DNA and Double-Stranded Oligonucleotides - Free-Radical-Induced DNA Damage and Its Repair - page 368

Piperidine that is typically used for this purpose has a double function. As
a nucleophile, it releases the damaged base (denoted as HNR 2 ) and assists
in the acidification of the H2

′ by forming a positively charged Schiff base

[reaction (8)].

The kinetics of the cleavage of the 2-dRL lesion is by -elimination has been

studied in some detail as a function of pH and temperature for a number of
ODNs of varying length (Roupioz et al. 2002; see also Sect. 12.9).
The Tg lesion rates among those ALS as shown with the help of an ODN con-
taining this lesion at a specific position (Matray and Greenberg 1994). Interest-
ingly, the FAPY-A lesion is readily identified as an ALS with this assay, while
FAPY-G is not (Haraguchi et al. 2002). In the absence of piperidine but in the
presence of phosphate buffer pH 7.5, the deglycosylation lifetime of FAPY-A is
about 103 h at 37 °C; FAPY-G is about 25 times more stable (measured at 55 °C;
Greenberg et al. 2001).
The C (1

β

) radical has been generated specifically within a short ss/dsODN
(Tronche et al. 1998). The ratio of ALSs to SSBs was 9:1, independent of whether
the radical was generated in a ss- or dsODN. The route from the C (1

′

′ ) radical to

frank SSBs is as yet unknown.

12.4.4
Strand Breaks

Concerning DNA strand breakage in the absence of O 2 , the sequence of reac-
tions resulting from the C (4

) radical were the first understood mechanistically
(Dizdaroglu et al. 1975), and this reaction still remains the most-widely studied
mechanism of DNA strand breakage. Strand breakage occurs by a heterolytic
cleavage of the neighboring phosphate group, whereby cleavage at C (3

′

′ ) strongly

dominates over that at C (5 ) [reactions (9) and (15); Beesk et al. 1979]. The het-

erolytic cleavage is favored over a homolytic

′

-cleavage due to the effective sol-
vation of the ensuing ions (Glatthar et al. 2000).

β