title: An investigation of the ionic and solvation patterns of dsDNG versus dsDNA by use of molecular dynamics simulations.
abstract: Molecular dynamics has been employed to analyze the counterion and water atmospheres around the deoxynucleic guanidine (DNG) duplex G(12)-C(12). These features are compared to those of DNA G(12)-C(12). The chloride counterions of cationic DNG demonstrate fewer penetrations and only fleeting residence times in the minor groove, as opposed to the multi-nanosecond visits seen by sodium ions in DNA minor grooves. The 10 ns simulations also show the differences in hydration patterns between the DNG and DNA duplexes.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA.
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Toporowski
authors.forename: Swarnalatha Y
authors.initials: SY
authors.lastname: Reddy
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Bruice
mesh_terms: D002414:Cations, Monovalent / Q000737:chemistry; D002712:Chlorides / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D004583:Electrons; D006146:Guanidines / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D012995:Solubility; D012997:Solvents / Q000737:chemistry; D014867:Water / Q000737:chemistry*
chemical_list: D002414:Cations, Monovalent; D002712:Chlorides; D006146:Guanidines; D012997:Solvents; C088820:deoxynucleic guanidine; D014867:Water; D004247:DNA