Synthesis and duplex stability of oligonucleotides containing cytosine-thymine analogues

Abstract

The synthesis of the deoxynucleoside derived from the base P, 6H, 8H-3, 4-dihydro-pyrimido[4, 5-c][1, 2] oxazin-7-one, 2, and its introduction by established phosphoramidite and H-phosphonate chemistry into oligonucleotides is described. The melting transition temperatures (Tm ) of a range of heptadecamer duplexes containing P/A and P/G base-pairs are compared with corresponding ones having N4 -methoxycytosine (M) 1 and mismatched normal bases. P/A and P/G pairs allow closely similar duplex stabilities and have the potential to reduce the multiplicity of probes and primers based on amino acid sequences by removing the T/C degeneracy. © 1989 IRL Press.