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Xie Y, Hou Y, Yu Y, Zhang J, Long J, Chen M, Lang X, Yang X, Chen H. Cascade branch migration-triggered strand displacement amplification for specific and sensitive detection of microRNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4116-4123. [PMID: 38855960 DOI: 10.1039/d4ay00765d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
MicroRNAs (miRNAs) have been involved in many biological processes and are regarded as promising biomarkers. The short sequence, low abundance and highly homologous interference sequences greatly hinder the accurate detection of miRNAs. Here, a cascade branch migration-triggered strand displacement amplification (CBM-TSDA) strategy was developed for the first time for specific and sensitive detection of miRNA-155 (miR-155). In the presence of target miR-155, the CBM was initiated and two Y-shaped probes were eventually produced. Next, the Y-shaped probes were transformed into three-way junction (3WJ) structures and triggered the SDA to produce a large number of G-quadruplex (G4) structures. Finally, the increased fluorescence signal of G4/Thioflavin T (ThT) was used to quantify miR-155. Meanwhile, the colorimetric responses of the G4-hemin DNAzyme could be used as supplementary detection to obtain a dual-mode signal readout. This detection strategy showed high detection sensitivity, and the limit of detection was 0.28 pM in the fluorescence detection mode and 0.34 pM in the colorimetric detection mode. Notably, it showed high detection specificity, being able to discriminate the single-base mutations of the target with a high discrimination factor. The strategy also possessed excellent capacity for miR-155 detection in cell lysates and real human blood samples. The developed strategy provides a promising detection platform for miRNA, which may be applied to early clinical diagnosis.
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Affiliation(s)
- Yaxing Xie
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Yulei Hou
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Yang Yu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Jianhong Zhang
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Jinyan Long
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Mengqi Chen
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Xueqing Lang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Hui Chen
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
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2
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A novel fluorescence biosensor based on double-stranded DNA branch migration-induced HCR and DNAzyme feedback circuit for sensitive detection of Pseudomonas aeruginosa (clean version). Anal Chim Acta 2022; 1232:340449. [DOI: 10.1016/j.aca.2022.340449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/18/2022] [Accepted: 09/25/2022] [Indexed: 12/30/2022]
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3
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Zhang Z, Mei M, Yao J, Ye T, Quan J, Liu J. An off/on thrombin activated energy driven molecular machine for sensitive detection of human thrombin via non-enzymatic catalyst recycling amplification. Analyst 2021; 145:6868-6874. [PMID: 32820297 DOI: 10.1039/d0an01054e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this article, we report a novel dual on/off thrombin fluorescence aptasensor by combining the energy driven target induced strand displacement reaction and a non-enzyme catalyst recycling DNA machine. Firstly, the specific binding of an aptamer strand and thrombin induce the release of a catalyst which was used as a DNA machine trigger. Subsequently, the catalyst as the trigger initiated the DNA machine through nucleic acid hybridization and branch migration of the DNA machine, resulting in the DNA substrate melting and re-hybridization. In such a working model, the DNA machine achieved cooperative control of the circular strand displacement reaction, realizing catalyst recycling and dual-amplification. The fluorescence signal change of FAM and ROX accumulation had a good linear relationship with the thrombin concentration in the range of 1 fM to 1 nM. On account of catalyst recycling and dual recognition, the detection limit for thrombin was determined to be as low as 0.45 fM (S/N = 3).This biosensor also showed good selectivity for thrombin without being affected by some other proteins, such as PSA, lysozyme etc. Moreover, this assay can be applied to the detection of thrombin in diluted human serum.
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Affiliation(s)
- Zhang Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China.
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4
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Lai W, Xiao M, Yang H, Li L, Fan C, Pei H. Circularized blocker-displacement amplification for multiplex detection of rare DNA variants. Chem Commun (Camb) 2021; 56:12331-12334. [PMID: 32959033 DOI: 10.1039/d0cc05283c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A superselective isothermal amplification technique, termed circularized blocker-displacement amplification, was developed for multiplex analysis of rare DNA variants.
