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Journal of Analytical Methods in Chemistry
Volume 2015, Article ID 675827, 10 pages
http://dx.doi.org/10.1155/2015/675827
Research Article

A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement

1Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
2College of Mathematics and System Science, Shandong University of Science and Technology, Qingdao, Shandong 266590, China
3College of Computer and Communication Engineering, China University of Petroleum, Qingdao, Shandong 266580, China
4Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, 93350 Kuching, Sarawak, Malaysia
5Key Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China

Received 6 May 2015; Accepted 7 July 2015

Academic Editor: Chih-Ching Huang

Copyright © 2015 Xin Li et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

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.