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DNA Research Advance Access published online on February 22, 2006
DNA Research, doi:10.1093/dnares/dsi022
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© The Author 2006. Kazusa DNA Research Institute.
Received December 6, 2005
Revised December 11, 2005

Full Papers

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

Yasushi Shigemori 1 and Michio Oishi 2 *

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

* To whom correspondence should be addressed.
Michio Oishi, E-mail: oishi{at}kazusa.or.jp


  Abstract

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.

Keywords: RecA protein; stable triple-stranded DNA; deoxyoligonucleotide probe; SNPs detection.
Communicated by Takao Sekiya
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