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Affiliation(s)
- Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
| | - Haihong Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
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5
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Zhang L, Wang Y, Guo Y, Chen H, Yu W, Zhang Z, Xie G. A comprehensive system for detecting rare single nucleotide variants based on competitive DNA probe and duplex-specific nuclease. Anal Chim Acta 2021; 1166:338545. [PMID: 34023002 DOI: 10.1016/j.aca.2021.338545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022]
Abstract
Single nucleotide variants (SNVs) have emerged as increasingly important biomarkers, particularly in the diagnosis and prognosis of cancers. However, most SNVs are rarely detected in blood samples from cancer patients as they are surrounded by abundant concomitant wild-type nucleic acids. Herein, we design a system that features a combination of competitive DNA probe system (CDPS) and duplex-specific nuclease (DSN) that we referred to as CAD. A theoretical model was established for the CAD system based on reaction networks. Guided by the theoretical model, we found that a minor loss in sensitivity significantly improved the specificity of the system, thus creating a theoretical discrimination factor (DF) > 100 for most conditions. This non-equivalent tradeoff between sensitivity and specificity provides a new concept for the analysis of rare DNA-sequence variants. As a demonstration of practicality, we applied as-proposed CAD system to identify low variant allele frequency (VAF) in a synthetic template (0.1% VAF) and human genomic DNA (1% VAF). This work promises complete guidance for the design of enzyme-based nucleic acid analysis.
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Affiliation(s)
- Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yufeng Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yongcan Guo
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, 646000, PR China
| | - Huajian Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Wen Yu
- Clinical Laboratory of Chongqing University Cancer Hospital, Chongqing, 400016, PR China
| | - Zhang Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
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6
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Zhang Z, Zhang L, Wang Y, Yao J, Wang T, Weng Z, Yang L, Xie G. Ultrasensitive electrochemical biosensor for attomolar level detection of let 7a based on toehold mediated strand displacement reaction circuits and molecular beacon mediated circular strand displacement polymerization. Anal Chim Acta 2021; 1147:108-115. [PMID: 33485569 DOI: 10.1016/j.aca.2020.12.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/26/2020] [Accepted: 12/27/2020] [Indexed: 12/12/2022]
Abstract
In this study, an ultrasensitive electrochemical miRNA biosensor based on toehold mediated strand displacement reaction circuits (SDRCs) and molecular beacon mediated isothermal circular strand displacement polymerization reaction (ICSDPR) has been proposed. During the SDRCs module, the cascade strand displacement reaction induces the recycling of the target let 7a and generation of a large amount of strand A (SA). The SA recognition opens the hairpin capture probe immobilized on the gold electrode, thus, varying the distance between the redox molecules and electrode surface. The primer mediated ICSDPR is observed to further generate a large amount of SA, thus, leading to a reduction in the signal. Considering these merits, the proposed method is observed to exhibit a log-linear linearity from 10 aM to 100 pM and ultrahigh sensitivity towards let 7a down to 6.2 aM, with a capability of distinguishing the let 7a family members, thereby, providing a new electrochemical route for early cancer screening.
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Affiliation(s)
- Zhang Zhang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China; Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Li Zhang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China
| | - Youqiang Wang
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, PR China
| | - Juan Yao
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, PR China
| | - Ting Wang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China; Department of Laboratory Medicine, Chongqing Fuling People's Hospital, Chongqing, PR China
| | - Zhi Weng
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China
| | - Liu Yang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China.
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7
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Zhang Z, Yao J, Huang X, Zhang L, Wang T, Weng Z, Xie G. Multiplex real-time PCR using double-strand primers and probes for the detection of nucleic acids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:5392-5396. [PMID: 33111715 DOI: 10.1039/d0ay01661f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Multiplex PCR encounters difficulties in primer designing with all the primer pairs working at the same annealing temperature. In this study, we have developed a double-strand primer-mediated multiple strand displacement reaction for the detection of SARS-COV-2 ORF, N and E genes (as examples). The double primer is composed of a 5'-modified fluorophore strand, which does not impact polymerase extension and a 3'-modified quencher strand, which cannot impact elongation. At the annealing temperature, the fluorophore strand combined with the template, extended and resulted in fluorescence signal release. Results showed that the double-strand primer relatively exhibits a wide annealing temperature range and good compatibility between three pairs of primers and probes. These merits allow the simple and multiplex real-time fluorescence quantification of nucleic acids. The detection limit was 400 copies/mL, and the detection time was approximately 2 h. In addition to its extreme specificity and simplicity, this method has a wide range of applications such as multiple PCR and SNP detection.
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Affiliation(s)
- Zhang Zhang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China.
