Diffusion of Knots along DNA Confined in Nanochannels

Zixue Ma; Kevin D. Dorfman

doi:10.1021/acs.macromol.0c00561

Diffusion of Knots along DNA Confined in Nanochannels

Zixue Ma, Kevin D. Dorfman

Chemical Engineering and Materials Science

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17 Scopus citations

Abstract

We study the diffusion of knots along relaxed deoxyribonucleic acid (DNA) in nanochannels using a nanofluidic "knot factory"device for knot generation. The apparent scaling exponent for the growth in the ensemble-averaged mean-squared displacement is 0.82 ± 0.01 when accounting for random errors and [0.79, 0.88] when accounting for systematic errors. Both estimates indicate subdiffusion and support a model of self-reptation. These results contradict the prevailing theory for knot diffusion along nanochannel-confined DNA, where knot region breathing is presumed to control knot diffusion in long polymers, but are consistent with previous observations of self-reptation of knots for unconfined DNA under tension.

Original language	English (US)
Pages (from-to)	6461-6468
Number of pages	8
Journal	Macromolecules
Volume	53
Issue number	15
DOIs	https://doi.org/10.1021/acs.macromol.0c00561
State	Published - Aug 11 2020

Bibliographical note

Funding Information:
The authors thank Dr. Hui-Min Chuang for her assistance in device fabrication protocols. This work was supported by NIH (R01-HG006851) and NSF (CBET-2016879). Device fabrication was conducted in the Minnesota Nano Center, which is supported by the National Science Foundation through the National Nano Coordinated Infrastructure Network (NNCI) under Award Number ECCS-1542202.

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Copyright © 2020 American Chemical Society.

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title = "Diffusion of Knots along DNA Confined in Nanochannels",

abstract = "We study the diffusion of knots along relaxed deoxyribonucleic acid (DNA) in nanochannels using a nanofluidic {"}knot factory{"}device for knot generation. The apparent scaling exponent for the growth in the ensemble-averaged mean-squared displacement is 0.82 ± 0.01 when accounting for random errors and [0.79, 0.88] when accounting for systematic errors. Both estimates indicate subdiffusion and support a model of self-reptation. These results contradict the prevailing theory for knot diffusion along nanochannel-confined DNA, where knot region breathing is presumed to control knot diffusion in long polymers, but are consistent with previous observations of self-reptation of knots for unconfined DNA under tension. ",

author = "Zixue Ma and Dorfman, {Kevin D.}",

note = "Funding Information: The authors thank Dr. Hui-Min Chuang for her assistance in device fabrication protocols. This work was supported by NIH (R01-HG006851) and NSF (CBET-2016879). Device fabrication was conducted in the Minnesota Nano Center, which is supported by the National Science Foundation through the National Nano Coordinated Infrastructure Network (NNCI) under Award Number ECCS-1542202. Publisher Copyright: Copyright {\textcopyright} 2020 American Chemical Society.",

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doi = "10.1021/acs.macromol.0c00561",

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AU - Ma, Zixue

AU - Dorfman, Kevin D.

N1 - Funding Information: The authors thank Dr. Hui-Min Chuang for her assistance in device fabrication protocols. This work was supported by NIH (R01-HG006851) and NSF (CBET-2016879). Device fabrication was conducted in the Minnesota Nano Center, which is supported by the National Science Foundation through the National Nano Coordinated Infrastructure Network (NNCI) under Award Number ECCS-1542202. Publisher Copyright: Copyright © 2020 American Chemical Society.

PY - 2020/8/11

Y1 - 2020/8/11

N2 - We study the diffusion of knots along relaxed deoxyribonucleic acid (DNA) in nanochannels using a nanofluidic "knot factory"device for knot generation. The apparent scaling exponent for the growth in the ensemble-averaged mean-squared displacement is 0.82 ± 0.01 when accounting for random errors and [0.79, 0.88] when accounting for systematic errors. Both estimates indicate subdiffusion and support a model of self-reptation. These results contradict the prevailing theory for knot diffusion along nanochannel-confined DNA, where knot region breathing is presumed to control knot diffusion in long polymers, but are consistent with previous observations of self-reptation of knots for unconfined DNA under tension.

AB - We study the diffusion of knots along relaxed deoxyribonucleic acid (DNA) in nanochannels using a nanofluidic "knot factory"device for knot generation. The apparent scaling exponent for the growth in the ensemble-averaged mean-squared displacement is 0.82 ± 0.01 when accounting for random errors and [0.79, 0.88] when accounting for systematic errors. Both estimates indicate subdiffusion and support a model of self-reptation. These results contradict the prevailing theory for knot diffusion along nanochannel-confined DNA, where knot region breathing is presumed to control knot diffusion in long polymers, but are consistent with previous observations of self-reptation of knots for unconfined DNA under tension.

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Diffusion of Knots along DNA Confined in Nanochannels

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Diffusion of Knots along DNA Confined in Nanochannels

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