title: The alternating conformation of analogues of poly[d(AT)].
abstract: Synthetic DNAs were prepared containing 6-methyl adenine (m6A) in place of adenine and 5-ethyl uracil (Et5U) or 5-methoxymethyl uracil (Mm5U) in place of thymine. All three modifications destabilized duplex DNAs to varying degrees. The binding of ethidium 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(m6AT)] was approximately 6 fold higher than to poly[d(AT)]. 31P NMR spectra were recorded in increasing concentrations of CsF. Poly[d(AEt5U)] showed two well-resolved signals separated by 0.55 ppm in 1 M CsF compared to 0.32 ppm for poly[d(AT)] under identical conditions. In contrast, poly[d(AMm5U)] and poly[d(m6AT)] 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 CsF were better resolved and were separated by 0.41 ppm. These results suggest that minor modifications to the bases may have conformational effects which could be recognized by DNA-binding proteins.
mesh_terms: D004996:Ethidium / Q000378:metabolism / Q000494:pharmacology; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation / Q000187:drug effects; D011067:Poly dA-dT / Q000138:chemical synthesis; D011089:Polydeoxyribonucleotides / Q000138:chemical synthesis / Q000378:metabolism
chemical_list: D011089:Polydeoxyribonucleotides; D011067:Poly dA-dT; D004996:Ethidium