Nucleic Acids in Chemistry and Biology

8.11.2 Base Excision Repair of Altered Residues

In mammalian cells, excision repairis the most important mechanism and involves enzyme recognition of
the modified base, usually resulting form oxidation, deamination, or alkylation (Table 8.1). There are two dis-
tincttypes of excision repair process and both appear to be error-free: base excisionand nucleotide excision.
Repair by base excision, BER, employs a DNA glycosylasethat cleaves the glycosylic bonds of modi-
fied purine or pyrimidine nucleosides to generate an abasic site.^95 The next step is incision of the phosphate
backbone by an AP endonuclease(Section 10.5.2), which operates close to apurinic and apyrimidinic
sites. Subsequent exonuclease action then excises nucleotides to create a gap at least 30 residues long.
Multiple human glycosylases have been identified, each with its own base-specificity. Four of these
enzymes operate on 2
-deoxyuridine, which arises through misincorporation of dUMP (giving a UA
base-pair) or from deamination of dC (giving a UG base-pair). It has been estimated that humans repair
some 500 uracil residues per cell per day. Uracil DNA glycohydrolase, UDG, is highly conserved from
archaebacteria to humans and is the product of the UNGgene. It is the most proficient of the uracil repair
enzymes, having a reaction acceleration close to 10^12 , while its efficiency of discrimination against
thymine and cytosine in favour of uracil exceeds 1:10^7.
3-Methyladenine is the principal target for two 3-methyladenine-DNA glycosylases from E.coli,one of
which also acts on 3-MeG, O^2 -MeC and O^2 -MeT residues. The human enzyme 3-methyladenine DNA gly-
cosylase, the MPGgene product, removes a remarkably diverse group of damaged bases from DNA, includ-
ing cytotoxic and mutagenic alkylation adducts of purines such as 3-MeA, 7-MeG and hypoxanthine. The
structure of the human 3-methyladenine DNA glycosylase complexed to a mechanism-based pyrrolidine
inhibitor (Figure 8.41a) shows the enzyme intercalated into the minor groove of DNA, causing the abasic
pyrrolidine nucleotide to flip into the enzyme active site, where a bound water is poised for nucleophilic attack.
8-Oxoguanine is the major mutagenic base lesion in DNA caused by exposure to reactive oxygen
species. It is excised by OGG1, a DNA glycosylase with an associated lyase activity for chain cleavage. It
releases free 8-hydroxyguaninespecifically from 8-OH-GC pairs and also introduces a chain break in a

328 Chapter 8

a

NN

O

O

H

O

OH

HO

H

N

N

O

O

H

O

OH

HO

H

F

H H

NH

N

H

N

N

O

N

H

H

O

H 2 C

OH

HO

pseudodeoxyuridine 4'-carba-8-oxoguanosine 2'-difluorouridine

b

N

N

O

O

H

O

O

PO 2

O

PO 2

N

N

O

O

H

O

OPO

2

O

PO 2

O

H

H

O

O

Asp^145

N

H

N

O

O

H

O

O

PO 2

O

PO 2

OH

HO

O Asp

88

SN^1

ionisation

solvation

H

F

HN

OPO

2

O

PO 2 H

iminium abasic analogue

Figure 8.41 (a) Structures of some nucleoside analogues used to inhibit glycosylic bond cleavage. (b) 2-Step SN 1
mechanism of glycosylic bond cleavage by UDG

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