Chemistry Reference
In-Depth Information
degradation) that the [Ru(phi)
2
(bpy
)] - P1 + Zn(II) 1:1 [54] (where P1 is a
de novo
designed a-helical peptide containing histidine residues for Zn
2+
coordination) is
the most effi cient DNA cleaving metal complex with totally 82% formation of
nicked plasmid and linear DNA (64% increase of modifi ed plasmid DNA compared
to control sample). On the other hand, high sequence selectivity is obtained in the
case of appended peptides derived from DNA-binding proteins, especially when
these peptides are either already structured (e.g. a
3
helix of the phage P
22
repres-
sor
46
) or initially designed to be a - helical, with a - helicity further increased upon
metal coordination (e.g. coordination of Zn(II) to appropriately designed pep-
tides
54
). However, it is important to keep in mind that sequence selectivity and
cleavage effi ciency of intercalating metal complexes tethered to peptides can be
further improved and optimized by the selection of the appropriate ancillary ligands,
intercalating ligands, linker and appended peptides.
Metal-peptide complexes show higher cleavage ability of DNA compared to
metal complex-peptide conjugates. As seen from Table 12.2, it is obvious that 100%
cleavage of plasmid DNA is not reported for any of the metal complex-peptide
conjugates (82% is the highest percentage of cleavage observed in the case of
[Rh(phi)
2
(bpy
′
)]-P1+Zn(II) 1:1). On the other hand, 100% conversion of super-
coiled plasmid DNA (form I) to nicked circular DNA (form II) and linear DNA
(form III) is reported for most metal-coordinated peptides.
56 - 58
Furthermore, Ni(II)
metallopeptides of the type Xaa-Xaa-His show remarkably high DNA-binding
constants,
56
comparable with those of intercalating metal complexes tethered to
peptides (10
7
- 10
8
M
− 1
).
46,47
Since metal complex-peptide conjugates and Ni(II) met-
allopeptides bind to DNA with similar affi nities, then the reason for the higher
cleavage effi ciency observed for Ni(II) metallopeptides probably lies in the different
mechanisms of DNA cleavage. A possible explanation is the shape selectivity upon
DNA binding of Ni(II) metallopeptides, reminiscent of the known minor-groove
binding drugs, that enables them to fi t into the DNA minor groove bringing the
metal centre in close proximity to the deoxyribose moiety (cleavage takes place
commonly by C4
′
-H abstraction). Even higher cleavage effi ciency can be accom-
plished when metallopeptides are conjugated to an intercalating ligand, such as in
the case of (bis-Ni(II)·GGH-NDI), in which two Ni(II)·GGH units are conjugated
to napthalene diimide (NDI).
59
The resultant nuclease is the most effi cient reported
so far among metallopeptides (100 times more effi cient than Ni(II)·GGH).
59
In
addition, sequence selectivity and cleavage effi ciency of metal-peptide complexes
can conveniently be modulated either by changing the position of amino-acids
bearing the appropriate side chain functionalities within the peptide sequence, thus
discriminating between different mixed A/T sequences or changing amino acid chi-
rality resulting in totally different sequence recognition (e.g. 5
′
′
- CCT - 3
′
in the case
of Ni(II) · Gly - D - Asn - His
56
).
Another important issue concerning the design of applicable artifi cial nucleases
is the mechanistic pathway followed. Formation of diffusible active oxygen species
results in base-directed reactivity, with guanines being the most vulnerable residues
toward oxidation. Consequently, any sequence selectivity observed upon DNA
binding cannot be reproduced after initiation of cleavage. This is obvious in the case
of peptides conjugated to the parent complex [Ru(bpy)
3
]
2+
.
24
Hence, formation of
