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DNA folding in a crowded environment

ORAL

Abstract

At the molecular level, biological systems operate in very crowded solution environments. It has long been recognized that this crowding can affect the conformational stability and phase transitions of the biopolymers comprising such systems. Similar issues must be addressed in developing biotechnology applications based of dense arrays of surface-tethered polymers. In our recent work we directly measure the entropy reduction resulting from crowding/confinement using Wang-Landau computer simulation techniques [1]. Here we will discuss the folding transition of a specific single-stranded DNA oligomer that has been studied extensively by the Plaxco group [2]. We develop a coarse-grained model for this ssDNA and use it to examine the entropic effects associated with both surface tethering and surface crowding. For the tethered ssDNA oligomer crowded by other tethered oligomers, we find, in agreement with experiment, that both stabilization and destabilization are possible depending on the conformational state of the crowders. [1] Taylor, Macromolecules 50, 6967 (2017); J. Chem. Phys. 147, 166101 (2017); [2] Watkins et al, JACS 134, 2120 (2012); JACS 136, 8923 (2014).

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Authors

  • Mark Taylor

    Dept. of Physics, Hiram College, Hiram, OH

  • Clemens Winkelmann

    University of Michigan, Department of Physics \& Astronomy, Michigan State University; CREATE for STEM Institute, Department of Physics \& Astronomy, Michigan State University, Kettering University, Kent State University - Physics, Kent State University - Chemistry, Institute for Physics, Martin-Luther-Universitaet, Halle, Germany, Institute for Quantum Science and Engineering, Department of Physics and Astronomy, Texas A&M University, College Station, TX 77843, USA, IPG Photonics, 50 Old Webster Rd., Oxford, MA 01540, OptiGrate, 562 S. Econ Circle, Oviedo, FL 32765, Northrop Grumman Synoptics, 1201 Continental Blvd., Charlotte, NC 28273, University of Toledo, The University of Toledo, Toledo, OH, Case Western Reserve University, Clarkson University, Univ of Dayton, Australian Ntl Univ, U.S. Army Combat Capabilities Dev Command - Armament Ctr, Wayne State University, The University of Akron, Institute of Physics, University of Belgrade, University of Wisconsin Oshkosh, Néel Institute, Grenoble, France