title: Enhanced sampling simulations of DNA step parameters.
abstract: A novel approach for the selection of step parameters as reaction coordinates in enhanced sampling simulations of DNA is presented. The method uses three atoms per base and does not require coordinate overlays or idealized base pairs. This allowed for a highly efficient implementation of the calculation of all step parameters and their Cartesian derivatives in molecular dynamics simulations. Good correlation between the calculated and actual twist, roll, tilt, shift, and slide parameters is obtained, while the correlation with rise is modest. The method is illustrated by its application to the methylated and unmethylated 5'-CATGTGACGTCACATG-3' double stranded DNA sequence. One-dimensional umbrella simulations indicate that the flexibility of the central CG step is only marginally affected by methylation.
authors.affiliation: Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE 205, Tampa, Florida, 33620.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Karolak
authors.forename: Arjan
authors.initials: A
authors.lastname: van der Vaart
mesh_terms: D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation
chemical_list: D004247:DNA
keywords: DNA; free energy; step paremeters; umbrella sampling