Figure 4.
(a) The secondary structure of the HDV genomic ribozyme (7). (b) The labeling of stems (l1, l2) and single-stranded sections (s1, s2, s3) for the pseudoknot whose entropic free energy is given in Eq. 1; it corresponds to the main pseudoknotted scaffold of the HDV ribozyme (a). (c) The secondary structure of the ribozyme (black) plus attenuator (blue) as it presumably occurs in the HDV genome, except during replication. It corresponds to the absolute free energy minimum obtained by Zuker (ref. 13; http://mfold2.wustl.edu/∼mfold/rna/form1.cgi). Figs. 4, 5, and 7 are drawn by using RnaViz (15).