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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] [What about the content of this article? (0)] [Affiliation(s)] [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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SHENG N, YUE HJ, PANG SY, QI XM, ZHANG YJ, WU YZ, SONG QX, ZOU BJ, ZHOU GH. Visualized Detection of Aldehyde Dehydrogenase 2 Gene Polymorphism By Serial Invasive Reaction Coupled with Gold Nanoparticle Probe Assembling. Chinese Journal of Analytical Chemistry 2021. [DOI: 10.1016/s1872-2040(20)60072-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Aro-Heinilä A, Lönnberg T, Virta P. Covalently Mercurated Molecular Beacon for Discriminating the Canonical Nucleobases. Chembiochem 2020; 22:354-358. [PMID: 32827233 DOI: 10.1002/cbic.202000575] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Indexed: 12/14/2022]
Abstract
A highly nucleobase-discriminating metalated nucleoside analogue, 3-fluoro-2-mercuri-6-methylaniline, was incorporated into an oligonucleotide molecular beacon. Fluorescence emission spectra were measured after the addition of four different complementary strands, in which the nucleobase opposite the metalated analogue varies. The fluorescence results showed a clear binding selectivity at room temperature, in the order G>T>C>A. The selectivity is based on the different affinities between the metalated nucleoside analogue and the canonical nucleobases. The synthesized probe is capable of robust discrimination between the two purine as well as the two pyrimidine bases by fluorescence at room temperature, and more sophisticated temperature analysis allows clear separation of every canonical nucleobase. The probe would, hence, be a suitable method for the detection of single nucleotide polymorphisms.
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Affiliation(s)
- Asmo Aro-Heinilä
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
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Murata Y, Jo JI, Tabata Y. Intracellular Controlled Release of Molecular Beacon Prolongs the Time Period of mRNA Visualization. Tissue Eng Part A 2019; 25:1527-1537. [DOI: 10.1089/ten.tea.2019.0017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Yuki Murata
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jun-ichiro Jo
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasuhiko Tabata
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
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Chou WC, Hu WP, Yang YS, Chan HWH, Chen WY. Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor. Sci Rep 2019; 9:11056. [PMID: 31363139 PMCID: PMC6667443 DOI: 10.1038/s41598-019-47522-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/12/2019] [Indexed: 12/15/2022] Open
Abstract
Silicon nanowire (SiNW) field-effect transistors (FETs) is a powerful tool in genetic molecule analysis because of their high sensitivity, short detection time, and label-free detection. In nucleic acid detection, GC-rich nucleic acid sequences form self- and cross-dimers and stem-loop structures, which can easily obtain data containing signals from nonspecific DNA binding. The features of GC-rich nucleic acid sequences cause inaccuracies in nucleic acid detection and hinder the development of precision medicine. To improve the inaccurate detection results, we used phosphate-methylated (neutral) nucleotides to synthesize the neutralized chimeric DNA oligomer probe. The probe fragment originated from a primer for the detection of hepatitis C virus (HCV) genotype 3b, and single-mismatched and perfect-matched targets were designed for single nucleotide polymorphisms (SNP) detection on the SiNW FET device. Experimental results revealed that the HCV-3b chimeric neutralized DNA (nDNA) probe exhibited better performance for SNP discrimination in 10 mM bis-tris propane buffer at 25 °C than a regular DNA probe. The SNP discrimination of the nDNA probe could be further improved at 40 °C on the FET device. Consequently, the neutralized chimeric DNA probe could successfully distinguish SNP in the detection of GC-rich target sequences under optimal operating conditions on the SiNW FET device.
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Affiliation(s)
- Wei-Cheng Chou
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li, 32001, Taiwan
| | - Wen-Pin Hu
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, 41354, Taiwan
| | - Yuh-Shyong Yang
- Institute of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30010, Taiwan
| | - Hardy Wai-Hong Chan
- Helios Bioelectronics, Inc. 3F., No. 2, Sec. 2, Shengyi Rd., Zhubei City, Hsinchu County, 302, Taiwan
| | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li, 32001, Taiwan.
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Hu J, Xiao K, Jin B, Zheng X, Ji F, Bai D. Paper-based point-of-care test with xeno nucleic acid probes. Biotechnol Bioeng 2019; 116:2764-2777. [PMID: 31282991 DOI: 10.1002/bit.27106] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 01/09/2023]
Abstract
Bridging the unmet need of efficient point-of-care testing (POCT) in biomedical engineering research and practice with the emerging development in artificial synthetic xeno nucleic acids (XNAs), this review summarized the recent development in paper-based POCT using XNAs as sensing probes. Alongside the signal transducing mode and immobilization methods of XNA probes, a detailed evaluation of probe performance was disclosed. With these new aspects, both researchers in synthetic chemistry / biomedical engineering and physicians in clinical practice could gain new insights in designing, manufacturing and choosing suitable reagents and techniques for POCT.
