https://doi.org/10.1140/epje/e2005-00026-9
Model for DNA hairpin denaturation
1
Dept. Física de la Materia Condensada, Universidad de Zaragoza, c/Pedro Cerbuna s/n, 50009, Zaragoza, Spain
2
Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain
3
Laboratoire de Physique, École Normale Supérieure de Lyon, 46 allée d’Italie, 69364, Lyon Cedex 07, France
4
Department of Physics, Cornell University, 14853, Ithaca, NY, USA
* e-mail: michel.peyrard@ens-lyon.fr
Received:
26
July
2004
Accepted:
7
December
2004
Published online:
22
February
2005
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.
PACS: 87.15.Aa Nonlinear dynamics and nonlinear dynamical systems – / 87.15.He Dynamics aaand conformational changes – / 05.45.-a Nonlinear dynamics and nonlinear dynamical systems –
© EDP Sciences, Società Italiana di Fisica and Springer-Verlag, 2005