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8
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Zhao Y, Feng Y, Zhang Y, Xia P, Xiao Z, Wang Z, Yan H. Combining competitive sequestration with nonlinear hybridization chain reaction amplification: an ultra-specific and highly sensitive sensing strategy for single-nucleotide variants. Anal Chim Acta 2020; 1130:107-116. [PMID: 32892930 DOI: 10.1016/j.aca.2020.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/06/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
Highly specific and sensitive detection of single-nucleotide variants (SNVs) is of central importance in disease diagnosis and pharmacogenomics. However, it remains a great challenge to successfully detect very low amounts of mutant SNV sequences in real samples in which a SNV sequence may be surrounded by high levels of closely related wild-type sequences. Herein, we propose an ultra-specific and highly sensitive SNV sensing strategy by combining the competitive sequestration with the nonlinear hybridization chain reaction (HCR) amplification. The rationally designed sequestration hairpin can effectively sequester the large amount of wild-type sequence and thus dramatically improve the hybridization specificity in recognizing SNVs. To improve the detection sensitivity, a new fluorescent signal probe is fabricated by intercalating SYBR Green I dye into the nonlinear HCR based DNA dendrimer to further bind with SNVs for signal amplification. The hyperbranched DNA dendrimer possesses large numbers of DNA duplexes for dye intercalation, thus the signal probe shows strong fluorescence intensity, leading to large fluorescence signal amplification. Taking advantage of the improved hybridization specificity of the competitive sequestration and the enhanced fluorescence response of the nonlinear HCR amplification, the developed sensing strategy enables ultra-specific and highly sensitive detection of SNVs. Taking human pancreatic cancers and colorectal carcinomas related KRAS gene mutations as models, the developed strategy shows remarkably high specificity against 17 SNVs (discrimination factors ranged from 126 to 1001 with a median of 310), and achieves high sensitivity for 6 KRAS mutations (the best resultant detection limit reached 15 pM for KRAS G13D (c.38G > A)). Notably, combined with PCR amplification, our SNV sensing strategy could detect KRAS G12D (c.35G > A) from extracted human genomic DNA samples at abundance as low as 0.05%. This work expands the rule set of designing specific and sensitive SNV sensing strategies and shows promising potential application in clinical diagnosis.
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Affiliation(s)
- Yan Zhao
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China.
| | - Yuanbo Feng
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Yuanbo Zhang
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Pu Xia
- Key Laboratory of Spectral Imaging Technology, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
| | - Zihan Xiao
- Queen Mary University of London Engineering School, NPU, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Ziheng Wang
- Queen Mary University of London Engineering School, NPU, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Hongxia Yan
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China.
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9
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Tang W, Zhong W, Tan Y, Wang GA, Li F, Liu Y. DNA Strand Displacement Reaction: A Powerful Tool for Discriminating Single Nucleotide Variants. Top Curr Chem (Cham) 2020; 378:10. [PMID: 31894426 DOI: 10.1007/s41061-019-0274-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023]
Abstract
Single-nucleotide variants (SNVs) that are strongly associated with many genetic diseases and tumors are important both biologically and clinically. Detection of SNVs holds great potential for disease diagnosis and prognosis. Recent advances in DNA nanotechnology have offered numerous principles and strategies amenable to the detection and quantification of SNVs with high sensitivity, specificity, and programmability. In this review, we will focus our discussion on emerging techniques making use of DNA strand displacement, a basic building block in dynamic DNA nanotechnology. Based on their operation principles, we classify current SNV detection methods into three main categories, including strategies using toehold-mediated strand displacement reactions, toehold-exchange reactions, and enzyme-mediated strand displacement reactions. These detection methods discriminate SNVs from their wild-type counterparts through subtle differences in thermodynamics, kinetics, or response to enzymatic manipulation. The remarkable programmability of dynamic DNA nanotechnology also allows the predictable design and flexible operation of diverse strand displacement probes and/or primers. Here, we offer a systematic survey of current strategies, with an emphasis on the molecular mechanisms and their applicability to in vitro diagnostics.
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Affiliation(s)
- Weiyang Tang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yun Tan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Guan A Wang
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada
| | - Feng Li
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada. .,College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China. .,Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Wuhan University, Wuhan, China.
