The self-complementary dodecanucleotide d(CGCO⁶MeGAATTTGCG)₂ which contains two O⁶-methyl-2'-deoxyguanosine-thymine base pairs, has been analysed by X-ray diffraction methods and the structure refined to a residual error of R = 0.185 at 2.0A resolution. The O⁶MedG.T mispair closely resembles a Watson/Crick base pair and there are very few structural differences between the O⁶MedG.T duplex and the native analogue. The similarity between the O⁶MedG.T base pair and a normal dG.dC base pair explains the failure of mismatch repair enzymes to recognise and remove this mutagenic lesion. A series of ultraviolet melting studies over a wide pH range on a related dodecamer indicate that the O⁶MedG.dC mispair can exist in two conformations, one of which is a wobble pair, and the other a protonated Watson/Crick pair. The former, which predominates at physiological pH, will be removed by normal proofreading and repair enzymes, whereas the latter is likely to escape detection. Hence, the occasional occurrence of the protonated O⁶MedG.dC base pair may explain why the presence of O⁶MedG in genomic DNA does not always give rise to a mutation. Synthesis of C(8) substituted 2'-deoxyguanosine derivatives was also undertaken in an effort to yield 8-oxo-7-hydro-2'-deoxyguanosine, a product of oxidative damage to DNA. Displacement of bromine, from 8-bromo-2'-deoxyguanosine, was achieved with methoxide, benzyloxide and p-nitrothiophenol. Conversion of 8-methoxy-2'-deoxyguanosine to 8-oxo-7-hydro-2'-deoxyguanosine was achieved by use of thiophenol, however conversion was not possible using oligonucleotides containing the 8MeOdG base. Oligonucleotides containing 8-bromo-2'-deoxyguanosine were synthesised and they demonstrated similar pairing properties as 2'-deoxyguanosine. As a result the oligonucleotide d[T8BrGTACA] was prepared and co-crystallised with the drug nogalomycin to act as a heavy atom marker and aid refinement of the native DNA/drug sequence.