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Design of nucleic acid sequences for DNA computing based on a thermodynamic approach

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Please use this identifier to cite or link to this item:http://hdl.handle.net/2115/64504

Title: Design of nucleic acid sequences for DNA computing based on a thermodynamic approach
Authors: Tanaka, Fumiaki Browse this author
Kameda, Atsushi Browse this author
Yamamoto, Masahito Browse this author →KAKEN DB
Ohuchi, Azuma Browse this author →KAKEN DB
Issue Date: 2005
Publisher: Oxford University Press
Journal Title: Nucleic Acids Research
Volume: 33
Issue: 3
Start Page: 903
End Page: 911
Publisher DOI: 10.1093/nar/gki235
Abstract: We have developed an algorithm for designing multiple sequences of nucleic acids that have a uniform melting temperature between the sequence and its complement and that do not hybridize non-specifically with each other based on the minimum free energy (ΔGmin). Sequences that satisfy these constraints can be utilized in computations, various engineering applications such as microarrays, and nano-fabrications. Our algorithm is a random generate-and-test algorithm: it generates a candidate sequence randomly and tests whether the sequence satisfies the constraints. The novelty of our algorithm is that the filtering method uses a greedy search to calculate ΔGmin. This effectively excludes inappropriate sequences before ΔGmin is calculated, thereby reducing computation time drastically when compared with an algorithm without the filtering. Experimental results in silico showed the superiority of the greedy search over the traditional approach based on the hamming distance. In addition, experimental results in vitro demonstrated that the experimental free energy (ΔGexp) of 126 sequences correlated well with ΔGmin (|R| = 0.90) than with the hamming distance (|R| = 0.80). These results validate the rationality of a thermodynamic approach. We implemented our algorithm in a graphic user interface-based program written in Java.
Type: article
URI: http://hdl.handle.net/2115/64504
Appears in Collections:情報科学院・情報科学研究院 (Graduate School of Information Science and Technology / Faculty of Information Science and Technology) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 山本 雅人

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