Aptamers to the sigma factor mimic promoter recognition and inhibit transcription initiation by bacterial RNA polymerase

Promoter recognition by bacterial RNA polymerase (RNAP) is a multi-step process involving multiple protein-DNA interactions and several structural and kinetic intermediates which remain only partially characterized. We used single-stranded DNA aptamers containing specific promoter motifs to probe the interactions of the Therms aquaticus RNAP sigma(A) subunit with the -10 promoter element in the absence of other parts of the promoter complex. The aptamer binding decreased intrinsic fluorescence of the sigma subunit, likely as a result of interactions between the -10 element and conserved tryptophan residues of the a DNA-binding region 2. By monitoring these changes, we demonstrated that DNA binding proceeds through a single rate-limiting step resulting in formation of very stable complexes. Deletion of the N-terminal domain of the sigma(A) subunit increased the rate of aptamer binding while replacement of this domain with an unrelated N-terminal region 1.1 from the Escherichia colt sigma(70) subunit restored the original kinetics of sigma-aptamer interactions. The results demonstrate that the key step in promoter recognition can be modelled in a simple sigma-aptamer system and reveal that highly divergent N-terminal domains similarly modulate the DNA-binding properties of the a subunit. The aptamers efficiently suppressed promoter-dependent transcription initiation by the holoenzyme of RNA polymerase, suggesting that they may be used for development of novel transcription inhibitors. (C) 2015 Elsevier Inc. All rights reserved.