Exploring potentially alternative non-canonical DNA duplex structures through simulation.

Exploring potentially alternative non-canonical DNA duplex structures through simulation.

J Biomol Struct Dyn. 2018 Jul 26;:1-15

Authors: Galindo-Murillo R, Cheatham TE, Hopkins RC

Abstract
Hopkins proposed an alternative and chirally distinct family of double stranded DNA models that have antiparallel chains with 5' → 3' senses opposite to those of the right-handed Watson-Crick (WC) family. Termed configuration II, this family of double stranded DNA models contains both right-handed, II-R, and left-handed, II-L, forms, with Z-DNA as an example of the latter. Relative interstrand binding energies for six DNA duplex models, two each of configuration I-R (standard Watson-Crick canonical B-DNA), II-R and II-L for the duplex d(CGCGAATTCGCG), have been estimated under identical conditions using MM-PBSA analysis from molecular dynamics (MD) trajectories using three different AMBER force fields. These simulations support the stereo chemical soundness of configuration II dsDNA forms. Recent force fields (bsc1 and OL15) successfully render stable II-L structures, whereas the previous force field, bsc0, generated stable II-R structures although with an energy difference between II-R and II-L of ∼30 kcal/mol.

PMID: 30047316 [PubMed - as supplied by publisher]

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