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10
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Yu W, Li J, Zuo C, Tao Y, Bai S, Li J, Zhang Z, Xie G. Specific discrimination and universal signal amplification for RNA detection by coupling toehold exchange with RCA through nucleolytic conversion of a structure-switched hairpin probe. Anal Chim Acta 2019; 1068:96-103. [PMID: 31072482 DOI: 10.1016/j.aca.2019.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/02/2019] [Accepted: 04/09/2019] [Indexed: 12/27/2022]
Abstract
Herein, we combined toehold exchange with ligation-free rolling circle amplification (RCA) by programming nucleolytic conversion of hairpin probe into sensors, allowed for both high specific recognition and universal signal amplification for RNA detection. The rational engineered HP ensured highly specific recognition based on toehold exchange and allowed the pre-formed circular template for RCA to be shared for different RNAs detection. Generally, detecting different RNA requires different circular template for signal amplification. In this paper, the circular template for RCA was independent of the sequences of the target, so the signal amplification system was an universal one for different RNAs detection. Taking miRNA let-7d as a model target, this method showed a wide linear range from 1 fM to 1 nM with a detection limit of 0.46 fM and exhibited a remarkable selectivity even in distinguishing homologous miRNAs with 1-nt or 2-nt difference. To evaluate the potential of the method, it was applied to analysis the let-7d concentration in human serum, total RNA, and cell lysates. In conclusion, we believe this method exhibits potential for both specific discrimination and universal signal amplification for RNA analysis in complex matrices.
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Affiliation(s)
- Wen Yu
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Juqiong Li
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Chen Zuo
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yiyi Tao
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Shulian Bai
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Junlong Li
- Department of Laboratory Medicine, The Affiliated University City Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhang Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, PR China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
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11
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Simmel FC, Yurke B, Singh HR. Principles and Applications of Nucleic Acid Strand Displacement Reactions. Chem Rev 2019; 119:6326-6369. [PMID: 30714375 DOI: 10.1021/acs.chemrev.8b00580] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.
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Affiliation(s)
| | - Bernard Yurke
- Micron School of Materials Science and Engineering , Boise State University , Boise , ID 83725 , United States
| | - Hari R Singh
- Physics Department , TU München , 85748 Garching , Germany
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12
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Yao J, Zhang Z, Deng Z, Wang Y, Guo Y. An enzyme free electrochemical biosensor for sensitive detection of miRNA with a high discrimination factor by coupling the strand displacement reaction and catalytic hairpin assembly recycling. Analyst 2018; 142:4116-4123. [PMID: 28991307 DOI: 10.1039/c7an01224a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An isothermal, enzyme free, ultra-specific and ultra-sensitive protocol for electrochemical detection of miRNAs is proposed based on the toehold-mediated strand displacement reaction (SDR) and non-enzymatic catalytic hairpin reaction (CHA) recycling. The SDR was first triggered only in the presence of target miRNA and this process also affects other miRNA interferences having similar target sequences, thus guaranteeing a high discrimination factor and could be used in rare content miRNA detection with various amounts of interferences having similar target sequences. The output protector strand then triggered enzyme free CHA amplification and generates plenty of hairpin self-assembly products. This process in turn influences SDR equilibrium to move to the right and generates large amounts of protector output to ensure analysis sensitivity. Compared with traditional CHA, our proposed method greatly improved the signal to noise ratio and shows excellent performance in rare miRNA detection with miRNA analogue interference. Under the optimal experimental conditions and using square wave voltammetry, the established biosensor could detect target miRNA-21 down to 30 fM (S/N = 3) with a dynamic range from 100 fM to 2 nM, and discriminate rare target miRNA-21 from mismatched miRNA with high selectivity. This method holds great promise in miRNA detection from human cancer cell lines and would be a versatile and powerful tool for clinical molecular diagnostics.
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Affiliation(s)
- Juan Yao
- Department of Laboratory Medicine, Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, P. R. China.
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13
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Zhou L, Wang J, Chen Z, Li J, Wang T, Zhang Z, Xie G. A universal electrochemical biosensor for the highly sensitive determination of microRNAs based on isothermal target recycling amplification and a DNA signal transducer triggered reaction. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2129-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Yu W, Tang L, Qiu JH, Zhang Z, Zhou LL, Li JL, Xie GM. Systematic comparison between toehold exchange and toehold displacement: exploration for highly specific and sensitive DNA detection. RSC Adv 2017. [DOI: 10.1039/c7ra07481f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The detection of nucleic acid variations with high specificity and sensitivity is essential for the good practice of precision medicine.
