Chemistry Reference
In-Depth Information
3'
N
N
N
N
N
N
N
N
N
N
N
N
Y
R
rR
N
N
N
N
N
N
N
N
N
N
N
N
N
N
5'
5'
3'
G
A
G
C
T
A
C
A
C
T
A
C
A
G
3'
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
5'
G rN
5'
T
3'
A
A
G
C
C
G
G
A
G
T
C
C
G
C
5'
YYY
Y
A A T A C
G
C
N
N
N
N
N
N
N
N
N
N
3'
R
Y
R
Y
R
Y
R
Y
A C
3'
5'
T
G
C
G
C
G
Figure 14.1
DNAzymes for Mg(II) (top), Pb(II) (middle) and Cu(II) (bottom). In each fi gure,
'N' represents any nucleotide provided they abide by Watson-Crick base pairing. All the
DNAzymes contain an enzyme strand (bottom strand) and a substrate strand (top strand).
Cleavage and ligation sites are marked by an arrow. Y denotes pyrimidine and R denotes
purine. (Yi Lu, Prof; New Transition-Metal-Dependent DNAzymes as Effi cient Endonucleases
and as Selective Metal Biosensors.
Chemistry - A European Journal
, 2002,
8
, 4589-4596.
Copyright Wiley-VCH Verlag GmbH & Co. KGaA. Reproduced with permission.)
14.2 Metal Ions as Important Cofactors of DNA zymes
Protein-based enzymes are constructed from 20 amino acids, whereas the variety of
structural features of nucleic acid enzymes is limited to only four different nucle-
otides. The lack of the 2
-OH functional group in DNA compared to RNA further
reduces the diversity of conformations that DNAzymes can take for effective target
recognition. Nature's solution to low effi ciency and diversity in biomolecular inter-
actions is the employment of cofactors. For example, protein enzymes are known to
recruit cofactors, such as NADH, porphyrins and especially metal ions, to broaden
the scope of reactions catalysed, increase catalytic effi ciency and fi ne - tune reactiv-
ity.
23 - 25
Therefore, to compete favourably with other families of enzymes, cofactors
are even more critical for the functions of DNAzymes. Among common cofactors,
metal ions are arguably the most important because of their capability to broaden
and fi ne-tune the activity of the emzymes.
23 - 25
In fact, other than a few reports that
some DNA/RNAzymes are active independent of the presence of metal ions,
13,14
for
the majority of DNA/RNAzymes, metal ions, including Mg
2+
, Mn
2+
and Ca
2+
, are
′
