Chemistry Reference
In-Depth Information
Table 2.1
Reaction rate constants of
e
a
−
with H
3
O
+
and transition metal ions. (Values of
K
e/aq
are given in 10
9
m
−
1
s
−
1
.)
H
+
Mn
2+
Co
2+
Ni
2+
Ni(en)
2+
Ni(en
3
)
2+
Cu
2+
Cu
+
Zn
2+
Ag
+
M
n
+
K
e/aq
24
0.038
12
22
22.4
0.02
30
-
1.5
36
DPT takes place spontaneously in one out of 10
4
bp. Transition metal ions are known
to interact with DNA (depending on anion charge, G-C composition of DNA, ionic
strength etc.
28
), the effect of which is to increase the number of mispaired Watson-
Crick base pairs. The interaction of H
3
O
+
and transition metal ions with DNA
depends on both the electronic structure of the ions and the structural, poly-
electrolytic and dynamic characteristics of DNA in water solution.
Table 2.1 presents the reaction rate constants of hydrated electrons (
e
a
−
) with
different types of ions.
29,30
The reactivities of the ions presented in the table actually
refl ect the affi nities of the hydrated electron with these ions in water solutions
31
and,
as will be shown in Section 2.3.3, they correlate well with the results of UV spectra
of DNA - metal ion complexes.
Native double helix DNA is a heavily charged polyanion (2e
−
charge per base
pair), which in solution exists in the form of an ordered closely packed structure, as
proved by the strong hyperchroism displayed upon melting of the double helix.
Quantum chemical evaluations show an identical sequence of arrangement of elec-
tron-donor atoms for unscreened B-DNA and for that screened by Na
+
ions:
32 - 33
G - N7; G - N3; A - N3; T - O2; G - O6; A - N7
The NH
2
group of adenine and guanine prevents interaction of metal ions with
A-N7 and G-N3 due to steric crowding. In addition, G-N3, A-N3 and T-O2 are
located in the minor groove, the width and the depth of which are 5.7 Å and 7.5 Å,
respectively, in the B-form. For steric reasons all these atoms are unreachable for a
hydrated transition metal ion, which has a diameter of approximately 7.5 Å. However,
the omnipresent H
3
O
+
ion can interact with electron-donor groups from both of the
grooves. Interaction of ions with DNA also depends on ionic strength, GC composi-
tion, the order of the nucleotides in the helix and the conformational parameters
of DNA (the angle of the coil twist, the propeller angle, the distance between adja-
cent phosphorus atoms of the same chain etc.). Nevertheless, one may say with a
certain assurance that dynamic characteristics of DNA are the most signifi cant
factors governing metal ion-DNA interactions. First of all, this is important for
modelling e.g. B
Z transitions, mechanisms of transcription, replication, carcino-
genesis and mutagenesis.
In this respect it is important to describe the characteristics of inner
mobility in DNA, e.g. various small-amplitude oscillating movements of atoms,
about
0.
′
inside the components of DNA (10
− 14
- 10
− 13
s); limited movements of
phosphates, sugars and nucleobases around an equilibrium position; torsion and
fl exural oscillations of the double helix (10
− 10
- 10
− 8
s); large - amplitude movements of
phosphates, sugars and bases occurring at the transition of DNA double helix from
→
