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Modeling DNA structure, elasticity, and deformations at the base-pair level

MPS-Authors
http://pubman.mpdl.mpg.de/cone/persons/resource/persons48419

Mergell,  B.
MPI for Polymer Research, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons47837

Ejtehadi,  M. R.
MPI for Polymer Research, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons47850

Everaers,  R.
MPI for Polymer Research, Max Planck Society;

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Citation

Mergell, B., Ejtehadi, M. R., & Everaers, R. (2003). Modeling DNA structure, elasticity, and deformations at the base-pair level. Physical Review E, 68(2): 021911.


Cite as: http://hdl.handle.net/11858/00-001M-0000-000F-6333-B
Abstract
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between the neighboring base pairs. The sugar-phosphate backbones are taken into account by semirigid harmonic springs with a nonzero spring length. The competition between these two interactions and the introduction of a simple geometrical constraint lead to a stacked right-handed B-DNA-like conformation. The mapping of the presented model to the Marko-Siggia and the stack-of-plates model enables us to optimize the free model parameters so as to reproduce the experimentally known observables such as persistence lengths, mean and mean-squared base-pair step parameters. For the optimized model parameters, we measured the critical force where the transition from B- to S-DNA occurs to be approximately 140 pN. We observe an overstretched S-DNA conformation with highly inclined bases which partially preserves the stacking of successive base pairs.