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Model for DNA hairpin denaturation

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Abstract.

We investigate the thermal denaturation of DNA hairpins using molecular dynamics simulations of a simple model describing the molecule at a scale of a nucleotide. The model allows us to analyze the different interacting features that determine how an hairpin opens, such as the role of the loop and the properties intrinsic to the stem.

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Authors and Affiliations

  1. Dept. Física de la Materia Condensada, Universidad de Zaragoza, c/Pedro Cerbuna s/n, 50009, Zaragoza, Spain

    S. Cuesta-López

  2. Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain

    S. Cuesta-López

  3. Laboratoire de Physique, École Normale Supérieure de Lyon, 46 allée d’Italie, 69364, Lyon Cedex 07, France

    S. Cuesta-López, M. Peyrard & D. J. Graham

  4. Department of Physics, Cornell University, 14853, Ithaca, NY, USA

    D. J. Graham

Authors
  1. S. Cuesta-López
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  2. M. Peyrard
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  3. D. J. Graham
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Correspondence to M. Peyrard.

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Cuesta-López, S., Peyrard, M. & Graham, D.J. Model for DNA hairpin denaturation. Eur. Phys. J. E 16, 235–246 (2005). https://doi.org/10.1140/epje/e2005-00026-9

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  • DOI: https://doi.org/10.1140/epje/e2005-00026-9

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