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Affiliation(s)
- Jie Hu
- Singapore Institute of Manufacturing Technology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kang Xiao
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, P. R. China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, P. R. China
| | - Birui Jin
- School of Materials and Chemical Engineering, Xi'an Technological University, Xi'an, P. R. China
| | - Xuyang Zheng
- Department of Infectious Diseases, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, P. R. China
| | - Fanpu Ji
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Dan Bai
- Xi'an Institute of Flexible Electronics (IFE) & Xi'an Key Laboratory of Flexible Electronics (KLoFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Shaanxi Key Laboratory of Flexible Electronics (KLoFE), Northwestern Polytechnical University (NPU), Xi'an, Shaanxi, P. R. China.,Xi'an Institute of Biomedical Materials and Engineering (IBME) & Xi'an Key Laboratory of Biomedical Materials and Engineering (KLBME), Northwestern Polytechnical University (NPU), Xi'an, Shaanxi, P. R. China
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Abrosimova LA, Migur AY, Kubareva EA, Zatsepin TS, Gavshina AV, Yunusova AK, Perevyazova TA, Pingoud A, Oretskaya TS. A study on endonuclease BspD6I and its stimulus-responsive switching by modified oligonucleotides. PLoS One 2018; 13:e0207302. [PMID: 30475809 PMCID: PMC6261011 DOI: 10.1371/journal.pone.0207302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/28/2018] [Indexed: 11/18/2022] Open
Abstract
Nicking endonucleases (NEases) selectively cleave single DNA strands in double-stranded DNAs at a specific site. They are widely used in bioanalytical applications and in genome editing; however, the peculiarities of DNA-protein interactions for most of them are still poorly studied. Previously, it has been shown that the large subunit of heterodimeric restriction endonuclease BspD6I (Nt.BstD6I) acts as a NEase. Here we present a study of interaction of restriction endonuclease BspD6I with modified DNA containing single non-nucleotide insertion with an azobenzene moiety in the enzyme cleavage sites or in positions of sugar-phosphate backbone nearby. According to these data, we designed a number of effective stimulus-responsive oligonucleotide inhibitors bearing azobenzene or triethylene glycol residues. These modified oligonucleotides modulated the functional activity of Nt.BspD6I after cooling or heating. We were able to block the cleavage of T7 phage DNA by this enzyme in the presence of such inhibitors at 20-25°C, whereas the Nt.BspD6I ability to hydrolyze DNA was completely restored after heating to 45°C. The observed effects can serve as a basis for the development of a platform for regulation of NEase activity in vitro or in vivo by external signals.
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Affiliation(s)
- Liudmila A. Abrosimova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Anzhela Yu. Migur
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Elena A. Kubareva
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Timofei S. Zatsepin
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia
| | - Aleksandra V. Gavshina
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alfiya K. Yunusova
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Tatiana A. Perevyazova
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig University, Giessen, Germany
| | - Tatiana S. Oretskaya
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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Napoli C, Lai S, Giannetti A, Tombelli S, Baldini F, Barbaro M, Bonfiglio A. Electronic Detection of DNA Hybridization by Coupling Organic Field-Effect Transistor-Based Sensors and Hairpin-Shaped Probes. Sensors (Basel) 2018; 18:E990. [PMID: 29584638 DOI: 10.3390/s18040990] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/20/2018] [Accepted: 03/23/2018] [Indexed: 11/16/2022]
Abstract
In this paper, the electronic transduction of DNA hybridization is presented by coupling organic charge-modulated field-effect transistors (OCMFETs) and hairpin-shaped probes. These probes have shown interesting properties in terms of sensitivity and selectivity in other kinds of assays, in the form of molecular beacons (MBs). Their integration with organic-transistor based sensors, never explored before, paves the way to a new class of low-cost, easy-to-use, and portable genetic sensors with enhanced performances. Thanks to the peculiar characteristics of the employed sensor, measurements can be performed at relatively high ionic strengths, thus optimizing the probes’ functionality without affecting the detection ability of the device. A complete electrical characterization of the sensor is reported, including calibration with different target concentrations in the measurement environment and selectivity evaluation. In particular, DNA hybridization detection for target concentration as low as 100 pM is demonstrated.
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Zhang M, Liu K, Hu Y, Lin Y, Li Y, Zhong P, Jin X, Zhu X, Zhang C. A novel quantitative PCR mediated by high-fidelity DNA polymerase. Sci Rep 2017; 7:10365. [PMID: 28871131 DOI: 10.1038/s41598-017-10782-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/14/2017] [Indexed: 01/19/2023] Open
Abstract
The biggest challenge for accurate diagnosis of viral infectious disease is the high genetic variability of involved viruses, which affects amplification efficiency and results in low sensitivity and narrow spectrum. Here, we developed a new simple qPCR mediated by high-fidelity (HF) DNA polymerase. The new method utilizes an HFman probe and one primer. Fluorescent signal was generated from the 3'-5' hydrolysis of HFman probe by HF DNA polymerase before elongation initiation. Mismatches between probe/primer and template have less influence on the amplification efficiency of the new method. The new qPCR exhibited higher sensitivity and better adaptability to sequence variable templates than the conventional TaqMan probe based-qPCR in quantification of HIV-1 viral load. Further comparison with COBAS TaqMan HIV-1 Test (v2.0) showed a good correlation coefficient (R2 = 0.79) between both methods in quantification of HIV-1 viral load among 21 clinical samples. The characteristics of tolerance to variable templates and one probe-one primer system imply that the probe/primer design for the new method will be easier and more flexible than the conventional method for highly heterogeneous viruses. Therefore, the HF DNA polymerase-mediated qPCR method is a simple, sensitive and promising approach for the development of diagnostics for viral infectious diseases.
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