A general mechanism for transcription bubble nucleation in bacteria

Abstract Transcription initiation is a major control point of gene expression. The cellular RNA polymerases (RNAPs), with the help of initiation factors (σ factors in bacteria), recognize promoter sequences and initiate (nucleate) melting of the duplex DNA for transcription bubble formation, a critical step of initiation. The σ factors fall into two classes, the σ70-family and the σN (σ54) family. Bubble nucleation by σ70-factors occurs by a well-characterized flip-and-capture mechanism where nucleotides of the promoter flip out of the duplex