TY - JOUR
T1 - A model for structure and thermodynamics of ssDNA and dsDNA near a surface
T2 - A coarse grained approach
AU - Ambia-Garrido, J.
AU - Vainrub, Arnold
AU - Pettitt, B. Montgomery
N1 - Funding Information:
J.A.-G. was partially supported by a training fellowship from the Keck Center for Interdisciplinary Bioscience Training of the Gulf Coast Consortia . The Robert A. Welch Foundation ( E-1028 ), and the National Institutes of Health ( GM-066813 ) are thanked for partial support of this work. This research was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory, located at the Pacific Northwest National Laboratory and in part by the National Science Foundation through TeraGrid resources provided by Pittsburgh Supercomputing Center.
PY - 2010/12
Y1 - 2010/12
N2 - 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.
AB - 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.
KW - Continuum solvent model
KW - DNA structure
KW - Poisson-Boltzmann
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U2 - 10.1016/j.cpc.2010.08.029
DO - 10.1016/j.cpc.2010.08.029
M3 - Article
AN - SCOPUS:77957903935
SN - 0010-4655
VL - 181
SP - 2001
EP - 2007
JO - Computer Physics Communications
JF - Computer Physics Communications
IS - 12
ER -