Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Aug;86(2 Pt 1):021903. doi: 10.1103/PhysRevE.86.021903. Epub 2012 Aug 3.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Biomechanical Phenomena
  • DNA, Single-Stranded / chemistry*
  • DNA, Single-Stranded / genetics
  • Mechanical Phenomena*
  • Molecular Dynamics Simulation*
  • Nucleic Acid Conformation*
  • Time Factors

Substances

  • DNA, Single-Stranded