double-stranded oligonucleotide (Table 8.1). The human enzyme MUTYH appears to be homologous to
the bacterial repair glycosylase MutY, and removes adenines mis-paired with 8-oxoguanine. The third
component of the resistance to 8-oxoG is an 8-oxoGTP hydrolase, which removes it from the nucleotide
pool to circumvent misincorporation of 8-OH-G opposite A residues.
Recent studies have confirmed the role of reactive oxygen species in the pathogenesis of Alzheimer’s
disease (AD) and the accumulation of 8-oxo-2-deoxyguanosine in AD brain has been discussed. It seems
that reduced expression of 8-oxoguanine DNA glycosylase(hOGG1-2a), an enzyme that repairs 8-oxo-2-
deoxyguanosine, may be involved in the pathomechanism of AD.^96
8.11.3 Mechanisms and Inhibitors of DNA Glycohydrolases
All DNA glycosylases employ a nucleotide-flippingmechanism. This is a general strategy for enzymes
operating on natural or modified DNA bases to gain access to target loci that are buried in the DNA stack
or inaccessible from a groove. Such glycosylases fall into two distinct mechanistic classes: (i) monofunc-
tional glycosylasesand (ii) bifunctional glycosylase/AP lyases.
Considerable detail has been achieved in understanding the mechanism of monofunctional BER glyco-
sylases through the use of inhibitory nucleotide analogues resistant to glycosylic bond cleavage.^95 Three
general strategies have been employed (Figure 8.41a).
C-Glycosides as in the case of pseudodeoxyuridine for UDG^97 and 2-deoxyformycin A for MutY,
Carbocyclic sugar nucleosides, as in the case of 8-oxocarbadG for OGG1^98 and
2-Fluoropentoses, as in the case of 2-fluoroadenosine for MutY^99 and 2-difluorodU for human
TDG glycosylase.^100UDG is an example of an enzyme that ‘flips-out’the aberrant nucleotide, as seen in an elegant sequence
of X-ray structures by John Tainer, one including a transition state analogue.^97 Both QM-MM computation
and kinetic isotope studies have identified the glycosylic bond cleavage as a dissociative process, much of
the energy for which derives from stabilisation of an oxocarbenium ion at C-1 of the deoxyribose by the
negative charges on the proximate phosphate residues in the same strand. The water that is captured by the
oxocarbenium ion to give the deoxyribose AP-product is activated by an essential aspartic acid in an SN 1
mechanism (Figure 8.41b). The uracil anion is an adequate leaving group not needing general acid activa-
tion. Thus, the UDG enzyme appears to provide no chemical catalysis but serves simply to orientate the
DNA substrate to maximise uracil recognition, stereoelectronic effects and the enabling contribution of
the phosphate negative charges to C–N bond ionisation. In general, repair enzymes that involve oxocar-
benium ion intermediatesare strongly inhibited by iminium abasic sugar analogues (Figure 8.41a), which
have proven to constitute a general strategy for studying glycohydrolases.101,102
The enzymes that catalyse depurination show greatly reduced base-specificities and also appear to use
general acid catalysis at the purine to effect glycosyl bond cleavage. Less mechanistic detail is yet avail-
able to establish whether they employ SN1 or SN2 reaction pathways.
The bifunctional BER enzymes that cause chain cleavage as well as base-excision generally operate viaa
sugar-enzyme intermediate. These include OGG1, NEI1 and NTH1 (Table 8.1). Their mechanism is well
exemplified for the bacteriophage T4 Endonuclease V, which cleaves the glycosylic bond of the 5-residue
in a thymine photodimer.^103 The N-terminal amino group of T4 Endo V attacks C-1, displaces the base
and forms an aldimine. This is followed by -elimination of the 3-phosphate to give the single-strand
break (Figure 8.42).
8.11.4 Nucleotide Excision Repair
Nucleotide excision, NER, is the repair pathway that deals with bulky lesions, including those formed by
UV radiation, various environmental mutagens, and some chemotherapeutic agents, and shows broad sub-
strate acceptability.^104 There seems to be a general correlation between the efficiency of repair and the
Covalent Interactions of Nucleic Acids with Small Molecules and Their Repair 329