title: Free-energy landscape and characteristic forces for the initiation of DNA unzipping.
abstract: DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and experimental techniques, the minute details of the very first steps of unzipping are still unclear. Here, we use atomistic molecular-dynamics simulations, coarse-grained simulations, and a statistical-mechanical model to study the initiation of DNA unzipping by an external force. Calculation of the potential of mean force profiles for the initial separation of the first few terminal basepairs in a DNA oligomer revealed that forces ranging between 130 and 230 pN are needed to disrupt the first basepair, and these values are an order of magnitude larger than those needed to disrupt basepairs in partially unzipped DNA. The force peak has an echo of ∼50 pN at the distance that unzips the second basepair. We show that the high peak needed to initiate unzipping derives from a free-energy basin that is distinct from the basins of subsequent basepairs because of entropic contributions, and we highlight the microscopic origin of the peak. To our knowledge, our results suggest a new window of exploration for single-molecule experiments.
authors: Department of Chemistry, University of California, Irvine, Irvine, California.
authors: Ahmet
authors: A
authors: Mentes
authors: Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Interdisciplinary Research Institute, Université des Sciences et des Technologies de Lille, CNRS USR 3078, Villeneuve d'Ascq, France.
authors: Ana Maria
authors: AM
authors: Florescu
authors: Fuels Synthesis Division, Joint BioEnergy Institute, Emeryville, California; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California; Department of Bioengineering, University of California, Berkeley, Berkeley, California.
authors: Elizabeth
authors: E
authors: Brunk
authors: Department of Physics, Illinois Institute of Technology, Chicago, Illinois.
authors: Jeff
authors: J
authors: Wereszczynski
authors: Laboratoire Interdisciplinaire de Physique (CNRS UMR5588), Université Joseph Fourier Grenoble 1, St. Martin d'Heres, France.
authors: Marc
authors: M
authors: Joyeux
authors: Department of Chemistry, University of California, Irvine, Irvine, California. Electronic address: andricio@uci.edu.
authors: Ioan
authors: I
authors: Andricioaei
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D004247:DNA