Nucleic Acids in Chemistry and Biology

The viral self-cleaving motifs catalyze sequence-specific RNA cleavage through a simple trans-
esterification reaction that involves nucleophilic attack of the scissile 2
-OH group on an activated phospho-
diester linkage, resulting in products with 2
-3
cyclic phosphate and 5
-hydroxyl termini (Figure 7.39).
This reaction differs markedly from the self-splicing introns and RNase P in eukaryotes, which stimulate
attack by an exogenous nucleophile and which produce a different set of reaction products (Figure 7.17,
Section 7.2.2).
While the chemical reaction pathway of self-cleaving motifs is very similar to base-catalyzed RNA hydroly-
sis (Sections 3.2.2 and 8.1) and to the first part of the mechanism of the cleavage reaction of Ribonuclease
A (Figure 3.51), studies on ribozyme constructs have revealed a rich and complex chemistry.^69 Whereas mag-
nesium ions or other divalent cations are important in folding of the ribozyme motifs, some ribozymes, for
example the hairpin ribozyme and the hepatitis delta genomic and complementary antigenomic ribozymes
(both the sense and antisense strand of this motif are catalytic), do not strictly require divalent cations for
the chemical cleavage reaction. Instead, these ribozymes appear to promote strand scission (or ligation,
being the reverse reaction) by precise alignment of functional groups within the ribozyme active site.^27
These ribozymes may also stimulate reaction through general acid–base catalysis and electrostatic stabil-
ization (Figure 7.40).^69 Remarkably, certain nucleobases in the active site undergo dramatic pKashifts
toward neutrality, as exemplified by residue C75 of hepatitis delta virus ribozyme (Figure 7.9), that may
allow them to behave much like imidazole moieties of histidine residues within Ribonuclease A.^69
The catalytic mechanism of the hammerhead ribozyme remains controversial, however. Earlier studies on
a smaller RNA section that was thought to be sufficient for cleavage suggested the involvement of magnesium
ions in both folding and the catalytic mechanism. We now know that a complete hammerhead is composed of
a larger section of RNA (Figure 7.37a) and that two of its loops dock as part of the folding pathway.70,71
This construct has a much lower magnesium-ion requirement for cleavage than for minimized hammerhead
constructs. Further high-resolution structure analysis and biochemical studies may soon resolve whether
or not divalent ions are involved in the hammerhead catalytic mechanism.

7.6.3 RNA Tertiary Structure and Viral Function

Structured RNA plays a particularly important role in the replication and pathogenicity of viruses. Some
of the most important viral threats to human health, such as the flaviviruses (e.g., Yellow Fever), Hepatitis C
virus (HCV), Influenza, the coronaviruses (e.g., SARS), and the retroviruses (e.g., HIV) have RNA genomes
that contain regulatory elements composed of RNA tertiary structures. Furthermore, all viruses (including
those with DNA genomes) produce mRNA molecules that are processed and translated by exploitation of
unusual RNA conformations.

RNA Structure and Function 287

O base

O O

OP

O

O

O

O base

O OH

O P

O

O

H

5'

3'

O base

O O

P

O

O

O

O base

O OH

O P

O

O

5'

3'

B

H

O

O base

HO

O

O base

O OH

O P

O

O

5'

3'

O O

OPO

Figure 7.39 The mechanism of strand scission by the hammerhead, hairpin, hepatitis delta and Varkud satellite
ribozymes