title: A kinetic model of transcription initiation by RNA polymerase.
abstract: We establish a sequence-dependent kinetic model for the later stage of transcription initiation by RNA polymerase. We suggest that there are three reaction pathways, the abortive pathway, the scrunching pathway and the escape pathway, competitive with each other at each site during the transcription initiation. Using this three-pathway model, we mainly calculate the maximum sizes of the abortive transcripts, the abortive probabilities and the abortive/productive ratios for different promoters by Monte Carlo simulation and analytical methods. These results are quantitatively comparable with the experimental observations. In particular, our model can account for the unproductive initial transcribing complex and the nucleoside triphosphate concentration dependence of the transcription initiation, which have been found in the experiments and were hardly understood by the previous two-pathway kinetic competition model.
authors.affiliation: Center for Advanced Study, Tsinghua University, Beijing 100084, China. xuexc05@mails.tsinghua.edu.cn
authors.forename: Xiao-chuan
authors.initials: XC
authors.lastname: Xue
authors.forename: Fei
authors.initials: F
authors.lastname: Liu
authors.forename: Zhong-can
authors.initials: ZC
authors.lastname: Ou-Yang
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D007700:Kinetics; D008957:Models, Genetic; D009010:Monte Carlo Method; D012313:RNA / Q000378:metabolism; D013816:Thermodynamics; D024363:Transcription Initiation Site / Q000502:physiology; D014158:Transcription, Genetic
chemical_list: D012313:RNA; D012321:DNA-Directed RNA Polymerases