title: Dynamics of backtracking long pauses of RNA polymerase.
abstract: The dynamics of backtracking long pauses by RNA polymerase is quantitatively studied based on our proposed model. Analytical formulas are obtained for the dependence of mean backtracking time and mean lifetime of backtracking long pauses on the binding affinity V(0) of RNAP to the DNA and RNA lattices, an important parameter for the transcription elongation complex. By comparison of the theoretically with experimentally obtained mean backtracking times, the value of binding affinity V(0) is predicted. Using the predicted V(0), the effects of external load on the mean backtracking time, on the lifetime of the backtracking long pauses and on the exit from the backtracking long pauses are studied. The results are in agreement with the available experimental data and, moreover, some predicted results are presented. In addition, using this V(0) we study the processivity of RNA polymerase under no and sideways forces.
authors.affiliation: Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. pxie@aphy.iphy.ac.cn
authors.forename: Ping
authors.initials: P
authors.lastname: Xie
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D001665:Binding Sites; D004247:DNA / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism*; D008957:Models, Genetic; D011485:Protein Binding; D011487:Protein Conformation; D012313:RNA / Q000096:biosynthesis* / Q000378:metabolism; D055672:Static Electricity; D013269:Stochastic Processes; D013698:Templates, Genetic; D013816:Thermodynamics; D013997:Time Factors; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors
chemical_list: D035602:Transcriptional Elongation Factors; D012313:RNA; D004247:DNA; D012321:DNA-Directed RNA Polymerases