Elasticity of DNA and the effect of dendrimer binding

  • Santosh Mogurampelly
  • Bidisha Nandy
  • Roland R. Netz
  • Prabal K. Maiti
Regular Article

Abstract.

Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic properties of short double-stranded DNA (dsDNA) and the effect of dendrimer binding using fully atomistic molecular dynamics and numerical simulations. In equilibrium at room temperature, the contour length distribution P(L) and the end-to-end distance distribution P(R) are nearly Gaussian, the former gives an estimate of the stretch modulus \(\gamma_{1}\) of dsDNA in quantitative agreement with the literature value. The bend angle distribution \(P(\theta)\) of the dsDNA also has a Gaussian form and allows to extract a persistence length, Lp of 43nm. When the dsDNA is compacted by positively charged dendrimer, the stretch modulus stays invariant but the effective bending rigidity estimated from the end-to-end distance distribution decreases dramatically due to backbone charge neutralization of dsDNA by dendrimer. We support our observations with numerical solutions of the worm-like-chain (WLC) model as well as using non-equilibrium dsDNA stretching simulations. These results are helpful in understanding the dsDNA elasticity at short length scales as well as how the elasticity is modulated when dsDNA binds to a charged object such as a dendrimer or protein.

Graphical abstract

Keywords

Soft Matter: Polymers and Polyelectrolytes 

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Copyright information

© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Santosh Mogurampelly
    • 1
  • Bidisha Nandy
    • 1
  • Roland R. Netz
    • 2
  • Prabal K. Maiti
    • 1
  1. 1.Centre for Condensed Matter Theory, Department of PhysicsIndian Institute of ScienceBangaloreIndia
  2. 2.Fachbereich PhysikFreie Universität BerlinBerlinGermany

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