A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement
DNA strand displacement technique is widely used in DNA programming, DNA biosensors, and gene analysis. In DNA strand displacement, leaky reactions can cause DNA signals decay and detecting DNA signals fails. The mostly used method to avoid leakage is cleaning up after upstream leaky reactions, and...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | Journal of Analytical Methods in Chemistry |
| Online Access: | http://dx.doi.org/10.1155/2015/675827 |
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| author | Xin Li Xun Wang Tao Song Wei Lu Zhihua Chen Xiaolong Shi |
| author_facet | Xin Li Xun Wang Tao Song Wei Lu Zhihua Chen Xiaolong Shi |
| author_sort | Xin Li |
| collection | DOAJ |
| description | DNA strand displacement technique is widely used in DNA programming, DNA biosensors, and gene analysis. In DNA strand displacement, leaky reactions can cause DNA signals decay and detecting DNA signals fails. The mostly used method to avoid leakage is cleaning up after upstream leaky reactions, and it remains a challenge to develop reliable DNA strand displacement technique with low leakage. In this work, we address the challenge by experimentally evaluating the basic factors, including reaction time, ratio of reactants, and ion concentration to the leakage in DNA strand displacement. Specifically, fluorescent probes and a hairpin structure reporting DNA strand are designed to detect the output of DNA strand displacement, and thus can evaluate the leakage of DNA strand displacement reactions with different reaction time, ratios of reactants, and ion concentrations. From the obtained data, mathematical models for evaluating leakage are achieved by curve derivation. As a result, it is obtained that long time incubation, high concentration of fuel strand, and inappropriate amount of ion concentration can weaken leaky reactions. This contributes to a method to set proper reaction conditions to reduce leakage in DNA strand displacement. |
| format | Article |
| id | doaj-art-1bff920d2e7b40c7990a2af0457840fa |
| institution | Kabale University |
| issn | 2090-8865 2090-8873 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Analytical Methods in Chemistry |
| spelling | doaj-art-1bff920d2e7b40c7990a2af0457840fa2025-02-03T06:11:47ZengWileyJournal of Analytical Methods in Chemistry2090-88652090-88732015-01-01201510.1155/2015/675827675827A Novel Computational Method to Reduce Leaky Reaction in DNA Strand DisplacementXin Li0Xun Wang1Tao Song2Wei Lu3Zhihua Chen4Xiaolong Shi5Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, ChinaCollege of Mathematics and System Science, Shandong University of Science and Technology, Qingdao, Shandong 266590, ChinaCollege of Computer and Communication Engineering, China University of Petroleum, Qingdao, Shandong 266580, ChinaKey Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, ChinaKey Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, ChinaKey Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, ChinaDNA strand displacement technique is widely used in DNA programming, DNA biosensors, and gene analysis. In DNA strand displacement, leaky reactions can cause DNA signals decay and detecting DNA signals fails. The mostly used method to avoid leakage is cleaning up after upstream leaky reactions, and it remains a challenge to develop reliable DNA strand displacement technique with low leakage. In this work, we address the challenge by experimentally evaluating the basic factors, including reaction time, ratio of reactants, and ion concentration to the leakage in DNA strand displacement. Specifically, fluorescent probes and a hairpin structure reporting DNA strand are designed to detect the output of DNA strand displacement, and thus can evaluate the leakage of DNA strand displacement reactions with different reaction time, ratios of reactants, and ion concentrations. From the obtained data, mathematical models for evaluating leakage are achieved by curve derivation. As a result, it is obtained that long time incubation, high concentration of fuel strand, and inappropriate amount of ion concentration can weaken leaky reactions. This contributes to a method to set proper reaction conditions to reduce leakage in DNA strand displacement.http://dx.doi.org/10.1155/2015/675827 |
| spellingShingle | Xin Li Xun Wang Tao Song Wei Lu Zhihua Chen Xiaolong Shi A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement Journal of Analytical Methods in Chemistry |
| title | A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement |
| title_full | A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement |
| title_fullStr | A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement |
| title_full_unstemmed | A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement |
| title_short | A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement |
| title_sort | novel computational method to reduce leaky reaction in dna strand displacement |
| url | http://dx.doi.org/10.1155/2015/675827 |
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