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Affiliation(s)
- Wen Yu
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Lan Tang
- The Public Health Center
- The First Affiliated Hospital of Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Ju-Hui Qiu
- State Key Laboratory of Membrane Biology
- Tsinghua-Peking Center for Life Sciences
- School of Life Sciences
- Tsinghua University
- Beijing 100084
| | - Zhang Zhang
- Department of Laboratory Medicine
- Affiliated Hospital of Southwest Medical University
- Luzhou
- P. R. China
| | - Li-Li Zhou
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Jun-Long Li
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Guo-Ming Xie
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
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Bi S, Yue S, Wu Q, Ye J. Initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction for logic operations and amplified biosensing. Biosens Bioelectron 2016; 83:281-6. [DOI: 10.1016/j.bios.2016.04.059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/16/2016] [Accepted: 04/19/2016] [Indexed: 12/19/2022]
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16
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Zhang P, Liu H, Ma S, Men S, Li Q, Yang X, Wang H, Zhang A. A label-free ultrasensitive fluorescence detection of viable Salmonella enteritidis using enzyme-induced cascade two-stage toehold strand-displacement-driven assembly of G-quadruplex DNA. Biosens Bioelectron 2016; 80:538-542. [PMID: 26894984 DOI: 10.1016/j.bios.2016.02.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 01/25/2016] [Accepted: 02/10/2016] [Indexed: 11/30/2022]
Abstract
The harm of Salmonella enteritidis (S. enteritidis ) to public health mainly by contaminating fresh food and water emphasizes the urgent need for rapid detection techniques to help control the spread of the pathogen. In this assay, an newly designed capture probe complex that contained specific S. enteritidis-aptamer and hybridized signal target sequence was used for viable S. enteritidis recognition directly. In the presence of the target S. enteritidis, single-stranded target sequences were liberated and initiated the replication-cleavage reaction, producing numerous G-quadruplex structures with a linker on the 3'-end. And then, the sensing system took innovative advantage of quadratic linker-induced strand-displacement for the first time to release target sequence in succession, leading to the cyclic reuse of the target sequences and cascade signal amplification, thereby achieving the successive production of G-quadruplex structures. The fluorescent dye, N-Methyl mesoporphyrin IX, binded to these G-quadruplex structures and generated significantly enhanced fluorescent signals to achieve highly sensitive detection of S. enteritidis down to 60 CFU/mL with a linear range from 10(2) to 10(7)CFU/mL. By coupling the cascade two-stage target sequences-recyclable toehold strand-displacement with aptamer-based target recognition successfully, it is the first report on a novel non-label, modification-free and DNA extraction-free ultrasensitive fluorescence biosensor for detecting viable S. enteritidis directly, which can discriminate from dead S. enteritidis.
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Affiliation(s)
- Peng Zhang
- College of Life Sciences, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu 610065, China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu 610065, China; "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Chengdu 610065, China
| | - Hui Liu
- College of Life Sciences, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu 610065, China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu 610065, China; "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Chengdu 610065, China
| | - Suzhen Ma
- College of Life Sciences, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu 610065, China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu 610065, China; "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Chengdu 610065, China
| | - Shuai Men
- College of Life Sciences, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu 610065, China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu 610065, China; "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Chengdu 610065, China
| | - Qingzhou Li
- College of Life Sciences, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu 610065, China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu 610065, China; "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Chengdu 610065, China
| | - Xin Yang
- College of Life Sciences, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu 610065, China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu 610065, China; "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Chengdu 610065, China
| | - Hongning Wang
- College of Life Sciences, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu 610065, China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu 610065, China; "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Chengdu 610065, China.
| | - Anyun Zhang
- College of Life Sciences, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu 610065, China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Chengdu 610065, China; "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Chengdu 610065, China
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Yao J, Zhang Z, Zhao Y, Jing W, Zuo G. Double-stranded probe modified AuNPs for sensitive and selective detection of microRNA 30a in solution and live cell. RSC Adv 2016. [DOI: 10.1039/c6ra05131f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this article, we reported a double-stranded DNA probe modified gold nanoparticle used as both “nano-flares” and transfection agents to quantify miR-30a in solution and visualize in live cells.
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Affiliation(s)
- Juan Yao
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Zhang Zhang
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Yingze Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology
- Institute of Zoology
- Chinese Academy of Sciences
- Beijing 100101
- P. R. China
| | - Wanli Jing
- Department of Orthopaedics
- Tianjin First Center Hospital
- Tianjin 300192
- P. R. China
| | - Guowei Zuo
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
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