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. 2012 Feb 13;109(9):3323-3328. doi: 10.1073/pnas.1113086109

Fig. 3.

Fig. 3.

Pausing-deficient, mutant RNAP transcription affects folding fraction of the btuB riboswitch. (A) Both mutant RNAPs significantly affect pausing at sites A–C. Lane 240+ corresponds to high [NTP] chase after 4 min. (B) Schematic representation of the two RNA constructs. The full-length construct has 302 residues and contains the entire aptamer domain, the expression platform, and the first 20 codons of the BtuB gene. The aptamer-only construct has 202 residues and contains just the aptamer domain as defined in the literature (6). The location of the pause sites A–C is also indicated. (C) Transcription by the fast RNAPs reduces the ratio of protection in the absence and presence of coenzyme B12 for both the aptamer domain and the expression platform. The cleavage reaction with the RBS probe was carried out with 25% the amount of RNase H, as compared to the cleavage reaction with the aptamer probe. (D) Transcription by fast RNAPs has little effect on differential fraction folded of the aptamer-only construct.