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Nucleic Acids Research, 2001, Vol. 29, No. 4 e15
© 2001 Oxford University Press

Detection of competing DNA structures by thermal gradient gel electrophoresis: from self-association to triple helix formation by (G,A)-containing oligonucleotides

Paola B. Arimondo, Thérèse Garestier, Claude Hélène and Jian-Sheng Sun*

Laboratoire de Biophysique UMR 8646 CNRS–Muséum National d’Histoire Naturelle, INSERM U201, 43 rue Cuvier, 75231 Paris Cedex 05, France

Sequence-specific recognition of DNA can be achieved by triple helix-forming oligonucleotides that bind to the major groove of double-helical DNA. These oligonucleotides have been used as sequence-specific DNA ligands for various purposes, including sequence-specific gene regulation in the so-called ‘antigene strategy’. In particular, (G,A)-containing oligonucleotides can form stable triple helices under physiological conditions. However, triplex formation may be in competition with self-association of these oligonucleotides. For biological applications it would be interesting to identify the conditions under which one structure is favoured as compared to the other(s). Here we have directly studied competition between formation of a parallel (G,A) homoduplex and that of a triple helix by a 13 nt (G,A)-containing oligonucleotide. Temperature gradient gel electrophoresis allows simultaneous detection of competition between the two structures, because of their different temperature dependencies and gel electrophoretic mobilities, and characterisation of this competition.

* To whom correspondence should be addressed. Tel: +33 1 40793711; Fax: +33 1 40793705; Email: sun{at}mnhn.fr


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