Incorporation of 2'-amido-nucleosides in oligodeoxynucleotides and oligoribonucleotides as a model for 2'-linked conjugates

The functionalisation of oligodeoxynucleotides and oligoribonucleotides by incorporation of 2'-amido-2'-deoxyribonucleosides, possibly containing a reporter group via the 2'-amido bond, was examined. Therefore 2'-acetamido-ribonucleosides containing a small methyl group at the 2'-amido bond were synthesized as model compounds. In order to evaluate the influence of this 2'-modification on the hybridization capacities, 2'-acetamido-2'-deoxyuridine was incorporated in both RNA and DNA strands. The suitability of phosphoramidite chemistry for the introduction of this modified nucleoside was proven using laser desorption mass spectrometry of the final oligonucleotide. The presence of the 2'-modification destabilised both RNA-RNA, DNA-DNA and mixed duplexes. Therefore, it can be concluded that the 2'-acetamido group is not a good linker for attachment of reporter groups to oligonucleotides.