title: Coarse-Grained Ions for Nucleic Acid Modeling.
abstract: 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.
authors.affiliation: Department of Chemical and Biological Engineering, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Hinckley
authors.affiliation: Institute for Molecular Engineering, University of Chicago , Chicago, Illinois 60637, United States.|Materials Science Division Argonne National Laboratory , Argonne, Illinois 60439, United States.
authors.forename: Juan J
authors.initials: JJ
authors.lastname: de Pablo
mesh_terms: D002713:Chlorine / Q000737:chemistry; D007477:Ions; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D009696:Nucleic Acids / Q000737:chemistry*; D012964:Sodium / Q000737:chemistry; D013095:Spermidine / Q000737:chemistry
chemical_list: D007477:Ions; D009696:Nucleic Acids; D002713:Chlorine; D012964:Sodium; D008274:Magnesium; D013095:Spermidine