Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution

Hye Ran Koh, Rahul Roy, Maria Sorokina, Guo Qing Tang, Divya Nandakumar, Smita S. Patel, Taekjip Ha

Research output: Contribution to journalArticle

Abstract

We provide a comprehensive analysis of transcription in real time by T7 RNA Polymerase (RNAP) using single-molecule fluorescence resonance energy transfer by monitoring the entire life history of transcription initiation, including stepwise RNA synthesis with near base-pair resolution, abortive cycling, and transition into elongation. Kinetically branching pathways were observed for abortive initiation with an RNAP either recycling on the same promoter or exchanging with another RNAP from solution. We detected fast and slow populations of RNAP in their transition into elongation, consistent with the efficient and delayed promoter release, respectively, observed in ensemble studies. Real-time monitoring of abortive cycling using three-probe analysis showed that the initiation events are stochastically branched into productive and failed transcription. The abortive products are generated primarily from initiation events that fail to progress to elongation, and a majority of the productive events transit to elongation without making abortive products. Koh et al. report single-molecule transcription that monitors most steps of initiation in real time with near base-pair resolution. They distinguish productive and failed transcription; they also show that a majority of productive transcription occurs without abortive initiation and that most of the abortive RNAs result from multiple rounds of failed transcription events.

Original languageEnglish (US)
Pages (from-to)695-706.e5
JournalMolecular Cell
Volume70
Issue number4
DOIs
StatePublished - May 17 2018

Fingerprint

DNA-Directed RNA Polymerases
Base Pairing
RNA
Fluorescence Resonance Energy Transfer
Recycling
Population

Keywords

  • abortive RNA
  • closed complex
  • fluorescence
  • FRET
  • open complex
  • promoter DNA
  • single-molecule
  • T7 RNA polymerase
  • transcription initiation
  • transition to elongation

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

Cite this

Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution. / Koh, Hye Ran; Roy, Rahul; Sorokina, Maria; Tang, Guo Qing; Nandakumar, Divya; Patel, Smita S.; Ha, Taekjip.

In: Molecular Cell, Vol. 70, No. 4, 17.05.2018, p. 695-706.e5.

Research output: Contribution to journalArticle

Koh, Hye Ran ; Roy, Rahul ; Sorokina, Maria ; Tang, Guo Qing ; Nandakumar, Divya ; Patel, Smita S. ; Ha, Taekjip. / Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution. In: Molecular Cell. 2018 ; Vol. 70, No. 4. pp. 695-706.e5.
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