Microscopic DNA fluctuations are in accord with macroscopic DNA stretching elasticity without strong dependence on force-field choice

  • John Marko
  • Michael Feig
  • B. Montgomery Pettitt
Part of the NATO Science Series book series (NAII, volume 116)

Abstract

Multiscale modeling requires the use of information at small length and time scales to parameterize less detailed models at large scales/ We present analysis of molecular dynamics simulation of the solvated double-stranded DNA decamer d(C5T5) (A5G5) to parameterize an elastic rod model of DNA. We show that thermal fluctuation of rise along the helix implies stretching elasticity in accord with the macroscopic stretching elasticity observed in single- molecule stretching experiments. We find consistent results from three different force-fields (AMBER, CHARMM and CHARMM-27). Notably, while the base-pair rise averages about 3 Å, it fluctuates between 2 and 4 Å, i.e. by ±30%. The lifetime of these fluctuations is roughly one nanosecond. We discuss how these strong thermal deformations may play a role in the binding dynamics of proteins and drugs that deform double helix structure.

Keywords

Multiscale Simulation Molecular Dynamics Field Theory 

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Copyright information

© Springer Science+Business Media Dordrecht 2003

Authors and Affiliations

  • John Marko
    • 1
  • Michael Feig
    • 2
  • B. Montgomery Pettitt
    • 3
  1. 1.Department of PhysicsThe University of Illinois at ChicagoChicagoUSA
  2. 2.Department of Molecular Biology TPC6The Scripps Research InstituteLa JollaUSA
  3. 3.Department of ChemistryThe University of HoustonHoustonUSA

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