The Backfolded Odijk Regime for Wormlike Chains Confined in Rectangular Nanochannels.

Abhiram Muralidhar,Michael Quevillon,Kevin Dorfman

doi:10.3390/polym8030079

Abhiram Muralidhar, Michael Quevillon + Show 1 more

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https://doi.org/10.3390/polym8030079

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Journal: Polymers	Publication Date: Mar 14, 2016
Citations: 62	License type: CC BY 4.0

Affiliation: University of Minnesota

Abstract

We confirm Odijk’s scaling laws for (i) the average chain extension; (ii) the variance about the average extension; and (iii) the confinement free energy of a wormlike chain confined in a rectangular nanochannel smaller than its chain persistence length through pruned-enriched Rosenbluth method (PERM) simulations of asymptotically long, discrete wormlike chains. In the course of this analysis, we also computed the global persistence length of ideal wormlike chains for the modestly rectangular channels that are used in many experimental systems. The results are relevant to genomic mapping systems that confine DNA in channel sizes around 50 nm, since fabrication constraints generally lead to rectangular cross-sections.

Highlights

The confinement of a wormlike chain in a channel smaller than its persistence length is commonly referred to as the Odijk regime [1,2]
By performing simulations of asymptotically long chains, we demonstrated that Odijk’s Flory theory correctly captures the mean extension, the variance of extension and free energy for chains confined in rectangular channels for channel sizes where both dimensions are smaller than the persistence length
The prefactors we obtained for the scaling laws associated with the mean extension, its variance and the confinement free energy can used to predict these quantities for the backfolded Odijk regime in rectangular channels

Summary

Introduction

The confinement of a wormlike chain in a channel smaller than its persistence length is commonly referred to as the Odijk regime [1,2]. For long chains, excluded volume interactions between backfolded segments of the chain become important as well [4]. Based on these two ideas, Odijk proposed that long wormlike chains, such as DNA, confined to channels smaller than the persistence length can exist in two different regimes: (i) a “classic” Odijk regime, where the excluded volume effect is strong and the chain is strongly extended; and (ii) a “backfolded” Odijk regime, where the excluded volume is weak and the chain is able to backfold [4]. Our work completes the validation of the backfolded Odijk regime

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