Untying Knotted DNA with Elongational Flows
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Doyle_Untying knotted.pdf
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Author(s)
Renner, Christopher Benjamin
Doyle, Patrick S
Date Issued
September 2014
Journal
ACS Macro Letters
Publisher
American Chemical Society (ACS)
Citation
Renner, C. Benjamin, and Patrick S. Doyle. “Untying Knotted DNA with Elongational Flows.” ACS Macro Letters 3.10 (2014): 963–967.
Version
Author's final manuscript
Abstract
We present Brownian dynamics simulations of initially knotted double-stranded DNA molecules untying in elongational flows. We show that the motions of the knots are governed by a diffusion–convection equation by deriving scalings that collapse the simulation data. When being convected, all knots displace nonaffinely, and their rates of translation along the chain are topologically dictated. We discover that torus knots “corkscrew” when driven by flow, whereas nontorus knots do not. We show that a simple mechanism can explain a coupling between this rotation and the translation of a knot, explaining observed differences in knot translation rates. These types of knots are encountered in nanoscale manipulation of DNA, occur in biology at multiple length scales (DNA to umbilical cords), and are ubiquitous in daily life (e.g., hair). These results may have a broad impact on manipulations of such knots via flows, with applications to genomic sequencing and polymer processing.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
Terms of Use
Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1021/mz500464p
