title: Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis.
abstract: Double stranded helical DNA and RNA are flexible molecules that can undergo global conformational fluctuations. Their bending, twisting and stretching deformabilities are of similar magnitude. However, recent single-molecule experiments revealed a striking qualitative difference indicating an opposite sign for the twist-stretch couplings of dsDNA and dsRNA [Lipfert et al. 2014. Proc. Natl. Acad. Sci. U.S.A. 111, 15408] that is not explained by existing models. Employing unconstrained Molecular Dynamics (MD) simulations we are able to reproduce the qualitatively different twist-stretch coupling for dsDNA and dsRNA in semi-quantitative agreement with experiment. Similar results are also found in simulations that include an external torque to induce over- or unwinding of DNA and RNA. Detailed analysis of the helical deformations coupled to twist indicate that the interplay of helical rise, base pair inclination and displacement from the helix axis upon twist changes are responsible for the different twist-stretch correlations. Overwinding of RNA results in more compact conformations with a narrower major groove and consequently reduced helical extension. Overwinding of DNA decreases the size of the minor groove and the resulting positive base pair inclination leads to a slender and more extended helical structure.
authors.affiliation: Physik-Department T38, Technische Universität München, James-Franck-Strasse, D-85748 Garching, Germany.
authors.forename: Korbinian
authors.initials: K
authors.lastname: Liebl
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo namesti 2, 166 10 Prague, Czech Republic Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University Prague, Albertov 6, 128 43 Prague, Czech Republic.
authors.forename: Tomas
authors.initials: T
authors.lastname: Drsata
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo namesti 2, 166 10 Prague, Czech Republic Laboratory of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic.
authors.forename: Filip
authors.initials: F
authors.lastname: Lankas
authors.affiliation: Department of Physics, Center for Nanoscience (CeNS), and Nanosystems Initiative Munich (NIM), Ludwig-Maximilian-University Munich, 80799 Munich, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Lipfert
authors.affiliation: Physik-Department T38, Technische Universität München, James-Franck-Strasse, D-85748 Garching, Germany martin.zacharias@ph.tum.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Zacharias
mesh_terms: D020029:Base Pairing; D001696:Biomechanical Phenomena; D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012330:RNA, Double-Stranded / Q000737:chemistry*; D019415:Torque
chemical_list: D012330:RNA, Double-Stranded; D004247:DNA