Kinetics of loop formation in worm-like chain polymers

2013 ◽  
Vol 138 (17) ◽  
pp. 174908 ◽  
Author(s):  
Reza Afra ◽  
Brian A. Todd
Keyword(s):  
Loop Formation ◽  
Kinetics Of

scholarly journals Kinetics of Internal-Loop Formation in Polypeptide Chains: A Simulation Study

2007 ◽  
Vol 92 (7) ◽  
pp. 2281-2289 ◽  
Author(s):  
Dana Doucet ◽  
Adrian Roitberg ◽  
Stephen J. Hagen
Keyword(s):  
Simulation Study ◽  
Loop Formation ◽  
Internal Loop ◽  
Polypeptide Chains ◽  
Kinetics Of

Kinetics of Loop Formation and Breakage in the Denatured State of Iso-1-cytochrome c

2005 ◽  
Vol 353 (3) ◽  
pp. 730-743 ◽  
Author(s):  
Eydiejo Kurchan ◽  
Heinrich Roder ◽  
Bruce E. Bowler
Keyword(s):  
Cytochrome C ◽  
Loop Formation ◽  
Denatured State ◽  
Kinetics Of

scholarly journals The accidental ally: Nucleosomal barriers can accelerate cohesin mediated loop formation in chromatin

2019 ◽  
Author(s):  
Ajoy Maji ◽  
Ranjith Padinhateeri ◽  
Mithun K. Mitra
Keyword(s):  
Effective Diffusion ◽  
Diffusion Constant ◽  
Loop Formation ◽  
Base Pairs ◽  
Diffusion Constants ◽  
Dna Backbone ◽  
The Mean ◽  
The Times ◽  
Lower Loop ◽  
Kinetics Of

AbstractAn important question in the context of the 3D organization of chromosomes is the mechanism of formation of large loops between distant base pairs. Recent experiments suggest that the formation of loops might be mediated by Loop Extrusion Factor proteins like cohesin. Experiments on cohesin have shown that cohesins walk diffusively on the DNA, and that nucleosomes act as obstacles to the diffusion, lowering the permeability and hence reducing the effective diffusion constant. An estimation of the times required to form the loops of typical sizes seen in Hi-C experiments using these low effective diffusion constants leads to times that are unphysically large. The puzzle then is the following, how does a cohesin molecule diffusing on the DNA backbone achieve speeds necessary to form the large loops seen in experiments? We propose a simple answer to this puzzle, and show that while at low densities, nucleosomes act as barriers to cohesin diffusion, beyond a certain concentration, they can reduce loop formation times due to a subtle interplay between the nucleosome size and the mean linker length. This effect is further enhanced on considering stochastic binding kinetics of nucleosomes on the DNA backbone, and leads to predictions of lower loop formation times than might be expected from a naive obstacle picture of nucleosomes.

scholarly journals Kinetics of Loop Formation in Polymer Chains†

2008 ◽  
Vol 112 (19) ◽  
pp. 6094-6106 ◽  
Author(s):  
Ngo Minh Toan ◽  
Greg Morrison ◽  
Changbong Hyeon ◽  
D. Thirumalai
Keyword(s):  
Polymer Chains ◽  
Loop Formation ◽  
Kinetics Of

scholarly journals Kinetics of interior loop formation in semiflexible chains

2006 ◽  
Vol 124 (10) ◽  
pp. 104905 ◽  
Author(s):  
Changbong Hyeon ◽  
D. Thirumalai
Keyword(s):  
Loop Formation ◽  
Interior Loop ◽  
Kinetics Of

scholarly journals Dynamic Processing of Displacement Loops During Recombinational DNA Repair

2018 ◽  
Author(s):  
Aurèle Piazza ◽  
Shanaya Shah ◽  
William Douglass Wright ◽  
Steven K. Gore ◽  
Romain Koszul ◽  
...  
Keyword(s):  
Strand Break ◽  
Loop Formation ◽  
Dna Double Strand Break ◽  
Loop Dynamics ◽  
D Loop ◽  
Srs2 Helicase ◽  
Dynamic Processing ◽  
Break Induced Replication ◽  
Kinetics Of

AbstractDisplacement-loops (D-loops) are pivotal intermediates of homologous recombination (HR), a universal DNA double strand break (DSB) repair pathway. We developed a versatile assay for the physical detection of D-loopsin vivo, which enabled studying the kinetics of their formation and defining the network of D-loop formation and reversal pathways. Nascent D-loops are detected within 2 hrs of DSB formation and extended over the next 2 hrs in a system allowing break-induced replication. The majority of D-loops are disrupted in wild type cells by two pathways: one supported by the Srs2 helicase and the other by the Mph1 helicase and the Sgs1-Top3-Rmi1 helicase-topoisomerase complex. Both pathways operate without significant overlap and are delineated by the Rad54 paralog Rdh54 in an ATPase-independent fashion. This study uncovers a novel layer of HR control in cells relying on nascent D-loop dynamics, revealing unsuspected complexities, and identifying a surprising role for a conserved Rad54 paralog.

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