DNA hairpins primarily promote duplex melting rather than inhibiting hybridization

@article{Schreck2014DNAHP,
  title={DNA hairpins primarily promote duplex melting rather than inhibiting hybridization},
  author={John S. Schreck and Thomas E. Ouldridge and Flavio Romano and Petr {\vS}ulc and Liam P. Shaw and Ard A. Louis and Jonathan P. K. Doye},
  journal={arXiv: Soft Condensed Matter},
  year={2014}
}
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good agreement with experiment. By contrast, melting rates are accelerated by factors of ~100 and ~2000. This surprisingly large speed-up occurs because hairpins form during the melting process, stabilizing partially melted states, and facilitating dissociation… 
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