of signals from nucleic acid composed sensors. Integr Biol (Camb) 2011; 3:982-92. [DOI: 10.1039/c1ib00049g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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48
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Hu J, Zhang CY. Sensitive Detection of Nucleic Acids with Rolling Circle Amplification and Surface-Enhanced Raman Scattering Spectroscopy. Anal Chem 2010; 82:8991-7. [DOI: 10.1021/ac1019599] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Juan Hu
- Institute of Biomedical Engineering and Health Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chun-yang Zhang
- Institute of Biomedical Engineering and Health Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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49
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Merkiene E, Gaidamaviciute E, Riauba L, Janulaitis A, Lagunavicius A. Direct detection of RNA in vitro and in situ by target-primed RCA: The impact of E. coli RNase III on the detection efficiency of RNA sequences distanced far from the 3'-end. RNA (NEW YORK, N.Y.) 2010; 16:1508-1515. [PMID: 20584897 PMCID: PMC2905751 DOI: 10.1261/rna.2068510] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 05/20/2010] [Indexed: 05/29/2023]
Abstract
We improved the target RNA-primed RCA technique for direct detection and analysis of RNA in vitro and in situ. Previously we showed that the 3' --> 5' single-stranded RNA exonucleolytic activity of Phi29 DNA polymerase converts the target RNA into a primer and uses it for RCA initiation. However, in some cases, the single-stranded RNA exoribonucleolytic activity of the polymerase is hindered by strong double-stranded structures at the 3'-end of target RNAs. We demonstrate that in such hampered cases, the double-stranded RNA-specific Escherichia coli RNase III efficiently assists Phi29 DNA polymerase in converting the target RNA into a primer. These observations extend the target RNA-primed RCA possibilities to test RNA sequences distanced far from the 3'-end and customize this technique for the inner RNA sequence analysis.
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Affiliation(s)
- Egle Merkiene
- Fermentas UAB, Graiciuno 8, Vilnius LT-02241, Lithuania
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50
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Armani M, Rodriguez-Canales J, Gillespie J, Tangrea M, Erickson H, Emmert-Buck MR, Shapiro B, Smela E. 2D-PCR: a method of mapping DNA in tissue sections. LAB ON A CHIP 2009; 9:3526-3534. [PMID: 20024032 PMCID: PMC2910845 DOI: 10.1039/b910807f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A novel approach was developed for mapping the location of target DNA in tissue sections. The method combines a high-density, multi-well plate with an innovative single-tube procedure to directly extract, amplify, and detect the DNA in parallel while maintaining the two-dimensional (2D) architecture of the tissue. A 2D map of the gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was created from a tissue section and shown to correlate with the spatial area of the sample. It is anticipated that this approach may be easily adapted to assess the status of multiple genes within tissue sections, yielding a molecular map that directly correlates with the histology of the sample. This will provide investigators with a new tool to interrogate the molecular heterogeneity of tissue specimens.
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Affiliation(s)
- Michael Armani
- Bioengineering Graduate Program, University of Maryland, College Park, MD, USA
- Fischell Department of Bio-Engineering, University of Maryland, College Park, MD, USA
- Pathogenetics Unit, Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Jaime Rodriguez-Canales
- Laser Microdissection Core, Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | | | - Michael Tangrea
- Pathogenetics Unit, Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Heidi Erickson
- University of Texas, M. D. Anderson Cancer Center, Department of Thoracic Head & Neck Medical Oncology, Houston, TX, USA
| | - Michael R. Emmert-Buck
- Pathogenetics Unit, Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Benjamin Shapiro
- Bioengineering Graduate Program, University of Maryland, College Park, MD, USA
- Fischell Department of Bio-Engineering, University of Maryland, College Park, MD, USA
| | - Elisabeth Smela
- Bioengineering Graduate Program, University of Maryland, College Park, MD, USA
- Department of Mechanical Engineering, University of Maryland, 2176 Martin Hall, College Park, MD, 20742, USA
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