DNA and Double-Stranded Oligonucleotides - Free-Radical-Induced DNA Damage and Its Repair - page 357

Simulation of frank SSBs and base damage as expressed by ALS has been
achieved with the RADACK (RADiation attACK) procedure (Begusova et al.
2001b). This takes into account that the various nucleobases and the hydrogens
of the sugar moiety react with different rate constants. The effect is shown in
Fig. 12.4, where B-DNA is represented in a space-filling model with only the re-
active atoms represented, with the same atoms but with sizes according to their
• OH cross-section or with the non-reactive atoms re-added. It is the last struc-
ture that • OH "encounters" in the RADACK procedure.
The variations in the probability of damage induction calculated with RA-
DACK are well ref lected in the variation of frank SSBs and damaged bases (as ex-
pressed by ALS) for different forms of DNA: B-DNA (Fig. 12.5), Z-DNA (Tartier
et al. 1994; Fig. 12.6) and for a DNA quadruplex (Tartier et al. 1998). The yield of
• OH-induced frank SSBs of various topoisomers of DNA minicircles is the same
(Culard et al. 1994). It has been concluded that the accessibility of H4

is already
sufficient in the relaxed topoisomer that an increase in accessibility in the T

′

− 2

topoisomer would be without effect.
For further modeling studies of this group see Begusova et al. (1999, 2000a,
b, 2005); Michalik et al. (1995a−c); Savoye et al. (1996); Sy et al. (2001); Tartier et
al. (1994).

12 . 3
Single Base Damage

12 . 3.1
General Remarks

Nearly all modifications that have been detected on the model level (Chap. 10)
are also found in free-radical damaged DNA. Obviously the DNA-bound lesions
are much more difficult to detect, and there is an ongoing discussion as to the
best procedure of their excision (Chap. 13.2; for a review on the excision and
repair of base lesions in vivo see Wallace, 2002). Mechanistic details concerning
the formation of the base lesions have been discussed in Chapters 10 and 11, and
only some additional information will be given below and in the section on clus-
tered lesions where the phenomenon of tandem lesions, two damaged bases that
are formed side by side, is dealt with. The yields of damaged bases formed upon
γ -irradiation in aqueous solution, as has been determined by the GC − MS/SIM

technique, are compiled in Table 12.5.
As can be seen from this table, the detectable products amount to 35% of
• OH at most. Moreover, dsDNA gave rise to markedly lower yields than ssDNA.
Whether this is due to incomplete • OH scavenging in these systems due to low-
molecu la r-weig ht i mpu r it ies is as yet u n k now n. Obv iously, as we k now f from ot h-
er studies, there are more products formed such as Iz, Z, cA, cG, 5HmU, 5ForU,
Fo and hydantoin lesions (see below) than have been determined in this study.
Moreover, there is an attack of • OH at the sugar moiety that is generally believed
not to exceed 20% by much (see, however, Sect. 12.4.4). Thus, there is a gap in the
material balance. The material balance is especially poor in the absence of O 2 .