Alternate structures of crcB RNAs. (A) Output of R2R for predicted alternate structures for a crcB RNA in Acidothermus cellulolyticus 11B. Stems are shaded so that their positions in the alternate structures are apparent. R2R commands were used to shade selected nucleotides, to position the multistem junction using the automated solver and to turn the direction of the backbone in two places within the 3' tail. (B) Finished drawing, assembled using Adobe Illustrator based on part A. The predicted Shine-Dalgarno (SD) sequence and start codon are shaded green and labelled. It is hypothesized that when the RNA binds its ligand "X" (left), the SD sequence is available for ribosome binding, allowing gene expression. In the absence of ligand (right), the SD sequence is sequestered, inhibiting gene expression. This latter drawing was made by combining the two drawings in part A. (C) Alternate hypothetical structures of a crcB RNA in Roseburia intestinalis L1-82, finished drawing. The hypothesized structure without the ligand X (right) allows the formation of a putative transcription terminator, which inhibits gene expression. The terminator stem is labelled, and its characteristic poly-U stretch is colored red.