Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 11, Issue 11, Pages 5436-5446Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.5b00341
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Funding
- UW-Madison
- Wisconsin Alumni Research Foundation
- National Science Foundation
- U.S. Department of Energy's Office of Science
- Graduate Research Fellowship from National Science Foundation (NSF) [DGE-1256259]
- Department of Energy, Basic Energy Sciences, Materials Science and Engineering Division
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We present a general coarse-grained model of sodium, magnesium, spermidine, and chlorine in implicit solvent. The effective potentials between ions are systematically parametrized using a relative entropy coarse-graining approach [Carmichael, S. P. and M. S. Shell, J. Phys. Chem. B, 116, 8383-93 (2012)] that maximizes the information retained in a coarse-grained model. We describe the local distribution of ions in the vicinity of a recently published coarse-grained DNA model and demonstrate a dependence of persistence length on ionic strength that differs from that predicted by Odijk-Skolnick-Fixman theory. Consistent with experimental observations, we show that spermidine induces DNA condensation whereas magnesium and sodium do not. This model can be used alongside any coarse-grained DNA model that has explicit charges and an accurate reproduction of the excluded volume of dsDNA.
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