ArticleNature structural & molecular biology2013
The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion.
Article in Nature structural & molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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66 citing papers in PubMed.
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- Force and the α-C-terminal domains bias RNA polymerase recycling.Nature communications · 2024Article
- De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features.Biophysical journal · 2024Article
- RNAP Promoter Search and Transcription Kinetics in LiveThe journal of physical chemistry. B · 2023Article
- The structural mechanism for transcription activation by Caulobacter crescentus GcrA.Nucleic acids research · 2023Article
- Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter.Nucleic acids research · 2022Article
- Anticipating response function in gene regulatory networks.Journal of the Royal Society, Interface · 2021Article
- RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding.Nucleic acids research · 2021Article
- Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription.International journal of molecular sciences · 2021Article
- Transcription activation by a sliding clamp.Nature communications · 2021Article
- The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA.Nucleic acids research · 2020Article
- How p53 Molecules Solve the Target DNA Search Problem: A Review.International journal of molecular sciences · 2020Review
- Alternative transcription cycle for bacterial RNA polymerase.Nature communications · 2020Article
- Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes - Observing Strong Local Effects of Nucleoid Structure on Gene Regulation.Frontiers in microbiology · 2020Article
- Binding Revisited-Avidity in Cellular Function and Signaling.Frontiers in molecular biosciences · 2020Review
- Combined Methylome, Transcriptome and Proteome Analyses Document Rapid Acclimatization of a Bacterium to Environmental Changes.Frontiers in microbiology · 2020Article
- Transcription of Bacterial Chromatin.Journal of molecular biology · 2019Review
6 more citing papers are in PubMed but not listed here.
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Abstract
Gene expression, DNA replication and genome maintenance are all initiated by proteins that must recognize specific targets from among a vast excess of nonspecific DNA. For example, to initiate transcription, Escherichia coli RNA polymerase (RNAP) must locate promoter sequences, which compose <2% of the bacterial genome. This search problem remains one of the least understood aspects of gene expression, largely owing to the transient nature of search intermediates. Here we visualize RNAP in real time as it searches for promoters, and we develop a theoretical framework for analyzing target searches at the submicroscopic scale on the basis of single-molecule target-association rates. We demonstrate that, contrary to long-held assumptions, the promoter search is dominated by three-dimensional diffusion at both the microscopic and submicroscopic scales in vitro, which has direct implications for understanding how promoters are located within physiological settings.
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