User:Michelle Meyer BC/S7

The RNA structure that regulating the str operon in E. coli (rpsL, rpsG, fusA, and tufA) occurs within the intergenic region between rpsL and rpsG. In vitro nuclease protection assays have proposed two S7 binding sites. The first, contained within the bulge and lower portion of helix H-III, is not well conserved. The second binding site is purported to be at the three-stem junction, and bases implicated in binding are well conserved. However, there is sequence variability outside of this binding site, and two of the three helices forming the three-stem junction (helices H-IV and H-V) are absent in some species and even when present helix H-IV is often thermodynamically unstable.