Synthesis and hybridisation properties of phosphonamidate ester modified nucleic acid

The replacement of the two backbone oxygen atoms of the phosphodiester linkage of DNA with carbon and nitrogen in the form of a phosphonamidate ester linkage, in both possible regioisomeric forms, is described. An alkylation reaction with the 3'-C-P-N-5' methyl phosphonamidate regioisomer yielded the corresponding N-methylated analogues. For each example separation into individual phosphonamidate ester diastereoisomers was performed prior to incorporation into oligonucleotides. The effect upon duplex stability for DNA oligonucleotides containing each of these modifications with complimentary RNA is reported.