Depletion effects and loop formation in self-avoiding polymers.
Langevin dynamics is employed to study the looping kinetics of self-avoiding polymers both in ideal and crowded solutions. A rich kinetics results from the competition of two crowding-induced effects: the depletion attraction and the enhanced viscous friction. For short chains, the enhanced friction slows down looping, while for longer chains, the depletion attraction renders it more frequent and persistent. We discuss the possible relevance of the findings for chromatin looping in living cells.
Toan
N M
NM
International School for Advanced Studies (SISSA) and CNR-INFM, Via Beirut 2-4, 34014 Trieste, Italy.
Marenduzzo
D
D
Cook
P R
PR
Micheletti
C
C
D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D011108:Polymers / Q000737:chemistry*; D013237:Stereoisomerism; D013816:Thermodynamics
D002843:Chromatin; D011108:Polymers; D004247:DNA; D012321:DNA-Directed RNA Polymerases; D004259:DNA-Directed DNA Polymerase