Template Misalignment in Multisubunit RNA Polymerases and Transcription Fidelity

Ekaterina Kashkina, Michael Anikin, Florian Brueckner, Richard T. Pomerantz, William T T. McAllister, Patrick Cramer, Dmitry Temiakov

Research output: Contribution to journalArticlepeer-review

33 Scopus citations


Recent work showed that the single-subunit T7 RNA polymerase (RNAP) can generate misincorporation errors by a mechanism that involves misalignment of the DNA template strand. Here, we show that the same mechanism can produce errors during transcription by the multisubunit yeast RNAP II and bacterial RNAPs. Fluorescence spectroscopy reveals a reorganization of the template strand during this process, and molecular modeling suggests an open space above the polymerase active site that could accommodate a misaligned base. Substrate competition assays indicate that template misalignment, not misincorporation, is the preferred mechanism for substitution errors by cellular RNAPs. Misalignment could account for data previously taken as evidence for additional NTP binding sites downstream of the active site. Analysis of the effects of different template topologies on misincorporation indicates that the duplex DNA immediately downstream of the active site plays an important role in transcription fidelity.

Original languageEnglish (US)
Pages (from-to)257-266
Number of pages10
JournalMolecular Cell
Issue number2
StatePublished - Oct 20 2006

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Cell Biology


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