Nucleobases, Nucleosides and Nucleotides - Free-Radical-Induced DNA Damage and Its Repair - page 203

The p K a values of Thy and Ura are close to 9.5. Thus, near neutrality they are
deprotonated by OH − formed in the pulse. Due to the low p K a values, the repro-
tonation of the anions by water is sufficiently slow (

10 5 s −1 ) to allow the
anions to build-up to higher than steady-state concentrations. Of the two anions
that are formed upon deprotonation [e.g., reaction (1)] only the one deproton-
ated at N (1) absorbs at longer wavelengths than the neutral molecules (Morita
et al. 1981). This explains, why with the nucleosides which have the same p K a
values as the nucleobases no such intermediates are formed, although deproton-
ation by OH − occurs as well.
With Cyt, the situation is quite different. The p K a value of Cyt is 12.2. Hence,
reprotonation of the Cyt anion by water is very fast (

∼ 3 ×

10 8 s −1 ), and the interme-
diate Cyt anion cannot reach a sufficiently high concentration to be observable
under the conditions of such an experiment. On the other hand, Cyt is readily
protonated, the p K a value of the protonated Cyt being 4.6. The protonated Cyt
absorbs at longer wavelengths than Cyt itself, and hence a short-lived intermedi-
ate is observed. This also applies to Cyd. However, while the subsequent depro-
tonation of the protonated Cyt by OH − just reverts back to Cyd, this is not the
case with Cyt (Schuchmann et al. 2005). There, a new absorption builds up due
to the formation of its isomer, isocytosine, which has an absorption maximum at
296 nm (Dreyfus et al. 1976), i.e. at considerable longer wavelengths compared to
Cyt (

∼

λ max = 267 nm). Of the two isomers, Cyt is the thermodynamically favored
species and isocytosine (richer in Gibb's free energy by 14 kJ mol −1 ) eventually
reverts to Cyt [reactions (4) and (5)].

10.1.2
Reduction Potentials

Gua has the lowest reduction potential among the four nucleobases (Table 10.2),
and hence it is preferentially oxidized to its radical cation (for the calculation
of ionization potentials of the DNA bases see Close 2004; Crespo-Hernández et
al. 2004), and this property makes Gua and its derivatives to stick out of the
other nucleobases with respect to its different free-radical chemistry. In con-
trast, Thy and Cyt are good electron acceptors, while the purines are only poor
ones in comparison (for the calculation of electron affinities, see Richardson et
al. 2004). This is of special importance in the effects caused by the absorption of
ionizing radiation by DNA.
The reduction potential of Guo and Ado, determined pulseradiolytically
(Steenken and Jovanovic 1997), corrects earlier much lower values (Jovanovic
and Simic 1986, 1989), but is only slightly higher than the value of 1.47 V deter-