DNA hybridization kinetics: zippering, internal displacement and sequence dependence

@article{Ouldridge2013DNAHK,
  title={DNA hybridization kinetics: zippering, internal displacement and sequence dependence},
  author={Thomas E. Ouldridge and Petr {\vS}ulc and Flavio Romano and Jonathan P. K. Doye and Ard A. Louis},
  journal={Nucleic Acids Research},
  year={2013},
  volume={41},
  pages={8886 - 8895}
}
Although the thermodynamics of DNA hybridization is generally well established, the kinetics of this classic transition is less well understood. Providing such understanding has new urgency because DNA nanotechnology often depends critically on binding rates. Here, we explore DNA oligomer hybridization kinetics using a coarse-grained model. Strand association proceeds through a complex set of intermediate states, with successful binding events initiated by a few metastable base-pairing… 

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