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Nucleic Acids Research 2005 33(3):903-911; doi:10.1093/nar/gki235
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Published online 8 February 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

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

Fumiaki Tanaka1,*, Atsushi Kameda2, Masahito Yamamoto1,2 and Azuma Ohuchi1,2

1 Graduate School of Engineering, Hokkaido University North 13, West 8, Kita-ku, Sapporo 060-8628, Japan 2 CREST, Japan Science and Technology Corporation 4-1-8, Honmachi, Kawaguchi, Saitama, 332-0012, Japan

*To whom correspondence should be addressed. Tel: +81 11 716 2111, ext 6498; Fax: +81 11 706 7834; Email: fumiaki{at}dna-comp.org

Received October 19, 2004. Revised January 20, 2005. Accepted January 20, 2005.

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 ({Delta}G min). 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 {Delta}G min. This effectively excludes inappropriate sequences before {Delta}G min 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 ({Delta}G exp) of 126 sequences correlated well with {Delta}G min (|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.


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