title: Moving beyond Watson-Crick models of coarse grained DNA dynamics.
abstract: DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.
authors: Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors: Margaret C
authors: MC
authors: Linak
authors: Richard
authors: R
authors: Tourdot
authors: Kevin D
authors: KD
authors: Dorfman
mesh_terms: D000465:Algorithms; D052157:Aptamers, Nucleotide / Q000737:chemistry; D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation
chemical_list: D052157:Aptamers, Nucleotide; C081676:thrombin aptamer; D004247:DNA