Sequence recognition in the pairing of DNA duplexes

Pairing of DNA fragments with homologous sequences occurs in gene shuffling , DNA repair, and other vital processes. While chemical individuality of ba se pairs is hidden inside the double helix, x ray and NMR revealed sequence -dependent modulation of the structure of DNA backbone. Here we show that t he resulting modulation of the DNA surface charge pattern enables duplexes longer than similar to 50 base pairs to recognize sequence homology electro statically at a distance of up to several water layers. This may explain th e local recognition observed in pairing of homologous chromosomes and the o bserved length dependence of homologous recombination.