Oligonucleotide analogues with 4-hydroxy-N-acetylprolinol as sugar substitute

Abstract

Modified oligonucleotides incorporating trans-4-hydroxy-N-acetyl-L-prolinol (trans-4-HO-L-NAP) or its D-analogue as sugar substitute were synthesised with adenine and thymine as nucleobases. All-adenine oligonucleotides built from (2S,4S) or (2R,4R)-cis-4-hydroxy-N-acetylprolinol were likewise prepared. Hybridisation studies revealed that heterocomplexes formed between polyU and homochiral trans-4-hydroxy-N-acetylprolinol-based oligomers of the same as well as of opposite chirality (polyU/trans-DA(13)* and polyU/trans-LA(13)*). The former, however, were triple-stranded. Other complexes with ribonucleic acids were polyA/trans-LT13* and polyU/cis-LA(13)*. Heteroduplexes with deoxynucleic acids were formed between trans-LA(13)* and oligothymidylate. Interaction was also observed for cis-LA(13)* and oligothymidylate, but not with the D-hydroxyprolinol analogues. Microcalorimetry proved this interaction to be the formation of a triple-stranded complex. Two heteroduplexes, trans-LA(13)*/dT(13) and trans-LA(13)*/polyU, had similar or slightly increased stability when compared to the natural dA(13)/dT(13) or dA(13)/polyU systems. Microcalorimetry clearly indicated the formation of a duplex, in contrast to interactions with N-acetylprolinol oligonucleotides of different stereochemistry. Moreover, the enthalpy change was of the same magnitude but the association constant was slightly lower. Natural nucleicacids thus clearly prefer hybridisation with L-hydroxyprolinol oligomers over D-hydroxyprolinol oligomers. For the series investigated, the L-trans oligomers (Figure 1) seem best to mimic natural oligonucleotides. These modified oligonucleotides formed homocomplexes if both strands were of the same chirality, that is, homocomplexes formed between trans-LA* and trans-LT* and between trans-DA* and trans-DT*, reflecting the isochiral pu-py pairing found in natural nucleic acids. Once more, however, calorimetry proved these to be triplex interactions. Heterochiral pairing was not observed between modified oligonucleotides, but only between modified oligonucleotides and natural polyU. The thermal stabilities of these heterochiral complexes differed clearly.status: publishe