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Published online 2 January 2004

Nucleic Acids Research, 2004, Vol. 32, No. 1 e4
© 2004 Oxford University Press

Specific cleavage of DNA molecules at RecA-mediated triple-strand structure

Yasushi Shigemori and Michio Oishi*

Laboratory of Human Gene Research II, Kazusa DNA Research Institute, Kazusakamatari 2-6-7, Kisarazu, Chiba 292-0812, Japan

*To whom correspondence should be addressed. Tel: +81 438 52 3945; Fax: +81 438 52 3946; Email: oishi{at}kazusa.or.jp
Present address:
Yasushi Shigemori, Biotechnology Division, Aisin Cosmos R & D Co. Ltd, 2-3-9 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan

A novel procedure to cleave DNA molecules at any desired base sequence is presented. This procedure is based upon our finding that double-stranded DNA molecules at a site where RecA-mediated triple-stranded DNA structure with a complimentary deoxyoligonucleotide is located can be cleaved by a single-strand specific nuclease, such as nuclease S1 or BAL31, between the first base at the 5' termini of the deoxyoligonucleotides and the nearest base proximal to the 5' termini. Accordingly, the sequence as well as the number of the cleavage sites to be cleaved can be custom designed by selecting deoxyoligonucleotides with specific base sequences for triple-stranded DNA formation. The basic characteristics of the cleavage reaction and typical applications of the procedure are presented with actual results, including those which involve cleavage of complex genomic DNA at the very sites one desires.


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