Sequence-dependent kinetic model for transcription elongation by RNA polymerase

Lu Bai, Alla Shundrovsky, Michelle D. Wang

Research output: Contribution to journalArticlepeer-review

127 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)335-349
Number of pages15
JournalJournal of Molecular Biology
Issue number2
StatePublished - Nov 19 2004

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology


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