Waves of DNA: Propagating Excitations in Extended Nanoconfined Polymers

TL;DR

This study demonstrates how nanoconfinement induces propagating waves of excess fluorescence along a single DNA molecule, revealing collective dynamic phenomena driven by confinement in nanofluidic systems.

Contribution

It introduces a novel experimental setup and modeling approach to observe and analyze propagating excitations in nanoconfined polymers, highlighting confinement-induced collective behavior.

Findings

Waves of fluorescence propagate along the DNA in nanocavities.

Correlation dynamics reveal transfer of contour between cavities.

Modeling confirms Langevin dynamics and minimal lattice models capture the phenomena.

Abstract

We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded nanocavities; the cavity lattice is designed so that a single chain occupies multiple cavities. Fluorescent video-microscopy data shows that waves of excess fluorescence propagate across the cavity-straddling molecule, corresponding to propagating fluctuations of contour overdensity in the cavities. The waves are quantified by examining the correlation in intensity fluctuations between neighbouring cavities. Correlations grow from an anti-correlated minimum to a correlated maximum before decaying, corresponding to a transfer of contour between neighbouring cavities at a fixed transfer time-scale. The observed dynamics can be modelled using Langevin dynamics simulations and a minimal lattice model of coupled diffusion. This study shows how confinement-based sculpting of the polymer equilibrium configuration, by renormalizing the physical system into a series of discrete cavity states, can lead to new types of dynamic collective phenomena.