Europhys. Lett.
Volume 70, Number 1, April 2005
Page(s) 15 - 21
Section General
Published online 09 March 2005
Europhys. Lett., 70 (1), pp. 15-21 (2005)
DOI: 10.1209/epl/i2004-10457-1

Statistical mechanics of coil-hairpin transition in a single-stranded DNA oligomer

S. Kumar1, D. Giri2 and Y. Singh1

1  Department of Physics, Banaras Hindu University - Varanasi 221 005, India
2  Physics Section, MMV, Banaras Hindu University - Varanasi 221 005, India

received 17 September 2004; accepted in final form 31 January 2005
published online 9 March 2005

A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single-stranded DNA molecule that forms hairpin structure and calculate the properties associated with coil-hairpin transition by enumerating all possible conformations of a chain of N monomers in two and three dimensions. The first and last five monomers of the chain have been allowed to pair and form the stem of the hairpin structure while the remaining monomers can form a loop. The coil-hairpin transition is found to be first order with large entropy change. While the rate of unzipping of the hairpin stem is found to be independent of the length of the loop and the dimensionality of the space, the rate of closing varies greatly with loop length and dimensionality of the space.

05.10.-a - Computational methods in statistical physics and nonlinear dynamics.
87.10.+e - Biological and medical physics: General theory and mathematical aspects.
87.14.Gg - DNA, RNA.

© EDP Sciences 2005