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

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タイトル: Design of nucleic acid sequences for DNA computing based on a thermodynamic approach
著者: Tanaka, Fumiaki 著作を一覧する
Kameda, Atsushi 著作を一覧する
Yamamoto, Masahito 著作を一覧する
Ohuchi, Azuma 著作を一覧する
発行日: 2005年
出版者: Oxford University Press
誌名: Nucleic Acids Research
巻: 33
号: 3
開始ページ: 903
終了ページ: 911
出版社 DOI: 10.1093/nar/gki235
抄録: 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.
資料タイプ: article
出現コレクション:雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

提供者: 山本 雅人


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