Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.

  title={Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.},
  author={Debayan Chakraborty and Naoto Hori and Dave Thirumalai},
  journal={Journal of chemical theory and computation},
  volume={14 7},
We develop a robust coarse-grained model for single- and double-stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann… 

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