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Performing DNA computation with RecA-mediated triple-stranded DNA structure

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Abstract

A new method of DNA computing using an unusual triple-stranded DNA structure mediated by RecA protein is introduced and a minor 3-variable instance of the satisfiability (SAT) problem is solved. Separations were performed by using biotinylated oligodeoxynucleotide probes coated with RecA protein. During the computation, sequence-specific recognition of double-stranded DNA by homologous oligodeoxynucleotides was fulfilled in the presence of ATPγS. Captured by the magnetic particles coated with streptavidin, the desirable double-stranded DNA strands were retained and extracted. It is suggested that the methods employed here may help decrease the errors in DNA computation and solve some larger size NP- complete problems.

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Acknowledgements

The project is partially supported by National Science Foundation of China (Grant number: 60533010, 30570431) and Foundation of Shaanxi Provincial Bureau of Education (Grant number: 06JK202). We acknowledge the financial support of Dalian University. And we gratefully acknowledge the kind help and valuable suggestions from Xiaohui Liu and Xiaodong Yuan of TaKaRa Biotechnology (Dalian) Co., Ltd. Finally, the authors wish to thank the anonymous referees of this paper who provided many useful and constructive suggestions for the improvement of this paper.

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Authors and Affiliations

  1. Department of Control Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China

    Gang Fang, Jin Xu & Shemin Zhang

  2. Department of Bioengineering, Dalian University, Dalian, Liaoning, 116622, China

    Gang Fang & Jin Xu

  3. Xi’an International Studies University, Xi’an, Shaanxi, 710061, China

    Shemin Zhang

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  1. Gang Fang
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  2. Jin Xu
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  3. Shemin Zhang
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Correspondence to Gang Fang.

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Fang, G., Xu, J. & Zhang, S. Performing DNA computation with RecA-mediated triple-stranded DNA structure. Nat Comput 8, 149–156 (2009). https://doi.org/10.1007/s11047-007-9060-x

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  • DOI: https://doi.org/10.1007/s11047-007-9060-x

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