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Long D, Shi P, Xu X, Ren J, Chen Y, Guo S, Wang X, Cao X, Yang L, Tian Z. Understanding the relationship between sequences and kinetics of DNA strand displacements. Nucleic Acids Res 2024; 52:9407-9416. [PMID: 39077949 DOI: 10.1093/nar/gkae652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 06/18/2024] [Accepted: 07/14/2024] [Indexed: 07/31/2024] Open
Abstract
Precisely modulating the kinetics of toehold-mediated DNA strand displacements (TMSD) is essential for its application in DNA nanotechnology. The sequence in the toehold region significantly influences the kinetics of TMSD. However, due to the large sample space resulting from various arrangements of base sequences and the resulted complex secondary structures, such a correlation is not intuitive. Herein, machine learning was employed to reveal the relationship between the kinetics of TMSD and the toehold sequence as well as the correlated secondary structure of invader strands. Key factors that influence the rate constant of TMSD were identified, such as the number of free hydrogen bonding sites in the invader, the number of free bases in the toehold, and the number of hydrogen bonds in intermediates. Moreover, a predictive model was constructed, which successfully achieved semi-quantitative prediction of rate constants of TMSD even with subtle distinctions in toehold sequence.
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Affiliation(s)
- Da Long
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Peichen Shi
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Xin Xu
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Jiayi Ren
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Yuqing Chen
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Shihui Guo
- School of Informatics, Xiamen University, Xiamen 361005, PR China
| | - Xinchang Wang
- School of Electronic Science and Engineering (National Model Microelectronics College), Xiamen University, Xiamen 361005, PR China
| | - Xiaoyu Cao
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Liulin Yang
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Zhongqun Tian
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
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Huang Z, Chen J, Luo Z, Wang X, Duan Y. Label-Free and Enzyme-Free Colorimetric Detection of Pb 2+ Based on RNA Cleavage and Annealing-Accelerated Hybridization Chain Reaction. Anal Chem 2019; 91:4806-4813. [PMID: 30834746 DOI: 10.1021/acs.analchem.9b00410] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A label-free and enzyme-free colorimetric sensor for rapid detection of Pb2+ is reported, which is based on the strategy of DNAzyme-mediated RNA cleavage combined with an annealing-accelerated DNA hybridization chain reaction (HCR). As a trigger DNA, the substrate strand (STM) of DNAzyme can initiate HCR effectively. However, when it is cleaved by DNAzyme in the presence of Pb2+, the separation of DNA functional domains leads to a serious decrease in HCR efficiency. As a result, the difference in Pb2+ concentration converts into the difference of DNA assembly, which eventually leads to the color change of colloidal gold nanoparticles (AuNPs). In this work, a DNA strand (cGR5) completely complementary to the catalytic strand (GR5) of DNAzyme is used to improve the dissociation of STM to enhance the HCR efficiency. In addition, the simple operation of DNA annealing is first used to accelerate the HCR process, enabling the Pb2+ detection to be completed in about 30 min. As advantages of high sensitivity, good selectivity, strong anti-interference ability, and good practical performance are achieved, it is anticipated that the cheap and simple colorimetric sensor will be helpful for on-site detection of environmental and food samples.
