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Ambia-Garrido J, Vainrub A, Pettitt BM. A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach. Comput Phys Commun. 2010;181(12):2001-2007doi: 10.1016/j.cpc.2010.08.029.
Ambia-Garrido, J., Vainrub, A., & Pettitt, B. M. (2010). A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach. Computer physics communications, 181(12), 2001-2007. https://doi.org/10.1016/j.cpc.2010.08.029
Ambia-Garrido, J, et al. "A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach." Computer physics communications vol. 181,12 (2010): 2001-2007. doi: https://doi.org/10.1016/j.cpc.2010.08.029
Ambia-Garrido J, Vainrub A, Pettitt BM. A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach. Comput Phys Commun. 2010 Dec 01;181(12):2001-2007. doi: 10.1016/j.cpc.2010.08.029. PMID: 20957064; PMCID: PMC2955266.
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Comput Phys Commun. 2010 Dec 01;181(12):2001-2007. doi: 10.1016/j.cpc.2010.08.029.

A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach.

Computer physics communications

J Ambia-Garrido, Arnold Vainrub, B Montgomery Pettitt

Affiliations

  1. Department of Physics and Department of Chemistry, University of Houston, Houston, Texas.

PMID: 20957064 PMCID: PMC2955266 DOI: 10.1016/j.cpc.2010.08.029

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.

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