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.J. Comp. Chem.2010,31, 1644]. Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model. A very efficientR-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.
Baker Laboratory of Chemistry, Cornell University , Ithaca, New York 14850, United States ; Department of Physics and Biophysics, Faculty of Food Sciences, University of Warmia and Mazury , 11-041 Olsztyn, Poland.
Maciej
M
Maciejczyk
Baker Laboratory of Chemistry, Cornell University , Ithaca, New York 14850, United States ; Department of Biochemistry and Biophysics, University of Rochester Medical Center , Rochester, New York 14642, United States.
Aleksandar
A
Spasic
Baker Laboratory of Chemistry, Cornell University , Ithaca, New York 14850, United States ; Faculty of Chemistry, University of Gdańsk , 80-308 Gdańsk, Poland.
Adam
A
Liwo
Baker Laboratory of Chemistry, Cornell University , Ithaca, New York 14850, United States.
Harold A
HA
Scheraga