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Figure 3.4 Parallel-eye stereo image of the crystal structure of the hairpin ribozyme in
the full four-way junction form. 34 The ribozyme folds by the coaxial stacking of helices
A with D (magenta) and B with C (cyan). Note the close association between the internal
loops of helices A and B. This includes the extrusion of Gþ1 from loop A and insertion
into loop B where it base pairs with C25 (shown as sticks).
Crystal structures have been solved for both the junction 34 ( Fig. 3.4 ) and
minimal hinged form 35 of the hairpin ribozyme. These confirmed the key
feature of the loop-loop interaction, and the general folding principle of the
junction form. The loop-loop association involves an extensive set of con-
tacts that include A-minor interactions, nucleobase contacts, and the extru-
sion of G
þ
1 (one of the nucleotides that flank the scissile phosphate) from
the A-loop and insertion into a pocket in the B-loop where it makes a
Watson-Crick pairing with C25. 34 The core nucleotides of the junction
and hinged forms can be superimposed with an RMS deviation of
1.28 ˚ . 35 As expected, the intimate interaction between the loops alters
the conformation of each loop from that of the isolated helices. 36,37 The
structure of a derivative of the hairpin ribozyme with a pentacoordinate
vanadium replacing the scissile phosphate as a transition state model was
obtained in the junction form, 38 and this will be discussed in the following
section.
2.3. Structure and dynamics of the VS ribozyme
Unlike the hairpin ribozyme, until very recently there was no crystal struc-
ture for the VS ribozyme. Nevertheless, we already had good idea of the
general fold of the ribozyme at low resolution from biophysical studies.
Initial biophysical studies focused on the II-III-VI and III-IV-V junc-
tions using a combination of comparative gel electrophoresis, FRET, and
homology-based modeling. 39,40 This suggested a core structure based upon
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