3.6.5.13 Kinetics of hairpin loop formation by oligomers

2005 ◽  
pp. 220-220
Author(s):  
D. H. Turner ◽  
N. Sugimoto ◽  
S. M. Freier
Keyword(s):  
Loop Formation ◽  
Hairpin Loop ◽  
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 Insights into DNA Platination within Unusual Structural Settings

2011 ◽  
Vol 2011 ◽  
pp. 1-17
Author(s):  
Stephanie Harvie ◽  
Owen Wilson ◽  
John A. Parkinson
Keyword(s):  
Nucleic Acid ◽  
Nmr Spectroscopy ◽  
Nucleic Acids ◽  
Product Formation ◽  
Loop Formation ◽  
Hairpin Loop ◽  
Cross Link ◽  
Site Specific ◽  
Phosphodiester Backbone ◽  
Dna Platination

2D HSQC NMR spectroscopy has been used to monitor reaction and product formation between and nucleic acids possessing irregular topologies and containing site-specific phosphorothioate substitution in the phosphodiester backbone. Comparison of the reaction profiles of dimer nucleic acids with and without phosphorothioate substitution is made with their short nucleic acid counterparts containing the key dimer components. Whereas d(GpA) is relatively unreactive towards , NMR evidence suggests that the tandem sheared mismatch duplex d(GCG3pAGC)2 reacts to form the head-to-tail interstrand G3-N7-Pt-G3-N7 cross-link. The equivalent phosphorothioate R,S-d(GsA) reacts to form a monoiodo, monosulphur adduct, whereas the tandem sheared mismatch phosphorothioate duplex d(GCGsAG5C)2 (VIs) reacts to form the unusual intrastrand macrochelate , in which platinum is attached at both sulphur and G5-N7. Experimental evidence supports the formation of a stabilized mismatch duplex in which platinum is attached to two nitrogen centres in the sequence d(CGCGpTGCG) in contrast to R,S-d(CGCGsT5GCG) for which NMR evidence supports macrochelate-stabilized hairpin loop formation cross-linked at both phosphorothioate sulphur and T5-N3.

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 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
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