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research article

A sequence-dependent rigid-base model of DNA

Gonzalez, O.
•
Petkeviciute, D.  
•
Maddocks, J. H.  
2013
Journal Of Chemical Physics

A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can successfully predict the nonlocal changes in the minimum energy configuration of an oligomer that are consequent upon a local change of sequence at the level of a single point mutation. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4789411]

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Type
research article
DOI
10.1063/1.4789411
Web of Science ID

WOS:000314746400061

Author(s)
Gonzalez, O.
Petkeviciute, D.  
Maddocks, J. H.  
Date Issued

2013

Publisher

Amer Inst Physics

Published in
Journal Of Chemical Physics
Volume

138

Issue

5

Article Number

055102

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCVMM  
Available on Infoscience
March 28, 2013
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/90762
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