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

PHYS 454

Alex Savelyev, and Garegin A. Papoian, 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

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