Resonant optimization in the mechanical unzipping of DNA

¹ Departamento de Física, Universidad de Oriente - 90500 Santiago de Cuba, Cuba
² Departamento de Física de la Materia Condensada, Universidad de Zaragoza - 50009 Zaragoza, Spain
³ Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza 50018 Zaragoza, Spain
⁴ School of Mathematical Sciences, Queen Mary University of London - Mile End Road, London E1 4NS, UK

^(a) A.Fiasconaro@qmul.ac.uk

Received: 16 January 2014
Accepted: 12 March 2014

Abstract

The mechanical separation of the double-stranded DNA in single-molecule experiments is of fundamental importance in the understanding of the replication or transcription processes. Time-dependent forces can influence in different ways the dynamics of this separation. We study here this unzipping of DNA in the framework of the mesoscopic Peyrard-Bishop-Dauxois model under the influence of a periodic driving. Two different protocols, both of them feasible experimentally, have been studied under two modes of pulling: controlled force and controlled position. A strong resonant activation phenomenon has been observed in the magnitudes that characterize the mechanical unzipping such as the mean opening time, the mean opening force, and the mean critical opening force, all of them as a function of the frequency of the driving. This optimal frequency region has been observed for all the cases studied both in a uniform DNA of adenine-thymine nucleotides and in a real DNA sequence. Importantly, a well precise resonant frequency can be determined with the use of one of this protocols.