Figure 4.

mFold prediction of the secondary structure of Broccoli (circled with green) fused to tRNA (red). For comparison purposes the color coding of nucleotides is the same as in Figure 3d. Green indicates conservative bases (or equivalent substitutions) participating in base pairing. Blue indicates conservative bases in bulges. Yellow in this structure indicates reengineered terminal stem-loop. The non-colored base is a mutation in a conservative bulge. Either a small-molecule aptamer or another Broccoli unit (without tRNA) can be inserted in place of the indicated stem-loop.