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Understanding chain looping kinetics in polymer solutions: crowding effects of microviscosity and collapse

Abstract

A theoretical framework based on generalized Langevin equation with fractional Gaussian noise is presented to describe the looping kinetics of chain in polymer solution. Particular attention is paid to quantitatively reveal the crowding effects on the loop formation rate in terms of microviscosity and collapse. By the aid of empirical relations for these two crowding associated physical quantities, we explicitly investigate the relationship between looping rate and polymer concentration, the degree of polymerization, and system parameters. According to our analysis, the dependence of the looping rate on crowder volume fraction exhibits three typical regimes: monotonic decreasing, non-monotonic trend and monotonic increasing. We reveal that these non-trivial behaviors can be attributed to the competition between the two opposing factors of the viscosity-associated inhibition and collapse-induced facilitation to the loop formation. We apply our theory to analyze the kinetics of single-stranded DNA hairpin base pairing in polyethylene glycol solutions. The theoretical results can reproduce the experimental data on the closing rate of hairpins quantitatively to a certain degree with reasonable fitting parameters. The unexpected increase of closing rate upon the addition of increasing amounts of polymer is well rationalised. Such good agreements clearly demonstrate the validity of our theory, appropriately addressing the very role of crowding effects to the relevant kinetics.

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Publication details

The article was received on 22 Jul 2018, accepted on 06 Sep 2018 and first published on 10 Sep 2018


Article type: Paper
DOI: 10.1039/C8SM01499J
Citation: Soft Matter, 2018, Accepted Manuscript
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    Understanding chain looping kinetics in polymer solutions: crowding effects of microviscosity and collapse

    Y. Bian, X. Cao, P. Li and N. Zhao, Soft Matter, 2018, Accepted Manuscript , DOI: 10.1039/C8SM01499J

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