Sequence-structure relationships in DNA oligomers: a computational approach.

摘要: A collective-variable model for DNA structure is used to predict the conformation of a set 30 octamer, decamer, and dodecamer oligomers which high-resolution crystal structures are available. The combines an all-atom base pair representation with empirical backbone, emphasizing role stacking in fixing sequence-dependent structure. We able reproduce trends roll twist within 5 degrees across large database both A- B-DNA oligomers. genetic algorithm approach search global minimum this augmented by grid identify local minimums. find that number minimums highly sequence dependent, certain sequences having span entire range between canonical conformations. Although does not always agree structure, 24 oligomers, we low-energy match experimental step parameters. Discrepancies throw some light on packing determining solid-state double-helical DNA.