The search result changed since you submitted your search request. Documents might be displayed in a different sort order.
  • search hit 3 of 34
Back to Result List

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

Export metadata

Additional Services

Search Google Scholar Statistics
Metadaten
Author details:Jaeoh Shin, Andrey G. CherstvyORCiD, Ralf MetzlerORCiDGND
DOI:https://doi.org/10.1039/c4sm02007c
ISSN:1744-683X
ISSN:1744-6848
Pubmed ID:https://pubmed.ncbi.nlm.nih.gov/25413029
Title of parent work (English):Soft matter
Publisher:Royal Society of Chemistry
Place of publishing:Cambridge
Publication type:Article
Language:English
Year of first publication:2015
Publication year:2015
Release date:2017/03/27
Volume:11
Issue:3
Number of pages:17
First page:472
Last Page:488
Funding institution:Academy of Finland (FiDiPro scheme); Deutsche Forschungsgemeinschaft (DFG) [CH 707/5-1]; Federal Ministry of Education and Research (BMBF Project)
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Physik und Astronomie
Peer review:Referiert
Accept ✔
This website uses technically necessary session cookies. By continuing to use the website, you agree to this. You can find our privacy policy here.