title: Single-Walled Carbon Nanotubes Modulate the B- to A-DNA Transition.
abstract: We study the conformational equilibrium between B-to-A forms of ds-DNA adsorbed onto a single-walled carbon nanotube (SWNT) using free energy profile calculations based on all-atom molecular dynamics simulations. The potential of mean force (PMF) of the B-to-A transition of ds-DNA in the presence of an uncharged (10,0) carbon nanotube for two dodecamers with poly-AT or poly-GC sequences is calculated as a function of a root-mean-square-distance (ΔRMSD) difference metric for the B-to-A transition. The calculations reveal that in the presence of a SWNT DNA favors B-form DNA significantly in both poly-GC and poly-AT sequences. Furthermore, the poly-AT DNA:SWNT complex shows a higher energy penalty for adopting an A-like conformation than poly-GC DNA:SWNT by several kcal/mol. The presence of a SWNT on either poly-AT or poly-GC DNA affects the PMF of the transition such that the B form is favored by as much as 10 kcal/mol. In agreement with published data, we find a potential energy minimum between A and B-form DNA at ΔRMSD ≈ -1.5 Å and that the presence of the SWNT moves this minimum by as much as ΔRMSD = 3 Å.
authors.affiliation: Department of Chemistry, University of California , Irvine, California 92617, United States.
authors.forename: Gavin
authors.initials: G
authors.lastname: Bascom
authors.affiliation: Department of Chemistry, University of California , Irvine, California 92617, United States.
authors.forename: Ioan
authors.initials: I
authors.lastname: Andricioaei