Waves of DNA: Propagating excitations in extended nanoconfined polymers
Name
PhysRevE.94.042603.pdf
Size
1.73 MB
Format
Adobe PDF
Checksum (MD5)
85daa2b75d76ef8f7ac8984b601521c5
Author(s)
de Haan, Hendrick W.
Reisner, Walter W.
Klotz, Alexander
Date Issued
October 2016
Journal
Physical Review E
Publisher
American Physical Society
Citation
Klotz, Alexander R., Hendrick W. de Haan, and Walter W. Reisner. “Waves of DNA: Propagating Excitations in Extended Nanoconfined Polymers.” Physical Review E 94.4 (2016): n. pag. © 2016 American Physical Society
Version
Final published version
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 fluctuations in intensity between cavities, including waves of excess fluorescence that propagate across the cavity-straddling molecule, corresponding to propagating fluctuations of contour overdensity in the cavities. The transfer of DNA between neighboring pits is quantified by examining the correlation in intensity fluctuations between neighboring cavities. Correlations grow from an anticorrelated minimum to a correlated maximum before decaying, corresponding to a transfer of contour between neighboring cavities at a fixed transfer time scale. The observed dynamics can be modeled 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.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
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DOI of Published Version
https://doi.org/10.1103/PhysRevE.94.042603
