Chemistry Reference
In-Depth Information
15
Two - Metal-Ion-Dependent Catalysis
in Nucleic Acid Enzymes
W e i Y a n g
15.1 Chemistry of Nucleic Acid Synthesis, Cleavage and Strand Transfer
DNA and RNA are synthesized by polymerases in the 5
′
to 3
′
direction. The
hydroxyl group at the 3
end of a primer strand attacks the a - phosphate of an incom-
ing (deoxy)nucleoside triphosphate ((d)NTP) to incorporate the (d)NMP into the
primer strand and release a pyrophosphate molecule (Figure 15.1A). Therefore,
nucleic acid synthesis transfers a phosphodiester bond from a (d)NTP to the 3
′
- OH
(the nucleophile) of a growing primer strand. All polymerases have been shown to
require Mg
2+
ions for catalysis.
1,2
The same phosphoryl transfer reaction occurs during DNA or RNA cleavage
except that the phosphate being attacked is the backbone of a nucleic acid and the
nucleophile is a hydroxyl group from water, protein or ribose (Figure 15.1B,C).
When a water molecule serves as a nucleophile, the nucleic acid is hydrolysed. When
the nucleophile is a hydroxyl group of protein sidechains, e.g. Ser and Tyr, as in DNA
recombination,
3 - 5
a 2
′
- OH of RNA or
DNA, as in splicing and integration,
7,8
the phosphorylated product is covalently
linked to the protein or nucleotide (Figure 15.1B). The chemistry of a phosphoryl
transfer reaction begins with deprotonation and activation of a nucleophile and
fi nishes with protonation of the leaving group. The mechanism for phosphoryl trans-
fer reactions in nucleic acids has been shown to be the S
N
2 type, involving a penta-
covalent phosphate intermediate (phosphate anion) and inversion of the stereo
′
-OH of ribose, as in RNA cleavage
6
or a 3
′
