DNA confined in a two-dimensional strip geometry

Department of Physics, University of Central Florida - Orlando, FL 32816-2385, USA

Received: 18 January 2014
Accepted: 24 March 2014

Abstract

Semiflexible polymers characterized by the contour length L and persistent length confined in a spatial region D have been described as a series of “spherical blobs” and “deflecting lines” by de Gennes and Odjik for and , respectively. Recently new intermediate regimes (extended de Gennes and Gauss-de Gennes) have been investigated by Tree et al. (Phys. Rev. Lett., 110 (2013) 208103). In this letter we derive scaling relations to characterize these transitions in terms of universal scaled fluctuations in d-dimension as a function of , and D, and show that the Gauss-de Gennes regime is absent and the extended de Gennes regime is vanishingly small for polymers confined in a 2D strip. We validate our claim by an extensive Brownian dynamics (BD) simulation which also reveals that the prefactor A used to describe the chain extension in the Odjik limit is independent of the physical dimension d and is the same as previously found by Yang et al. (Phys. Rev. E, 76 (2007) 011804). Our studies are relevant for optical maps of DNA stretched inside a nanostrip.