Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
10141504 | Journal of Molecular Liquids | 2018 | 22 Pages |
Abstract
Modified water models with different bond length are used to investigate solvent activity effects on DNA structure. The dodecamer d(CGCGAATTCGCG) DNA segment is merged into the different model solvents and its conformation transition is studied with molecular dynamics (MD) simulations in detail. We find that DNA undergos BâA-DNA transition when the solvent activity is reduced with decreasing bond length, while the DNA is restrained in B form by over activity solvent with strong hydrogen bonding when bond length is increased. Under conditions of over activity solvent, the solvent molecules are highly occupied around oxygen atoms of phosphate group leading to the lower interphosphate repulsion on DNA backbone. With decreasing solvent activity, the hydration shell around DNA becomes weak and the counterions are given the chance to interact with DNA's negative charge sites. When rOâH = 0.7 Ã
, the counterions are strongly coordinated to free phosphate oxygen atoms and bases. Its arrangement around DNA major groove is more compact, leading to the electrostatic repulsion on the backbones be restrained. Hence, the DNA favours A form conformation.
Related Topics
Physical Sciences and Engineering
Chemistry
Physical and Theoretical Chemistry
Authors
Ming-Ru Li, Nan Zhang, Feng-Shou Zhang,