Lac Repressor Mediated DNA Looping: Monte Carlo Simulation of Constrained DNA Molecules Complemented with Current Experimental Results

• Published in: PloS one Vol. 9; no. 5; p. e92475
• Main Authors: Biton, Yoav Y., Kumar, Sandip, Dunlap, David, Swigon, David
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 06.05.2014; Public Library of Science (PLoS)
• Subjects: Analysis; Base pairs; Binding; Biology and life sciences; Computer and Information Sciences; Computer simulation; Deoxyribonucleic acid; Dissociation; DNA; DNA structure; DNA, Bacterial - chemistry; DNA, Bacterial - metabolism; E coli; Elasticity; Experiments; Gene expression; Genetic research; Geometric constraints; Lac Repressors - metabolism; Lactose repressor; Mathematical models; Mathematics; Medical research; Microscopy; Models, Biological; Molecular biology; Monte Carlo Method; Monte Carlo methods; Monte Carlo simulation; Nucleic Acid Conformation; Operators; Particle motion; Physical Sciences; Protein Binding; Proteins; Statistical mechanics; Atlanta Georgia; Pittsburgh Pennsylvania; Georgia; United States > US; Pennsylvania

Tethered particle motion (TPM) experiments can be used to detect time-resolved loop formation in a single DNA molecule by measuring changes in the length of a DNA tether. Interpretation of such experiments is greatly aided by computer simulations of DNA looping which allow one to analyze the structu...