A Mechanistic Comparison of the Varkud Satellite and Hairpin Ribozymes - Progress in Molecular Biology and Translational Science - page 94

mitochondria of some field-isolated strains of the fungus Neurospora crassa
from Varkud in Kerala, India. Collins and coworkers found that the VS
RNA contains an element capable of self-cleavage, 9 which serves a role
in the processing of replication intermediates. 10

2.1. The secondary structures of the hairpin and VS
ribozymes the role of helical junctions

The nucleolytic ribozymes are relatively small, autonomously folding RNA
species. Two members of this class, the HDV and GlmS ribozymes, have
folds based on complex, nested pseudoknots, whereas the remaining mem-
bers have one or more helical junctions. There appears to be alternative solu-
tions to the problem of generating a stable fold that permits catalysis, and
based on this rather small set of ribozymes, the solutions seem to be mutually
exclusive.
The secondary structure of the hairpin ribozyme shows it to be centered
on a four-way helical junction, with arms sequentially labeled A, B, C, and
D( Fig. 3.2 ). 3 Adjacent arms A and B contain loops that include all but one of
the nucleotides shown to be essential for catalytic activity, and the site of
cleavage/ligation is located in arm A. Much of the initial work on this ribo-
zyme was carried out in the Burke lab 14-18 studying a minimal form com-
prising only helices A and B connected by a single-stranded hinge.
The sequence and deduced secondary structure of the VS ribozyme 19
suggests that it too should be based upon helical junctions ( Fig. 3.3 ).
Two three-way junctions interconnect five helical sections (helices II
through VI) forming a nominal H shape. Cleavage and ligation reactions
occur within the internal loop of stem-loop I that is connected to the
end of helix II. Collins and coworkers showed that the terminal loop of helix
I interacts with that of helix V, 23 and they have suggested that this results in
an altered pattern of base pairing that propagates down the helix to change
the structure within the internal loop that contains the scissile phosphate. 24
This involves the opening of the terminal base pair, extrusion of C634, and
rearrangement of base pairing in stem I such that CCC (635-637) pairs with
GGG (623-625). Jones and Strobel 25 pointed out that an additional helix
(VII) in the natural VS RNA sequence might play a role in the function
of the ribozyme by forming a third three-way junction with helices I and
II. Helix I may be physically disconnected from the rest of the ribozyme,
such that a ribozyme comprising helices II through VI acts in trans upon
stem-loop I. 26 Helix I may also be reconnected to the ribozyme in a variety

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