Measuring looping probability of short double-stranded DNA

COFFEE_KLATCH · Invited

Abstract

Bending of double-stranded DNA (dsDNA) is associated with fundamental biological processes such as genome packaging and gene regulation, and therefore studying sequence-dependent dsDNA bending is a key to understanding biological impact of DNA sequence beyond the genetic code. Average mechanical behavior of long dsDNA is well described by the wormlike chain model, but the behavior of dsDNA at length scales around or below its persistence length remains controversial. In this talk, I will explain how we can measure looping probability of dsDNA using a fluorescence technique called FRET (F\"orster Resonance Energy Transfer) and infer its elastic properties. I will also explain how we compare the experimental results against a discrete wormlike chain model which successfully explains the behavior of long dsDNA. I will show that the behavior of short dsDNA ($<$200 base pairs) cannot be described by the wormlike chain model, but demonstrates subelastic deformation mechanism.

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Authors

  • Chris Neu

    Florida State University, NHMFL, Institut Neel, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, China, Florida State University, Department of Physics, Florida State University, Tallahassee, FL, Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, Florida State University, National High Magnetic Field Laboratory, Institute of Physics, Chinese Academy of Sciences, China, Austin Peay State University, University of Pardubice, Davidson College, Covenant College, Lookout Mtn, GA 30750, Russian Academy of Sciences, Moscow, RU, University of Tennessee Space Institute, Tullahoma, TN, USA, Sandia National Laboratories,* Albuquerque, NM, Arkansas State University, Jonesboro, AK, None, Mississippi State University, Mississippi State University Department of Physics and Astronomy, Florida State University and the National High Magnetic Field Laboratory, Faculte des Sciences et Techniques and Universite Aix-Marseille, MIT Haystack Observatory, Departments of Chemistry and Physics, University of Tennessee of Chattanooga, Departments of Chemistry and Physics, University of Tennessee at Chattanooga, Western Kentucky University, Thomas Jefferson National Accelerator Facility, Newport News, VA, Fermilab, University of Virginia and Fermilab, Indiana University Bloomington, Indiana University Health Proton Therapy Center, University of North Florida, National Superconducting Cyclotron Laboratory, Michigan State University, Flordia State University, Louisiana State University, Washington University, Argonne National Laboratory, Lawrence Berkeley National Laboratory, Department of Physics, Florida State University., JINR, Tsinghua University, LBNL, LBNL/Vanderbilt University, Vanderbilt University, Florida A\&M University, Georgia Institute of Technology, Department of Physics, Virginia Tech, Gatton Academy, Exeter University, Florida International University, Office of Research, University of North Florida, Physics Department, University of North Florida, NSCL, Michigan State University, Physics Department, Florida State University, University of Tennessee-Knoxville, Neel Institut, Kazan Federal University, Bielefeld University, Ben Gurion University, LCIB - CEA, University of Georgia, Lawrence Livermore National Laboratory, Livermore, CA 94550, NHMFL, Tallahassee, USA, Department of Chemistry, University of Waterloo, Ontario, Canada, NHMFL, Tallahassee FL 32310 USA, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany, Wigner Research Center for Physics, Budapest, Hungary, Experimental physics II, University of Augsburg, Germany, Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, National High Magnetic Field Laboratory Florida State University, Tallahassee, Florida 32310, IM2NP-CNRS (UMR 7334) and Universite Aix-Marseille, National High Magnetic Field Laboratory Applied Superconductivity Center, Heifei National Lab for Physical Science at Microscale, USTC, Institute of Physics, Chinese Academy of Sciences, Department of Electrical Engineering, Rice University, National High Magnetic Field Laboratory, National High Magnetic Field Laboratory/FSU, University of Virginia