Nucleic Acids Research, 2003, Vol. 31, No. 3 1006-1012
© 2003 Oxford University Press
Stimulation of D-loop formation by polypurine/polypyrimidine sequences
UMR 2027 CNRS - Institut Curie, section Recherche, Bâtiment 110, Centre Universitaire, 91405 Orsay, France and 1 Laboratoire de Biophysique, UMR8646 CNRS - Muséum National d’Histoire Naturelle, U565 INSERM, 43, rue Cuvier, 75231 Paris cedex 05, France
*To whom correspondence should be addressed. Tel: +33 1 69 86 71 86; Fax: +33 1 69 86 94 29; Email: marie.dutreix{at}curie.u-psud.fr
Most of the approaches used to correct gene mutations in mammalian cells involve the targeting of short nucleotide molecules to homologous chromosomal sequences and the replacement of resident sequences via homologous recombination and mismatch repair. The limited efficiency and inconsistent reproducibility of these techniques are major constraints to their use in gene therapy. One of the main problems is that it is impossible to obtain reproducible results when the targeted gene loci differ. We investigated the effects of flanking sequences on homologous recombination by means of an in vitro assay of the efficiency of oligonucleotide targeting to its homologous sequence on a large duplex molecule in a reaction catalysed by the Escherichia coli RecA protein. We demonstrated that polypurine·polypyrimidine tracts (PPTs) in duplex DNA strongly stimulate the formation of D-loops with short oligodeoxynucleotides. This result was reproduced with various PPT sequences and oligonucleotides. The stimulatory effect was observed at loci as far as 4000 bp from the PPT. The formation of complexes between the oligonucleotide and the duplex molecule depended on the extent of sequence similarity between the two DNAs and the presence of the RecA protein. The stimulatory effect was inhibited by excess RecA and restored by adding heterologous DNA. We suggest that PPT sequences induce conformational changes in duplex DNA, leading to the aggregation of molecules, facilitating homology searches. We com pared, in vivo, the efficiency of the oligonucleotide-mediated correction of a URA3 chromosomal mutation for sequences with and without a PPT sequence in the vicinity. Consistent with our in vitro results, the efficiency of correction was eight times higher in the presence of the PPT sequence.
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