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Deng Y, Zhou T, Peng Y, Wang M, Xiang L, Zhang Y, Li J, Yang J, Li G. Dual-Gene-Controlled Rolling Circle Amplification Strategy for SARS-CoV-2 Analysis. Anal Chem 2023; 95:3358-3362. [PMID: 36723441 PMCID: PMC9897047 DOI: 10.1021/acs.analchem.2c04572] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/24/2023] [Indexed: 02/02/2023]
Abstract
The development of sensitive, accurate, and conveniently operated methods for the simultaneous assay of two nucleic acids is promising while still challenging. In this work, by using two genes (the N gene and RdRp gene) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as examples, we have designed an ingenious dual-gene-controlled rolling circle amplification (RCA) strategy to propose an accurate and sensitive electrochemical method. Specifically, the coexistence of the two target genes can trigger the RCA reaction to generate a number of repeated G-quadruplex (G4)-forming sequences. These sequences then switch into G4/hemin complexes with redox activity after the incubation of hemin, which can catalyze the TMB/H2O2 substrates to produce significantly enhanced current responses. Experimental results reveal that the proposed method exhibits satisfying feasibility and analytical performance, enabling the sensitive detection of SARS-CoV-2 in the range of 0.1-5000 pM, with the detection limit of 57 fM. Meanwhile, because only the simultaneous existence of the two target genes can effectively trigger the downstream amplification reaction, this method can effectively avoid false-positives and ensure specificity as well as accuracy. Furthermore, our method can distinguish the COVID-19 samples from healthy people, and the outcomes show a satisfying agreement with the results of RT-PCR, manifesting that our label-free dual-gene-controlled RCA strategy exhibits great possibility in clinical application.
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Affiliation(s)
- Ying Deng
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
| | - Tianci Zhou
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
| | - Ying Peng
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
| | - Minghui Wang
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
| | - Liangliang Xiang
- The Second Hospital of Nanjing, Nanjing
University of Chinese Medicine, Nanjing210003, P. R.
China
| | - Yuanyuan Zhang
- Department of Obstetrics and Gynecology,
The First Affiliated Hospital of Nanjing Medical University,
Nanjing210029, P. R. China
| | - Jinlong Li
- The Second Hospital of Nanjing, Nanjing
University of Chinese Medicine, Nanjing210003, P. R.
China
| | - Jie Yang
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
| | - Genxi Li
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
- Center for Molecular Recognition and Biosensing,
School of Life Sciences, Shanghai University, Shanghai200444,
P. R. China
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Kamar O, Sun SC, Lin CH, Chung WY, Lee MS, Liao YC, Kolpashchikov DM, Chuang MC. A mutation-resistant deoxyribozyme OR gate for highly selective detection of viral nucleic acids. Chem Commun (Camb) 2017; 53:10592-10595. [PMID: 28900642 PMCID: PMC5645154 DOI: 10.1039/c7cc05576e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Highly selective probes hybridize only to fully complementary DNA or RNA sequences and, therefore, often fail to recognize mutated viral genomes. Here we designed a probe that possesses two seemingly incompatible properties: it tolerates some point mutations in genome, while it remains selective towards others. An OR deoxyribozyme logic gate was designed to fluorescently report the sequences of enterovirus 71 (EV71) covering ∼90% of all known EV71 strains. Importantly, sequences of closely related coxsackieviruses that differed by single nucleotides were reliably differentiated in 7 out of 8 cases.
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Affiliation(s)
- Ola Kamar
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA.
