Towards computational modeling of chromatin: All-atom MD simulations of counterion condensation around DNA

PHYS 454

Alex Savelyev, alexsav@unc.edu and Garegin A. Papoian, gpapoian@unc.edu. Department of Chemistry, The University of North Carolina at Chapel Hill, Campus Box 3290, Chapel Hill, NC 27599-3290
DNA folds into a highly compact chromatin structure in the eukariotic cells. Counterions and the aqueous solvent provide a stabilizing medium for the maintanence of the highly compact and organized DNA structures. Thus, detailed understanding of counterion condensation around DNA is required to build a coarse-grained computational model of a chromatin fiber. We carried out large-scale all-atom Molecular Dynamics simulations of a 16-mer DNA in explicit water with Na+ and K+ counterions to gain insight into generic aspects of monovalent counterion condensation around the whole DNA molecule, focusing on the discrete nature of water and ions. We found that the Na+ ions penetrate the DNA interior and condense around the DNA exterior to a significantly larger degree compared with the K+ ions. We have provided a microscopic explanation for the larger Na+ affinity towards DNA, that is based on a combination of steric, electrostatic, and hydration effects. Our simulations are consistent with the prior DNA compaction and electrophoretic mobility experiments.
 

Poster Session
7:30 PM-10:00 PM, Wednesday, 13 September 2006 Moscone Center -- Hall D, Poster

Sci-Mix
8:00 PM-10:00 PM, Monday, 11 September 2006 Moscone Center -- Hall D, Sci-Mix

Division of Physical Chemistry

The 232nd ACS National Meeting, San Francisco, CA, September 10-14, 2006