Protein-mediated DNA loops: effects of protein bridge size and kinks.
This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size of a protein bridge and/or the presence of a kink at half DNA length. The DNA is modeled by the wormlike chain model, and the probability of loop formation is calculated in two ways: exact numerical evaluation of the constrained path integral and the extension of the Shimada and Yamakawa saddle point approximation. For example, we find that the looping free energy of a 100-base-pairs DNA decreases from 24 kBT to 13 kBT when the loop is closed by a protein of r=10 length. It further decreases 5 kBT to when the loop has a kink of 120 degrees at half-length.
Douarche
Nicolas
N
CNRS-Laboratoire de Physique Statistique de l'ENS, 24 rue Lhomond, 75005 Paris, France.
Cocco
Simona
S
D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000648:ultrastructure; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation
D004268:DNA-Binding Proteins; D004247:DNA