ArticleJournal of molecular biology2013
The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection.
Article in Journal of molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Molecular insight into 5' RNA capping with NpNature chemical biology · 2026Article
- Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity.Molecular cell · 2026Article
- Structural basis of pausing during transcription initiation in mycobacterium tuberculosis.Nature communications · 2026Article
- DNA as a perfect quantum computer based on the quantum physics principles.Scientific reports · 2024Article
- Structural basis of σProceedings of the National Academy of Sciences of the United States of America · 2024Article
- smFRET Detection of Cis and Trans DNA Interactions by the BfiI Restriction Endonuclease.The journal of physical chemistry. B · 2023Article
- Multi-parameter photon-by-photon hidden Markov modeling.Nature communications · 2022Article
- Real-Time Single-Molecule Studies of RNA Polymerase-Promoter Open Complex Formation Reveal Substantial Heterogeneity Along the Promoter-Opening Pathway.Journal of molecular biology · 2022Article
- Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications.International journal of molecular sciences · 2022Review
- Structural origins ofProceedings of the National Academy of Sciences of the United States of America · 2021Article
- A Bayesian model based computational analysis of the relationship between bisulfite accessible single-stranded DNA in chromatin and somatic hypermutation of immunoglobulin genes.PLoS computational biology · 2021Article
- Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER.Science advances · 2021Article
- The smfBox is an open-source platform for single-molecule FRET.Nature communications · 2020Article
- Redefining fundamental concepts of transcription initiation in bacteria.Nature reviews. Genetics · 2020Review
- Whole-genome Identification of Transcriptional Start Sites by Differential RNA-seq in Bacteria.Bio-protocol · 2020Article
- The dynamic landscape of transcription initiation in yeast mitochondria.Nature communications · 2020Article
- Dynamic insights on transcription initiation and RNA processing during bacterial adaptation.RNA (New York, N.Y.) · 2020Article
- Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase.Nucleic acids research · 2019Article
- Rapid functionalisation and detection of viruses via a novel CaScientific reports · 2019Article
- Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms.Journal of molecular biology · 2019Review
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Authors and funding
10 authors.
Funding
Abstract
Bacterial transcription is initiated after RNA polymerase (RNAP) binds to promoter DNA, melts ~14 bp around the transcription start site and forms a single-stranded "transcription bubble" within a catalytically active RNAP-DNA open complex (RP(o)). There is significant flexibility in the transcription start site, which causes variable spacing between the promoter elements and the start site; this in turn causes differences in the length and sequence at the 5' end of RNA transcripts and can be important for gene regulation. The start-site variability also implies the presence of some flexibility in the positioning of the DNA relative to the RNAP active site in RP(o). The flexibility may occur in the positioning of the transcription bubble prior to RNA synthesis and may reflect bubble expansion ("scrunching") or bubble contraction ("unscrunching"). Here, we assess the presence of dynamic flexibility in RP(o) with single-molecule FRET (Förster resonance energy transfer). We obtain experimental evidence for dynamic flexibility in RP(o) using different FRET rulers and labeling positions. An analysis of FRET distributions of RP(o) using burst variance analysis reveals conformational fluctuations in RP(o) in the millisecond timescale. Further experiments using subsets of nucleotides and DNA mutations allowed us to reprogram the transcription start sites, in a way that can be described by repositioning of the single-stranded transcription bubble relative to the RNAP active site within RP(o). Our study marks the first experimental observation of conformational dynamics in the transcription bubble of RP(o) and indicates that DNA dynamics within the bubble affect the search for transcription start sites.
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