title: Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations.
abstract: Bending of the seemingly stiff DNA double helix is a fundamental physical process for any living organism. Specialized proteins recognize DNA inducing and stabilizing sharp curvatures of the double helix. However, experimental evidence suggests a high protein-independent flexibility of DNA. On the basis of coarse-grained simulations, we propose that DNA experiences thermally induced kinks associated with the spontaneous formation of internal bubbles. Comparison of the protein-induced DNA curvature calculated from the Protein Data Bank with that sampled by our simulations suggests that thermally induced distortions can account for ~80% of the DNA curvature present in experimentally solved structures.
authors.affiliation: Institut Pasteur de Montevideo, Calle Mataojo 2020, Montevideo, Codigo Postal 11400, Uruguay.
authors.forename: Ari
authors.initials: A
authors.lastname: Zeida
authors.forename: Matías Rodrigo
authors.initials: MR
authors.lastname: Machado
authors.forename: Pablo Daniel
authors.initials: PD
authors.lastname: Dans
authors.forename: Sergio
authors.initials: S
authors.lastname: Pantano
mesh_terms: D001483:Base Sequence; D001696:Biomechanical Phenomena; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000235:genetics; D055595:Mechanical Phenomena; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D013997:Time Factors
chemical_list: D004277:DNA, Single-Stranded