Entropy-driven denaturation and bubble nucleation in DNA melting

¹ Department of Physics, JIS College of Engineering (Autonomous), West Bengal University of Technology Nadia-741235, India
² Physics and Applied Mathematics Unit, Indian Statistical Institute - 203 B.T. Road, Kolkata-700108, India

^(a) hsr_cal@yahoo.in
ssroy.science@gmail.com (corresponding author)
^(b) b_pratul@yahoo.co.in

Received: 9 November 2014
Accepted: 2 February 2015

Abstract

The conformational properties of a DNA molecule when mapped onto a Heisenberg spin system denaturation transition can be formulated in terms of quantum phase transition induced by a quench where the temperature effect is incorporated in the quench time. Here torsion takes on the role of the external field. The denaturation transition occurs when the entanglement entropy of the spin system vanishes. As the critical region corresponds to a two-limit behaviour the entanglement entropy gradually decreases with the gradual increase in the fraction of open base pairs and when the entropy vanishes the two strands are separated. The sequence heterogeneity interplays with the entropy effects and we have the onset of denaturation bubbles. We have studied the melting profiles for different sequence-specific DNA molecules and the results are found to be in excellent agreement with experiment.