title: DNA Structural Correlation in Short and Long Ranges.
abstract: Recent single-molecule measurements have revealed the DNA allostery in protein/DNA binding. MD simulations showed that this allosteric effect is associated with the deformation properties of DNA. In this study, we used MD simulations to further investigate the mechanism of DNA structural correlation, its dependence on DNA sequence, and the chemical modification of the bases. Besides a random sequence, poly d(AT) and poly d(GC) are also used as simpler model systems, which show the different bending and twisting flexibilities. The base-stacking interactions and the methyl group on the 5-carbon site of thymine causes local structures and flexibility to be very different for the two model systems, which further lead to obviously different tendencies of the conformational deformations, including the long-range allosteric effects.
authors.forename: Chan
authors.initials: C
authors.lastname: Gu
authors.forename: Jun
authors.initials: J
authors.lastname: Zhang
authors.forename: Y Isaac
authors.initials: YI
authors.lastname: Yang
authors.forename: Xi
authors.initials: X
authors.lastname: Chen
authors.forename: Hao
authors.initials: H
authors.lastname: Ge
authors.forename: Yujie
authors.initials: Y
authors.lastname: Sun
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Su
authors.forename: Lijiang
authors.initials: L
authors.lastname: Yang
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States.
authors.forename: Sunney
authors.initials: S
authors.lastname: Xie
authors.forename: Yi Qin
authors.initials: YQ
authors.lastname: Gao
mesh_terms: D000494:Allosteric Regulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D011506:Proteins; D004247:DNA