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Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size

  • The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping–unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how theThe looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping–unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions.show moreshow less

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Metadaten
Author:Jaeoh Shin, Andrey Cherstvy, Ralf MetzlerORCiDGND
ISSN:1744-683X
Parent Title (English):Soft Matter
Publisher:The Royal Society of Chemistry
Place of publication:Cambridge
Editor:Ralf Metzler
Document Type:Article
Language:English
Date of first Publication:2014/10/20
Year of Completion:2014
Release Date:2015/05/19
Tag:anomalous diffusion; dna coiling; dynamics; folding kinetics; gene-regulation kinetics; in-vitro; living cells; mixtures; physiological consequences; spatial-organization
Pagenumber:17
First Page:472
Last Page:488
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Chemie
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 54 Chemie / 540 Chemie und zugeordnete Wissenschaften
Peer Review:Referiert
Publication Way:Open Access
Grantor:RSC
Licence (English):License LogoCreative Commons - Attribution 3.0 unported
Notes extern:Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Humanwissenschaftliche Reihe ; 185