Sequence-dependent kinetic model for transcription elongation by RNA polymerase

被引：121

作者：

Bai, L ^{[1
]}

Shundrovsky, A ^{[1
]}

Wang, MD ^{[1
]}

机构：

[1] Cornell Univ, Atom & Solid State Phys Lab, Dept Phys, Ithaca, NY 14853 USA

来源：

JOURNAL OF MOLECULAR BIOLOGY | 2004年 / 344卷 / 02期

基金：

美国国家卫生研究院;

关键词：

RNA polymerase; transcription; kinetics; sequence-dependence; model;

D O I：

10.1016/j.jmb.2004.08.107

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We present a kinetic model for the sequence-dependent motion of RNA polymerase (RNAP) during transcription elongation. For each NTP incorporation, RNAP has a net forward translocation of one base-pair along the DNA template. However, this process may involve the exploration of back-tracked and forward-tracked translocation modes. In our model, the kinetic rates for the reaction pathway, calculated based on the stabilities of the transcription elongation complex (TEC), necessarily lead to sequence-dependent NTP incorporation rates. Simulated RNAP elongation kinetics is in good agreement with data from transcription gels and single-molecule studies. The model provides a kinetic explanation for well-known back-tracked pauses at transcript positions with unstable TECs. It also predicts a new type of pause caused by an energetically unfavorable transition from pre to post-translocation modes. (C) 2004 Elsevier Ltd. All rights reserved.

引用

页码：335 / 349

页数：15

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