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Knots modify the coil–stretch transition in linear DNA polymers

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Abstract

We perform single-molecule DNA experiments to investigate the relaxation dynamics of knotted polymers and examine the steady-state behavior of knotted polymers in elongational fields. The occurrence of a knot reduces the relaxation time of a molecule and leads to a shift in the molecule's coil–stretch transition to larger strain rates. We measure chain extension and extension fluctuations as a function of strain rate for unknotted and knotted molecules. The curves for knotted molecules can be collapsed onto the unknotted curves by defining an effective Weissenberg number based on the measured knotted relaxation time in the low extension regime, or a relaxation time based on Rouse/Zimm scaling theories in the high extension regime. Because a knot reduces a molecule's relaxation time, we observe that knot untying near the coil–stretch transition can result in dramatic changes in the molecule's conformation. For example, a knotted molecule at a given strain rate can experience a stretch–coil transition, followed by a coil–stretch transition, after the knot partially or fully unties.

Graphical abstract: Knots modify the coil–stretch transition in linear DNA polymers

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Publication details

The article was received on 07 Nov 2017, accepted on 04 Feb 2018 and first published on 09 Feb 2018


Article type: Paper
DOI: 10.1039/C7SM02195J
Citation: Soft Matter, 2018, Advance Article
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    Knots modify the coil–stretch transition in linear DNA polymers

    B. W. Soh, V. Narsimhan, A. R. Klotz and P. S. Doyle, Soft Matter, 2018, Advance Article , DOI: 10.1039/C7SM02195J

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