Chemistry Reference
In-Depth Information
that a nanowire made of T-Hg
II
-T base pairs might be a mediator for excess electron
transfer.
93
Utilizing the Hg
II
specifi city of the T-Hg
II
- T base pair, DNA oligomer - based
Hg
II
sensors were made by several groups. In 2004, an Hg
II
sensor with fl uorescent
probes (a fl uorophore at the 3
- end) was reported.
94
In this sensor, the sensor-DNA molecule forms a hairpin structure upon Hg
II
binding, which induces quenching of the fl uorescence. Therefore, the concentration
of Hg
II
can be quantitated from the fl uorescence intensity (the degree of quenching).
As mentioned above, T-T mismatches are highly specifi c to Hg
II
, and this Hg
II
sensor
specifi cally detected Hg
II
in the presence or absence of various metal cations.
94
In
2007, gold nanoparticles were utilized as an Hg
II
sensor in a study that employed
two kinds of gold nanoparticles modifi ed with different DNA oligomers on their
surfaces.
95
The fi rst particle is modifi ed with d(AAAAAAAAAA
T
AAAAAAAA
AA), and the second with d(TTTTTTTTTT
T
TTTTTTTTTT). In the presence of
Hg
II
, a T - Hg
II
-T base pair and Watson-Crick base pairs are formed between the
DNA oligomers on the particles. This induces the aggregation of the gold nanopar-
ticles and the colour of the particle-containing solution changes (colorimetric
sensing).
95
A third sensor was made from a catalytic DNA molecule (DNAzyme)
and its substrate RNA molecule with fl uorescent probes (a fl uorophore at the 5
′
-end and a quencher at the 5
′
′
- end
- end).
96
In the presence of Hg
II
, the DNAzyme strand takes
an active structure and cleaves the substrate RNA, which leads to an increase in
fl uorescence intensity. The interesting point of the enzymatic sensor is that the Hg
II
detection signal (fl uorescence intensity) can be enlarged upon Hg
II
sensing.
96
and a quencher at the 3
′
16.7 Biological Relevance of the T - H g
II
- T Base Pairs
NMR, FTIR and Raman studies have revealed modes of interaction between Hg
II
and nucleobases. Among these structures, a A-Hg
II
-T base pair with a N6(A)-Hg
II
-
O4(T) and a T - Hg
II
-T base pair with a N3(T)-Hg
II
- N3(T) can be formed under
physiological conditions.
69 - 72,81 - 83,94
The A- Hg
II
-T base pair with the N6(A)-Hg
II
-
O4(T) linkage was found to exist in studies by Sletten's group. This result indicates
that, in the case of A,G,C,T-mixed DNA sequences, T-Hg
II
- T base pairing with
strand displacements is not necessarily a favourable process. Instead, penetration of
Hg
II
into Watson-Crick A-T base pairs can take place. Thus it is possible that revers-
ible Hg
II
binding to natural DNA molecules (
E. coli
DNA, calf thymus DNA, etc.)
might involve such a mode of interaction.
It has also been demonstrated that a T-Hg
II
-T base pair with a N3(T)-Hg
II
- N3(T)
does exist, and its chemical structure was clearly determined in a DNA duplex.
83
However, the proton-Hg
II
exchange has not been observed in crystal structures of
functional RNA molecules and DNA/RNA oligomers. Even in the cases with coor-
dination bonds, those between metal cations and nucleic acids are rarely observed.
Therefore, the observation of the T-Hg
II
-T base pair in the context of the DNA
duplex suggests that metal cation-binding with nucleic acids though a proton-Hg
II
exchange can occur if the conditions are appropriate for such proton-Hg
II
exchanges.
