1 research outputs found
DNA Duplex Formation with a Coarse-Grained Model
A middle-resolution
coarse-grained model of DNA is proposed. The
DNA chain is built of spherical and planar rigid bodies connected
by elastic virtual bonds. The bonded part of the potential energy
function is fit to potentials of mean force of model systems. The
rigid bodies are sets of neutral, charged, and dipolar beads. Electrostatic
and van der Waals interactions are parametrized by our recently developed
procedure [Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H.A. <i>J. Comp. Chem.</i> <b>2010</b>, <i>31</i>, 1644].
Interactions with the solvent and an ionic cloud are approximated
by a multipole–multipole Debye–Hückel model.
A very efficient <i>R</i>-RATTLE algorithm, for integrating
the movement of rigid bodies, is implemented. It is the first coarse-grained
model, in which both bonded and nonbonded interactions were parametrized
ab initio and which folds stable double helices from separated complementary
strands, with the final conformation close to the geometry of experimentally
determined structures