A Mechanistic Comparison of the Varkud Satellite and Hairpin Ribozymes - Progress in Molecular Biology and Translational Science - page 95

Figure 3.2 The sequence and secondary structure of the hairpin ribozyme. The ribo-
zyme is based upon a perfect (4H) four-way helical junction with arms labeled
A through D. Arms A and B contain internal loops that interact to generate the active
site of the ribozyme. The site of cleavage within loop A is indicated by the arrow. All the
critical nucleotides required for catalytic activity are located in the two loops, including
G8 within loop A and A38 within loop B, and the two loops make an intimate interaction
in the folded ribozyme. 11 - 13
of different ways with retention of cleavage activity, and in some cases with
markedly enhanced rates. 8
2.2. Structure and dynamics of the hairpin ribozyme
The location of the nucleotides critical to ribozyme activity in the loops of
the A and B helices led to a strong suspicion that the active form of the ribo-
zyme would be generated by an intimate interaction between the loops. The
interaction would probably remodel the structures of both loops and create
the chemical environment in which catalysis of the transesterification reac-
tion could occur. However, the minimal hinged form of the ribozyme
required unphysiologically high concentrations of divalent ions to facilitate
catalysis, and attention turned back to the form with an intact four-way