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3
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Nucleic acid sensing with enzyme-DNA binding protein conjugates cascade and simple DNA nanostructures. Anal Bioanal Chem 2017; 409:3623-3632. [DOI: 10.1007/s00216-017-0304-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/03/2017] [Accepted: 03/08/2017] [Indexed: 11/26/2022]
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4
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Kuo TM, Shen MY, Huang SY, Li YK, Chuang MC. Facile Fabrication of a Sensor with a Bifunctional Interface for Logic Analysis of the New Delhi Metallo-β-Lactamase (NDM)-Coding Gene. ACS Sens 2015. [DOI: 10.1021/acssensors.5b00080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tsui-Ming Kuo
- Department
of Chemistry, Tunghai University, Taichung 40704, Taiwan
| | - Mo-Yuan Shen
- Department
of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Shih-Ying Huang
- Department
of Chemistry, Tunghai University, Taichung 40704, Taiwan
| | - Yaw-Kuen Li
- Department
of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Min-Chieh Chuang
- Department
of Chemistry, Tunghai University, Taichung 40704, Taiwan
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5
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Lee CC, Liao YC, Lai YH, Lee CCD, Chuang MC. Recognition of dual targets by a molecular beacon-based sensor: subtyping of influenza A virus. Anal Chem 2015; 87:5410-6. [PMID: 25879394 DOI: 10.1021/acs.analchem.5b00810] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A molecular beacon (MB)-based sensor to offer a decisive answer in combination with information originated from dual-target inputs is designed. The system harnesses an assistant strand and thermodynamically favored designation of unpaired nucleotides (UNs) to process the binary targets in "AND-gate" format and report fluorescence in "off-on" mechanism via a formation of a DNA four-way junction (4WJ). By manipulating composition of the UNs, the dynamic fluorescence difference between the binary targets-coexisting circumstance and any other scenario was maximized. Characteristic equilibrium constant (K), change of entropy (ΔS), and association rate constant (k) between the association ("on") and dissociation ("off") states of the 4WJ were evaluated to understand unfolding behavior of MB in connection to its sensing capability. Favorable MB and UNs were furthermore designed toward analysis of genuine genetic sequences of hemagglutinin (HA) and neuraminidase (NA) in an influenza A H5N2 isolate. The MB-based sensor was demonstrated to yield a linear calibration range from 1.2 to 240 nM and detection limit of 120 pM. Furthermore, high-fidelity subtyping of influenza virus was implemented in a sample of unpurified amplicons. The strategy opens an alternative avenue of MB-based sensors for dual targets toward applications in clinical diagnosis.
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Affiliation(s)
- Chun-Ching Lee
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
| | - Yu-Chieh Liao
- ‡Institute of Population Health Science, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan
| | - Yu-Hsuan Lai
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
| | | | - Min-Chieh Chuang
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
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Dong S, Zhao R, Zhu J, Lu X, Li Y, Qiu S, Jia L, Jiao X, Song S, Fan C, Hao R, Song H. Electrochemical DNA Biosensor Based on a Tetrahedral Nanostructure Probe for the Detection of Avian Influenza A (H7N9) Virus. ACS APPLIED MATERIALS & INTERFACES 2015; 7:8834-42. [PMID: 25844798 DOI: 10.1021/acsami.5b01438] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A DNA tetrahedral nanostructure-based electrochemical biosensor was developed to detect avian influenza A (H7N9) virus through recognizing a fragment of the hemagglutinin gene sequence. The DNA tetrahedral probe was immobilized onto a gold electrode surface based on self-assembly between three thiolated nucleotide sequences and a longer nucleotide sequence containing complementary DNA to hybridize with the target single-stranded (ss)DNA. The captured target sequence was hybridized with a biotinylated-ssDNA oligonucleotide as a detection probe, and then avidin-horseradish peroxidase was introduced to produce an amperometric signal through the interaction with 3,3',5,5'-tetramethylbenzidine substrate. The target ssDNA was obtained by asymmetric polymerase chain reaction (PCR) of the cDNA template, reversely transcribed from the viral lysate of influenza A (H7N9) virus in throat swabs. The results showed that this electrochemical biosensor could specifically recognize the target DNA fragment of influenza A (H7N9) virus from other types of influenza viruses, such as influenza A (H1N1) and (H3N2) viruses, and even from single-base mismatches of oligonucleotides. Its detection limit could reach a magnitude of 100 fM for target nucleotide sequences. Moreover, the cycle number of the asymmetric PCR could be reduced below three with the electrochemical biosensor still distinguishing the target sequence from the negative control. To the best of our knowledge, this is the first report of the detection of target DNA from clinical samples using a tetrahedral DNA probe functionalized electrochemical biosensor. It displays that the DNA tetrahedra has a great potential application as a probe of the electrochemical biosensor to detect avian influenza A (H7N9) virus and other pathogens at the gene level, which will potentially aid the prevention and control of the disease caused by such pathogens.
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Affiliation(s)
- Shibiao Dong
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
- ‡Institute of Applied Mechanics and Biomedical Engineering, Taiyuan University of Technology, Taiyuan, Shanxi 030024, China
| | - Rongtao Zhao
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Jiangong Zhu
- ∥Clinical Diagnostic Center, 302 Hospital of PLA, Beijing 100039, China
| | - Xiao Lu
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yang Li
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Shaofu Qiu
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Leili Jia
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Xiong Jiao
- ‡Institute of Applied Mechanics and Biomedical Engineering, Taiyuan University of Technology, Taiyuan, Shanxi 030024, China
| | - Shiping Song
- §Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- §Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - RongZhang Hao
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - HongBin Song
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
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