Closing and opening of the RNA polymerase trigger loop

Abhishek Mazumder, Miaoxin Lin, Achillefs N. Kapanidis, Richard H. Ebright

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


The RNA polymerase (RNAP) trigger loop (TL) is a mobile structural element of the RNAP active center that, based on crystal structures, has been proposed to cycle between an “unfolded”/“open” state that allows an NTP substrate to enter the active center and a “folded”/“closed” state that holds the NTP substrate in the active center. Here, by quantifying single-molecule fluorescence resonance energy transfer between a first fluorescent probe in the TL and a second fluorescent probe elsewhere in RNAP or in DNA, we detect and characterize TL closing and opening in solution. We show that the TL closes and opens on the millisecond timescale; we show that TL closing and opening provides a checkpoint for NTP complementarity, NTP ribo/deoxyribo identity, and NTP tri/di/ monophosphate identity, and serves as a target for inhibitors; and we show that one cycle of TL closing and opening typically occurs in each nucleotide addition cycle in transcription elongation.

Original languageEnglish (US)
Pages (from-to)15642-15649
Number of pages8
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number27
StatePublished - Jul 7 2020

All Science Journal Classification (ASJC) codes

  • General


  • Conformational dynamics
  • RNA polymerase
  • Single-molecule fluorescence resonance energy transfer
  • Transcription
  • Trigger loop


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