Conformational analysis of DNA using genetic algorithms

Abstract

Among techniques for conformational analysis of DNA molecules, restrained molecular dynamics and distance geometry are, up to now, most widely used. Both techniques are essentially based on local search strategies which use evaluation criteria that are simplified for pragmatic reasons. In practice, this approach appears to be decreasingly adequate when increasingly complex conformational spaces are dealt with.

These shortcomings can be largely circumvented by employing large-scale search techniques based on non-linear adaption. In particular, we wish to bring into attention the potential of genetic algorithms for conformational analysis of aqueous DNA. It appears that this approach, as compared to aforementioned “traditional” conformational techniques, exhibits significantly better sampling of conformational space, leads to conformations that are not biased by the expert chemist's intuition, and, as a rule, manages to satisfy all experimental constraints imposed within experimental error.