{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Wang A"],"funding":["UGC","UK","DBT/Wellcome Trust India Alliance","Wellcome Trust","Biotechnology and Biological Sciences Research Council"],"pagination":["gkaf857"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12445709"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["53(17)"],"pubmed_abstract":["Most bacterial sigma factors (σ) contain a highly conserved structural module, the 'σ-finger', which forms a loop that protrudes towards the RNA polymerase active centre in the open complex and has been implicated in pre-organization of template DNA, abortive initiation of short RNAs, initiation pausing, and promoter escape. Here, we introduce a novel single-molecule FRET (smFRET) assay to monitor σ-finger motions during transcription initiation and promoter escape. By performing real-time smFRET measurements, we determine that for all promoters studied, displacement occurs before promoter escape and can occur either before or after a clash with the extending RNA. We show that the kinetics of σ-finger displacement are highly dependent on the promoter, with implications for transcription kinetics and regulation. Analogous mechanisms may operate in the similar modules present across all kingdoms of life."],"journal":["Nucleic acids research"],"pubmed_title":["The displacement of the σ70 finger in initial transcription is highly heterogeneous and promoter-dependent."],"pmcid":["PMC12445709"],"funding_grant_id":["BB/M01116X/1","IA/I/21/2/505898","221610073587","110164/Z/15/Z","BB/R008655/1","212193/Z/18/Z"],"pubmed_authors":["Kapanidis AN","Wang A","Grainger DC","Mukherjee P","Mazumder A","Fletcher A"],"additional_accession":[]},"is_claimable":false,"name":"The displacement of the σ70 finger in initial transcription is highly heterogeneous and promoter-dependent.","description":"Most bacterial sigma factors (σ) contain a highly conserved structural module, the 'σ-finger', which forms a loop that protrudes towards the RNA polymerase active centre in the open complex and has been implicated in pre-organization of template DNA, abortive initiation of short RNAs, initiation pausing, and promoter escape. Here, we introduce a novel single-molecule FRET (smFRET) assay to monitor σ-finger motions during transcription initiation and promoter escape. By performing real-time smFRET measurements, we determine that for all promoters studied, displacement occurs before promoter escape and can occur either before or after a clash with the extending RNA. We show that the kinetics of σ-finger displacement are highly dependent on the promoter, with implications for transcription kinetics and regulation. Analogous mechanisms may operate in the similar modules present across all kingdoms of life.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Sep","modification":"2026-06-04T07:29:44.605Z","creation":"2026-06-04T03:05:57.715Z"},"accession":"S-EPMC12445709","cross_references":{"pubmed":["40966499"],"doi":["10.1093/nar/gkaf857"]}}