期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2010
卷号：107
期号：28
页码：12523-12528
DOI：10.1073/pnas.1003533107
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：RNA synthesis, carried out by DNA-dependent RNA polymerase (RNAP) in a process called transcription, involves several stages. In bacteria, transcription initiation starts with promoter recognition and binding of RNAP holoenzyme, resulting in the formation of the closed (R{middle dot}Pc) RNAP-promoter DNA complex. Subsequently, a transition to the open R{middle dot}Po complex occurs, characterized by separation of the promoter DNA strands in an approximately 12 base-pair region to form the transcription bubble. Using coarse-grained self-organized polymer models of Thermus aquatics RNAP holoenzyme and promoter DNA complexes, we performed Brownian dynamics simulations of the R{middle dot}Pc [->] R{middle dot}Po transition. In the fast trajectories, unwinding of the promoter DNA begins by local melting around the -10 element, which is followed by sequential unzipping of DNA till the +2 site. The R{middle dot}Pc [->] R{middle dot}Po transition occurs in three steps. In step I, dsDNA melts and the nontemplate strand makes stable interactions with RNAP. In step II, DNA scrunches into RNA polymerase and the downstream base pairs sequentially open to form the transcription bubble, which results in strain build up. Subsequently, downstream dsDNA bending relieves the strain as R{middle dot}Po forms. Entry of the dsDNA into the active-site channel of RNAP requires widening of the channel, which occurs by a swing mechanism involving transient movements of a subdomain of the {beta} subunit caused by steric repulsion with the DNA template strand. If premature local melting away from the -10 element occurs first then the transcription bubble formation is slow involving reformation of the opened base pairs and subsequent sequential unzipping as in the fast trajectories.
关键词：DNA scrunching ; transcription initiation ; self-organized polymer model ; molecular simulations ; sequential DNA unzipping
