ArticleNucleic acids research2018
The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 51 citations in OpenAlex.
- Single-Molecule Methods to Investigate Mechanisms of Transcription by RNA Polymerase ofbioRxiv : the preprint server for biology · 2026Article
- Structural Insights into De Novo Promoter Escape by Mycobacterium tuberculosis RNA Polymerase.Nature communications · 2025Article
- The displacement of the σ70 finger in initial transcription is highly heterogeneous and promoter-dependent.Nucleic acids research · 2025Article
- A phage transcription factor displaces the host σ factor and stabilizes its own σ factor.Nucleic acids research · 2025Article
- Single-stranded DNA drives σ subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations.Nucleic acids research · 2025Article
- Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens.Biochemistry · 2025Review
- Article
- Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment.Nucleic acids research · 2024Article
- Bleaching-resistant, Near-continuous Single-molecule Fluorescence and FRET Based on Fluorogenic and Transient DNA Binding.Chemphyschem : a European journal of chemical physics and physical chemistry · 2023Article
- Entropic control of the free-energy landscape of an archetypal biomolecular machine.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization.Nature communications · 2023Article
- Rapid Adaptation Often Occurs through Mutations to the Most Highly Conserved Positions of the RNA Polymerase Core Enzyme.Genome biology and evolution · 2022Article
- Article
- Structural and mechanistic basis of reiterative transcription initiation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding.Nucleic acids research · 2021Article
- Diverse and unified mechanisms of transcription initiation in bacteria.Nature reviews. Microbiology · 2021Review
- Optimization of N-hydroxysuccinimide ester coupling with aminoallyl-modified RNA for fluorescent labeling.Bioengineered · 2020Article
- Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations.Biomolecules · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
RNA polymerase (RNAP) contains a mobile structural module, the 'clamp,' that forms one wall of the RNAP active-center cleft and that has been linked to crucial aspects of the transcription cycle, including promoter melting, transcription elongation complex stability, transcription pausing, and transcription termination. Using single-molecule FRET on surface-immobilized RNAP molecules, we show that the clamp in RNAP holoenzyme populates three distinct conformational states and interconvert between these states on the 0.1-1 s time-scale. Similar studies confirm that the RNAP clamp is closed in open complex (RPO) and in initial transcribing complexes (RPITC), including paused initial transcribing complexes, and show that, in these complexes, the clamp does not exhibit dynamic behaviour. We also show that, the stringent-response alarmone ppGpp, which reprograms transcription during amino acid starvation stress, selectively stabilizes the partly-closed-clamp state and prevents clamp opening; these results raise the possibility that ppGpp controls promoter opening by modulating clamp dynamics.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.