ArticleNucleic acids research2014
Dissecting the chemical interactions and substrate structural signatures governing RNA polymerase II trigger loop closure by synthetic nucleic acid analogues.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A single cluster of RNA Polymerase II molecules is stably associated with active genes.Nature communications · 2026Article
- A single cluster of RNA Polymerase II molecules is stably associated with active genes.bioRxiv : the preprint server for biology · 2025Article
- Widespread epistasis shapes RNA polymerase II active site function and evolution.Nature communications · 2025Article
- Article
- Higher-order epistasis within Pol II trigger loop haplotypes.bioRxiv : the preprint server for biology · 2024Article
- Closing and opening of the RNA polymerase trigger loop.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Functional assays for transcription mechanisms in high-throughput.Methods (San Diego, Calif.) · 2019Review
- Mechanism of RNA polymerase II stalling by DNA alkylation.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop.PLoS genetics · 2016Article
- Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution.Nucleic acids research · 2016Article
- Impact of template backbone heterogeneity on RNA polymerase II transcription.Nucleic acids research · 2015Article
- Trigger loop folding determines transcription rate of Escherichia coli's RNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications.Critical reviews in biochemistry and molecular biology · 2015Review
- Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase.Nucleic acids research · 2014Article
- Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
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6 authors.
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Abstract
The trigger loop (TL) of RNA polymerase II (Pol II) is a conserved structural motif that is crucial for Pol II catalytic activity and transcriptional fidelity. The TL remains in an inactive open conformation when the mismatched substrate is bound. In contrast, TL switches from an inactive open state to a closed active state to facilitate nucleotide addition upon the binding of the cognate substrate to the Pol II active site. However, a comprehensive understanding of the specific chemical interactions and substrate structural signatures that are essential to this TL conformational change remains elusive. Here we employed synthetic nucleotide analogues as 'chemical mutation' tools coupling with α-amanitin transcription inhibition assay to systematically dissect the key chemical interactions and structural signatures governing the substrate-coupled TL closure in Saccharomyces cerevisiae Pol II. This study reveals novel insights into understanding the molecular basis of TL conformational transition upon substrate binding during Pol II transcription. This synthetic chemical biology approach may be extended to understand the mechanisms of other RNA polymerases as well as other nucleic acid enzymes in future studies.
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