Synthesis and Incorporation of C(5′)‐Ethynylated Uracil‐Derived Phosphoramidites into RNA.

Abstract

The d-allo-and l-talo-hept-6-ynofuranosyluracil-derived phosphoramidites 11A and 11T were prepared in 9 ± 10% yield over eight steps from the previously described propargylic alcohols 1A and 1T, respectively. The corresponding nucleotides were incorporated into rU 14 by standard solid-phase synthesis. While the duplex consisting of rU 14 with one l-talo-hept-6-ynofuranosyluracil in the middle of the strand and rA 14 (I´V) had the same melting point as the reference duplex rU 14´r A 14 (I´II), the duplex with one d-allo-hept-6-ynofuranosyluracil in the middle of rU 14 and rA 14 (I´III) melted 1.58 lower than the reference duplex. The duplex I´VI consisting of rU 14 with six l-talo-hept-6-ynofuranosyluracils distributed over the entire strand and rA 14 showed a melting point that is 118 lower than the reference duplex. The corresponding duplex I´IV of rU 14 possessing six d-allo-hept-6-ynofuranosyluracils and rA 14 showed a melting point which is more than 208 below the one of the reference duplex. These results are in qualitative agreement with the predictions based on the conformational analysis of the nucleosides and the interference of the ethynyl moiety with the hydration of the oligonucleotides.Introduction. ± We are exploring the chemistry of ethynylene-linked oligonucleotide analogues 1 ) to further test our hypothesis that the structural differentiation between backbone and nucleobases is not required for duplex formation [3]. In this context, we prepared the monomers 1A and 1T [4]. Their availability leads to the question about the influence of the ethynyl substituents at C(5') on the conformation and pairing of RNA analogues derived from these monomers (Fig. 1). Information about the influence of substituents at C(5') in DNA and RNA analogues on pairing is of interest in the context of antisense or antigene therapy [5 ± 14] and in view of preparing RNA analogues possessing new functional properties [15 ± 18]. Only a few nucleosides modified at C(5') 2 ) were incorporated into RNA or DNA, and had either little effect on duplex stability [35]