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DNA Research Advance Access originally published online on February 22, 2006
DNA Research 2005 12(6):441-449; doi:10.1093/dnares/dsi022
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© The Author 2006. Kazusa DNA Research Institute
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@oxfordjournals.org

Stable Triple-Stranded DNA Formation and its Application to the SNP Detection

Yasushi Shigemori1,2 and Michio Oishi1,*

1Department of Human Gene Research, Kazusa DNA Research Institute 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
2Aisin Cosmos R&D Co. Ltd 2-1-5 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan

We have found that a short stretch (30mer or larger) of triple-stranded DNA structure formed at the terminus (or very near) of linear DNA molecules is unusually stable, withstanding heat treatment at as high as 95°C. The stable triple-stranded structure is formed only when deoxyoligonucleotides are complementary to the strand terminating with 5'-phosphate and not to the strand terminating with 3'-OH. Presence of a single mismatched base in the complementary deoxyoligonucleotides drastically reduces the stability. We show that these unique properties of the terminal triple-stranded structure can be applied to the detection of single nucleotide polymorphisms in genomes without DNA dissociation and/or hybridization.

Key words: RecA protein; stable triple-stranded DNA; deoxyoligonucleotide probe; SNPs detection

*To whom correspondence should be addressed. Tel. +81-438-52-3944, Fax. +81-438-52-3911, E-mail: oishi{at}kazusa.or.jp

Communicated by Takao Sekiya


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