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Affiliation(s)
- Zhijun Huang
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Science , Sichuan University , Chengdu , People's Republic of China 610065
| | - Junman Chen
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Science , Sichuan University , Chengdu , People's Republic of China 610065
| | - Zewei Luo
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Science , Sichuan University , Chengdu , People's Republic of China 610065
| | - Xiaqing Wang
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Science , Sichuan University , Chengdu , People's Republic of China 610065
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Science , Sichuan University , Chengdu , People's Republic of China 610065
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Chen J, Huang Z, Luo Z, Yu Q, Xu Y, Wang X, Li Y, Duan Y. Multichannel-Structured Three-Dimensional Chip for Highly Sensitive Pathogenic Bacteria Detection Based on Fast DNA-Programmed Signal Polymerization. Anal Chem 2018; 90:12019-12026. [DOI: 10.1021/acs.analchem.8b02650] [Citation(s) in RCA: 19] [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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Guo Y, Wei B, Xiao S, Yao D, Li H, Xu H, Song T, Li X, Liang H. Recent advances in molecular machines based on toehold-mediated strand displacement reaction. QUANTITATIVE BIOLOGY 2017. [DOI: 10.1007/s40484-017-0097-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Strand-Exchange Nucleic Acid Circuitry with Enhanced Thermo-and Structure- Buffering Abilities Turns Gene Diagnostics Ultra-Reliable and Environmental Compatible. Sci Rep 2016; 6:36605. [PMID: 27812041 PMCID: PMC5095676 DOI: 10.1038/srep36605] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/13/2016] [Indexed: 12/19/2022] Open
Abstract
Catalytic hairpin assembly (CHA) is one of the most promising nucleic acid amplification circuits based on toehold-mediated strand exchange reactions. But its performance is usually ruined by fluctuated environmental temperatures or unexpected self-structures existing in most real-world targets. Here we present an amide-assistant mechanism that successfully reduces the prevalence of these problems for CHA and maximizes its thermo- and structure- buffering abilities. Such an organic amide-promoted CHA (shortened as OHT-CHA) can unprecedentedly amplify through 4 °C to 60 °C without rebuilding sequences or concerning target complexity. We are then for the first time able to employ it as a direct and universal signal booster for loop mediated isothermal reaction (LAMP). LAMP is one of the most promising point-of-care (POC) gene amplifiers, but has been hard to detect precisely due to structured products and haunted off-target amplicons. OHT-CHA guarantees a significant and reliable signal for LAMP reaction amplified from as little as 10−19 M virus gene. And one single set of OHT-CHA is qualified to any detection requirement, either in real-time at LAMP running temperature (~60 °C), or at end-point on a POC photon counter only holding environmental temperatures fluctuating between 4 °C to 42 °C.
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Guo W, Hong F, Liu N, Huang J, Wang B, Duan R, Lou X, Xia F. Target-specific 3D DNA gatekeepers for biomimetic nanopores. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:2090-2095. [PMID: 25683922 DOI: 10.1002/adma.201405078] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/19/2015] [Indexed: 06/04/2023]
Abstract
3D cross-linked DNA superstructures switch off the ionic flux through solid-state nanopores with extremely high ON-OFF ratios of 10(3) -10(5) . This gating mechanism can be generally applicable in a wide range of nanopores with opening diameters up to 650 nm. The 3D bio-supramolecular gatekeepers outperform previous low-dimensional or simple-structured DNA functional components.
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Affiliation(s)
- Wei Guo
- Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P.R. China; Laboratory of Bio-Inspired Smart Interface Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P.R. China
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Zhang S, Wang K, Li Z, Feng Z, Sun T. Lab in a tube: a fast-assembled colorimetric sensor for highly sensitive detection of oligonucleotides based on a hybridization chain reaction. RSC Adv 2015. [DOI: 10.1039/c5ra04613k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Upon adding THBV, the self-assembly of THBV with H1 allows the rest of the DNA sequence of H1 to accelerate H1–H2 complex formation. The G-quadruplex at the end of the H1–H2 complex could catalyze TMB into a colored product.
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Affiliation(s)
- Siqi Zhang
- College of Sciences
- Northeastern University
- Shenyang
- China
| | - Kun Wang
- Department of Chemistry and Environmental Engineering
- Changchun University of Science and Technology
- Changchun
- China
| | - Zhenyu Li
- College of Sciences
- Northeastern University
- Shenyang
- China
| | - Zhongmin Feng
- College of Sciences
- Northeastern University
- Shenyang
- China
| | - Ting Sun
- College of Sciences
- Northeastern University
- Shenyang
- China
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