8.11 DNA Repair 325
8.11.1 Direct Reversal of Damage 326
8.11.2 Base Excision Repair of Altered Residues 328
8.11.3 Mechanisms and Inhibitors of DNA Glycohydrolases 329
8.11.4 Nucleotide Excision Repair 329
8.11.5 Crosslink Repair 330
8.11.6 Base Mismatch Repair 330
8.11.7 Preferential Repair of Transcriptionally Active DNA 331
8.11.8 Post-Replication Repair 332
8.11.9 Bypass Mutagenesis 332
References 334296 Chapter 8
The simple purpose of this chapter is to provide an outline of the more important examples of covalent
interactions of small molecules with nucleic acids. Topics have been chosen as they bear on the modifica-
tions of intact nucleic acids, and especially as they relate to mutagenic and carcinogenic effects. While
much of the early information has come from studies on nucleosides, more recent work has shown that the
net effect of a reagent on an intact nucleic acid in many cases may be quite different from either the sum
or the average of its interactions with separate components. Above all, we have to recognise that studies
on the more subtle effects of DNA and RNA secondary and tertiary structures on covalent interactions are
still in their infancy.
8.1 Hydrolysis of Nucleosides, Nucleotides and Nucleic Acids
Nucleic acids are easily denatured in aqueous solution at extremes of pH or on heating. While the phos-
phate ester bonds are only slowly hydrolysed (Section 3.2.2), the N-glycosylic bonds are relatively labile.
Purine nucleosides are cleaved faster than pyrimidines while deoxyribonucleosides are less stable than
ribonucleosides.^1 Thus, dA and dG are hydrolysed in boiling 0.1M hydrochloric acid in 30min; rA and rG
require 1h with 1M hydrochloric acid at 100°C, while rC and rU have to be heated at 100°C with 12M
perchloric acid (Figure 8.1). It follows that the glycosylic bonds of carbocyclic nucleoside analogues
(Section 3.1.2), which cannot donate electrons from the furanose 4-oxygen, are much more stable to
acidic (and also enzymatic) hydrolysisand this property has been used to advantage in many applications.
Formic acid has been used to prepare apurinic acid, which has regions of polypentose phosphate
diesters linking pyrimidine oligonucleotides. Such phosphate diesters are relatively labile since the pen-
tose undergoes a -elimination in the presence of secondary amines such as diphenylamine. This gives
tracts of pyrimidine oligomerswith phosphate monoesters at both 3- and 5-ends. Total acidic hydrolysis
with minimum degradation of the four bases is best achieved with formic acid at 170°C.
DNA is resistant to alkaline hydrolysis but RNA is easily cleaved because of the involvement of its
2 -hydroxyl groups (Section 3.2.2).
8.2 Reduction of Nucleosides
Purine and pyrimidine bases are sufficiently aromatic to resist reductionunder the mild conditions used,
as for example in the hydrogenolysis of benzyl or phenyl phosphate esters. However, hydrogenation with
a rhodium catalyst converts uridine or thymidine into 5,6-dihydropyrimidines.^2 Alternatively, sodium
borohydride in conjunction with ultraviolet irradiation gives the same products,which can lead on by further
reduction in the dark to cleavage of the heterocyclic ring. Dihydrouridine and 4-thiouridine are easily and
selectively reduced in tRNA with sodium borohydride in the dark.^3