Nucleic Acids Research

Synthetic DNAs were prepared containing 6-methyl adenlne (n A).in place of adenine and 5-ethyl uracil (Et U) or 5-methoxyiBethyl uracil (Mm U) in place of thymine. All three modifications destabilired duplex DNAs to varying degrees. The binding of ethldiun was studied to analogues of poly[d(AT)]. There, was no evidence of cooperative binding and the "neighbour exclusion rule" was obeyed in all cases although the binding constant to poly[d(m AT)] was approximately 6 fold higher than to poly[d(AT)J. P NMR spectra were recorded in increasing concentration* of CsF. Poly[d(AEt U)] showed two well-resolved signals separated by 0.55 ppm in 1 M CaF compared to 0.32 ppm for poly[d(AT)] under identical conditions. In contrast, poly[d(AMm U)J and poly[d(m AT)] showed two signals separated by 0.28 ppm and 0.15 ppm respectively, only when the concentration of CsF was raised to 2 M. The signals for poly[d(AT)] in 2 M CaF were better resolved and were separated by 0.41 ppm. These results suggest that ainor modifications to the bases may have conformatlonal effects which could be recognized by DNA-binding proteins. Introduction The alternating conformation of DNA was proposed by Klug et_ a_l., (1) mainly on the basis of DNAse I digestion patterns (2). These studies showed that in alternating poly[d(AT)] the ApT step adopted a different conformation from the TpA step. Although this is difficult to visualize without models, it was suggested that this difference was due to increased stacking of T residues on the A residues below them, with a concommlttant decrease in stacking with the A residues above. This gives rise to an alternating conformation for the DNA backbone because the repeat unit of the helix is a dinucleotide. It seems likely that the 5-methyl group of T plays an important role. In the alternating conformation the methyl group is positioned above the five-membered ring of the A residues, thereby increasing the favourable stacking interactions. These ideas have been confirmed and extended by P NMR spectroscopy (3,4,5). Since the phosphorous atoms in the ApT and TpA steps have slightly © I R L Press Limited, Oxford, England. 4325 Nucleic Acids Research