The 7-tripropargylamine-7-deaza-2'-deoxyguanosine (2) containing two terminal triple bonds in the side chain was synthesized by the Sonogashira cross-coupling reaction from the corresponding 7-iodo nucleoside 1b. This was protected at the 2-amino group with an iso-butyryl residue, affording the protected intermediate 5. Then, compound 5 was converted to the 5'-O-DMT derivative 6, which on phosphitylation afforded the phosphoramidite 7. This was employed in solid-phase synthesis of a series of oligonucleotides. T(m) measurements demonstrate that a covalently attached tripropargylamine side chain increases duplex stability. Both terminal triple bonds of nucleoside 2 and corresponding oligonucleotides were functionalized by the Cu(I)-mediated 1,3-dipolar cycloaddition "double click reaction" with 1-azidomethyl pyrene 3, decorating the side chain with two proximal pyrenes. While the monomeric tripropargylamine nucleoside with two proximal pyrenes (4) shows strong excimer fluorescence, the ss-oligonucleotide containing 4 does not. This was also observed for ds-oligonucleotides when the complementary strand was unmodified. However, duplex DNA bearing pyrene residues in both strands exhibits strong excimer fluorescence when each strand contains two pyrene residues linked to the tripropargylamine moiety. This pyrene-pyrene interstrand interaction occurs when the pyrene modification sites of the duplex are separated by two base pairs which bring the fluorescent dyes in a proximal position. Molecular modeling indicates that only two out of four pyrene residues are interacting forming the exciplex while the other two do not communicate.

No abstract

No abstract

Clickable oligonucleotides with ethynyl residues in the 5-position of pyrimidines ((eth)dC and (eth)dU) or the 7-position of 7-deazaguanine ((eth)c(7)G(d)) are hydrated during solid-phase oligonucleotide synthesis and workup conditions. The side products were identified as acetyl derivatives by MALDI-TOF mass spectra of oligonucleotides and by detection of modified nucleosides after enzymatic phosphodiester hydrolysis. Ethynyl → acetyl group conversion was also studied on ethynylated nucleosides under acidic and basic conditions. It could be shown that side chain conversion depends on the nucleobase structure. Triisopropylsilyl residues were introduced to protect ethynyl residues from hydration. Pure, acetyl group free oligonucleotides were isolated after desilylation in all cases.