280576 A Next-Generation Coarse Grain DNA Model for Engineering and Biology

Monday, October 29, 2012: 4:35 PM
411 (Convention Center )
Daniel M. Hinckley, Gordon S. Freeman and Juan J. de Pablo, Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI

We present a new version of the 3-Site-Per-Nucleotide (3SPN) coarse grain model for simulation of DNA.  By incorporating anisotropic potentials between bead sites, we are able to remove Go-type interactions, thus freeing DNA to explore non-canonical configurations such as hairpins and holliday junctions.  We demonstrate that the resulting model displays the correct trends of sequence-dependent mechanical properties.  These include the effect of sequence on the persistence length of double-stranded DNA.  We use metadynamics to show unambiguously that the model reproduces experimental thermodynamic trends, including the dependence of melting temperature on oligomer and salt concentration.  Furthermore, we use Forward Flux Sampling (FFS) to calculate DNA hybridization rate constants and find that these calculated rate constants are in close agreement with values from experiment.  The ability to capture the structural, thermodynamic, and kinetic behavior of DNA makes this new model appropriate to any coarse grain simulation where structural resolution of DNA is desired, including both biological and nanoengineering applications.

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See more of this Session: Model Development for Biomolecular Systems
See more of this Group/Topical: Engineering Sciences and Fundamentals