A model for structure and thermodynamics of ssDNA and dsDNA near a surface

A coarse grained approach

J. Ambia-Garrido, Arnold Vainrub, Bernard Pettitt

Research output: Contribution to journalArticle

34 Citations (Scopus)

Abstract

New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6-8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all-atom simulations. Our average tilt results are also in agreement with all-atom simulations for the case of dense systems.

Original languageEnglish (US)
Pages (from-to)2001-2007
Number of pages7
JournalComputer Physics Communications
Volume181
Issue number12
DOIs
StatePublished - Dec 2010
Externally publishedYes

Fingerprint

Thermodynamics
thermodynamics
DNA
deoxyribonucleic acid
Atoms
worms
Molecules
simulation
beads
atoms
molecules
Demonstrations
sampling
Sampling
polymers
Polymers

Keywords

  • Continuum solvent model
  • DNA structure
  • Poisson-Boltzmann

ASJC Scopus subject areas

  • Hardware and Architecture
  • Physics and Astronomy(all)

Cite this

A model for structure and thermodynamics of ssDNA and dsDNA near a surface : A coarse grained approach. / Ambia-Garrido, J.; Vainrub, Arnold; Pettitt, Bernard.

In: Computer Physics Communications, Vol. 181, No. 12, 12.2010, p. 2001-2007.

Research output: Contribution to journalArticle

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