MODELING DNA CONFORMATIONAL MECHANICS

Using a modelling technique specifically adapted to DNA helices, we ha ve systematically studied the impact of base sequence on the geometry of the double helix. The results obtained show that each repetitive ba se sequence leads to several stable conformations belonging to the B-D NA family. These conformational sub-states generally have similar stab ilities, but often differ considerably in terms of their helical and b ackbone parameters. Each sub-state can be characterised by the puckeri ng of its sugar rings. Surface energy mapping and combinatorial search techniques are used to further understand the DNA conformational hype rsurface and to extend our study from dinucleotide repeats to tetranuc leotide sequences. The resulting structural database should be useful for predicting the properties of longer and more irregular base sequen ces and thus should contribute to understanding how DNA target sites a re recognised.