Sequence-structure relationships in DNA oligomers: a computational approach.
A collective-variable model for DNA structure is used to predict the conformation of a set of 30 octamer, decamer, and dodecamer oligomers for which high-resolution crystal structures are available. The model combines an all-atom base pair representation with an empirical backbone, emphasizing the role of base stacking in fixing sequence-dependent structure. We are able to reproduce trends in roll and twist to within 5 degrees across a large database of both A- and B-DNA oligomers. A genetic algorithm approach is used to search for global minimum structures and this is augmented by a grid search to identify local minimums. We find that the number of local minimums is highly sequence dependent, with certain sequences having a set of minimums that span the entire range between canonical A- and B-DNA conformations. Although the global minimum does not always agree with the crystal structure, for 24 of the 30 oligomers, we find low-energy local minimums that match the experimental step parameters. Discrepancies throw some light on the role of crystal packing in determining the solid-state conformation of double-helical DNA.
Packer
M J
MJ
Contribution from the Krebs Institute for Biomolecular Science, Department of Chemistry, University of Sheffield, Sheffield, S3 7HF England. m.j.packer@shef.ac.uk
Hunter
C A
CA
D000465:Algorithms; D001483:Base Sequence; D001704:Biopolymers; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation
D001704:Biopolymers; D004247:DNA