title: Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures.
abstract: The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic. sponer@ncbr.muni.cz
authors.forename: Jiří
authors.initials: J
authors.lastname: Sponer
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Cang
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Cheatham
mesh_terms: D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry; D006860:Hydrogen Bonding; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D016615:Telomere / Q000737:chemistry
chemical_list: D008024:Ligands; D012997:Solvents; D006147:Guanine; D012313:RNA; D004247:DNA