Crosslink Mapping at Amino Acid-Base Resolution Reveals the Path of Scrunched DNA in Initial Transcribing Complexes.

Summary RNA polymerase binds tightly to DNA to recognize promoters with high specificity but then releases these contacts during the initial stage of transcription. We report a site-specific crosslinking approach to map the DNA path in bacterial transcription intermediates at amino acid and nucleotide resolution. After validating the approach by showing that the DNA path in open complexes (RP O ) is the same as in high-resolution X-ray structures, we define the path following substrate addition in “scrunched” complexes (RP ITC ). The DNA bulges that form within the transcription bubble in RP ITC are positioned differently on the two strands. Our data suggest that the non-template strand bulge is extruded into solvent in complexes containing a 5-mer RNA, whereas the template strand bulge remains within the template strand tunnel, exerting stress on interactions between the β flap, β′ clamp, and σ 3.2 . We propose that this stress contributes to σ 3.2 displacement from the RNA exit channel, facilitating promoter escape. [ABSTRACT FROM AUTHOR]