Electro-entropic excluded volume effects on DNA looping and relaxation in nanochannels

Yeng-Long Chen

doi:10.1063/1.4826157

Abstract

We investigate the fluctuation-relaxation dynamics of entropically restricted DNA molecules in square nanochannels ranging from 0.09 to 19.9 times the persistence length. In nanochannels smaller than the persistence length, the chain relaxation time is found to have cubic dependence on the channel size. It is found that the effective polymer width significantly alter the chain conformation and relaxation time in strong confinement. For thinner chains, looped chain configurations are found in channels with height comparable to the persistence length, with very slow relaxation compared to un-looped chains. Larger effective chain widths inhibit the formation of hairpin loops.

Highlights

Stiff biological macromolecules such as actin filaments and DNA are restricted in partitions comparable to or much smaller than their longest characteristic length, inside a natural environment such as the cell and a cell nucleus
We investigate the fluctuation-relaxation dynamics of entropically restricted DNA molecules in square nanochannels ranging from 0.09 to 19.9 times the persistence length
It is found that the effective polymer width significantly alter the chain conformation and relaxation time in strong confinement

Summary

Introduction

Stiff biological macromolecules such as actin filaments and DNA are restricted in partitions comparable to or much smaller than their longest characteristic length, inside a natural environment such as the cell and a cell nucleus. The strong confinement constraint rearranges the structure of the molecules and affects the dynamics of processes such as nucleosome folding/unfolding, DNA transcription, and actin polymerization. Advances in nano-fabrication have greatly facilitated studies that directly probe changes to a single polymer structure and dynamics in confinement in well-defined nanoslits and nanochannels. These studies typically adopt double stranded viral phage DNA molecules as model polymers due to its mono-dispersity, long persistence length (P % 50 nm at high ionic strength), and the ease of direct observation. We investigated how changes in the effective polymer width and the bulk persistence length, which may be controlled by varying solvent ionic strength, affect the confined polymer properties. The chain relaxation mechanisms are found to depend on both the strong confinement and the effective polymer width

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Results

Conclusion