Synthesis and duplex stability of oligonucleotides containing adenine-guanine analogues

The nucleosides N6-methoxy-2'-deoxyadenosine (dZ) and 2-amino-9-(2-deoxy-beta-ribofuranosyl)-6-methoxyaminopurine (dK) have been synthesised and converted into 5'-O-dimethoxytrityl 3'-(2-cyanoethyl N,N-diisopropylphosphoramidites). These monomers have been used in machine DNA synthesis to give a set of heptadecanucleotides containing up to three analogue nucleotides. The melting transitions (Tm) show that the 17-mer duplexes containing Z.T and Z.C base-pairs have closely similar stabilities, as have those containing K.T and K.C pairs. They are less stable than the corresponding fully complementary duplexes, but more stable than those containing mismatched pairs. This, in the case of dZ, is in accord with the amino-imino tautomeric ratio of approximately 1:4 observed for the nucleoside in methyl sulfoxide. The application of oligomers containing such "degenerate" bases in oligonucleotide probes and primers is discussed.