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 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.
Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China.
Xin
X
Li
College of Mathematics and System Science, Shandong University of Science and Technology, Qingdao, Shandong 266590, China.
Xun
X
Wang
College of Computer and Communication Engineering, China University of Petroleum, Qingdao, Shandong 266580, China ; Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, 93350 Kuching, Sarawak, Malaysia.
Tao
T
Song
Key Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
Wei
W
Lu
Key Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
Zhihua
Z
Chen
Key Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
Xiaolong
X
Shi