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Mimicking DNA stretching with the Static Mode method: Shear stress versus transverse pulling stress

  • M. BrutEmail author
  • A. Estève
  • G. Landa
  • M. Djafari Rouhani
Regular Article

Abstract

DNA sequencing using nanopores is closer than ever to become a reality, but further research and development still need to be done, especially to unravel the atomic-scale mechanisms of induced DNA stretching. At this level, molecular modeling and simulation are essential to investigate DNA conformational flexibility and its response to the forces involved. In this work, through a “Static Mode” approach, we present a directed exploration of the deformations of a 27-mer subjected to externally imposed forces, as it could be in a nanopore. We show how the DNA sugar-phosphate backbone undergoes the majority of the induced deformation, before the base pairing is affected, and to what extent unzipping initiation depends on the force direction.

Keywords

Living systems: Structure and Function 

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Copyright information

© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • M. Brut
    • 1
    • 2
    Email author
  • A. Estève
    • 1
    • 3
  • G. Landa
    • 1
    • 3
  • M. Djafari Rouhani
    • 1
    • 2
  1. 1.CNRS; LAASToulouseFrance
  2. 2.UPS, LAASUniversité de ToulouseToulouseFrance
  3. 3.LAASUniversité de ToulouseToulouseFrance

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