DNA and Double-Stranded Oligonucleotides - Free-Radical-Induced DNA Damage and Its Repair - page 354

Fig. 12.4a-d. RADACK procedure: a B-DNA represented in a space-filling model; b the reactive
atoms only; c the same atoms but with sizes according to their • OH cross-section; d with the non-
reactive atoms re-added according to Begusova et al. (2001b, with permission)

to the structure of DNA in nucleosomes (Hayes et al. 1990b, 1991; Bashkin et
al. 1993), bent DNA (Tullius and Burkhoff 1988) and mapping the gene regula-
tion domains (Spotheim-Maurizot et al. 1995b). A similarly unspecific cleaving
agent for probing DNA

protein contacts seems to be the photoexcited uranyl ion
(Nielsen et al. 1988). Intercalating drugs may be much more selective in their
binding and hence in their cleavage reaction. As an example may serve photoex-
cited acridine derivatives (Jeppesen et al. 1988).

−

12 . 2 .1
Accessibility of the Sugar Moiety to Radical Attack
and Probability of Damage Induction

From the above, it is obvious that, beyond a global modulation of accessibility by
bound molecules such as protection by proteins, structural details of the DNA
determine the accessibility of radicals to sugar moieties. Among others, acces-
sibility will determine the H-abstraction from the various C H sites of the sugar

moiety even by the highly reactive • OH. Its overall relative accessibility, defined
as the accessible surface determined by rolling a sphere simulation of an • OH
onto the van de Waals surface of the H atoms, calculated for a molecular model
of a 68 bp DNA in B-form, shows that H5

−

′ 1 is the most exposed one, followed by

H5 ′ 2 and H4 ′ ; intermediate access is observed for H2 ′ 2 and H3 ′ , and the most

hidden ones are H2 (Sy et al. 1997; Begusova et al. 2001b).

A 80-bp DNA fragment has been used to study in detail the relation between
DNA damage (frank SSBs induced by • OH attack on the sugar moiety, notably at
H4

′ 1 and H1 ′

) and the accessibility of the H atoms involved in breakage (Sy et al.
1997). The experimental results were compared to the calculated accessibility of
the H atoms, and a good fit was observed between the frequency of SSBs at each

and H5

′ ′