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

M J Packer·C A Hunter
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Abstract

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.

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AlgorithmsBase SequenceBiopolymersDNANucleic Acid ConformationJournal Article

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M J Packer, C A Hunter. 2001-08-01. Sequence-structure relationships in DNA oligomers: a computational approach.. https://doi.org/10.1021/ja003385u

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