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Issue 9, 2008
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Pyrrolo-dC oligonucleotides bearing alkynyl side chains with terminal triple bonds: synthesis, base pairing and fluorescent dye conjugates prepared by the azidealkyne “click” reaction

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Abstract

5-(Octa-1,7-diynyl)-2′-deoxyuridine was converted into the furano-dU derivative 7 by copper-catalyzed cyclization; the pyrolodC-derivative 3 was formed upon ammonolysis. The bicyclic nucleosides 3 and 7 as well as the corresponding non-cyclic precursors 4 and 6 all containing terminal C[triple bond, length as m-dash]C bonds were conjugated with the non-fluorescent 3-azido-7-hydroxycoumarin 5 employing the copper(I)-catalyzed Huisgen–Sharpless–Meldal cycloaddition “click reaction”. Strongly fluorescent 1H-1,2,3-triazole conjugates (30–33) are formed incorporating two fluorescent reporters—the pyrdC nucleoside and the coumarin moiety. Oligonucleotides incorporating 6-alkynyl and 6-alkyl 7H-pyrrolo[2,3-d]pyrimidin-2(3H)-one nucleosides (3 and 2f) have been prepared by solid-phase synthesis using the phosphoramidite building blocks 10 and 13; the pyrrolo-dC oligonucleotides are formed during ammonia treatment. The duplex stability of oligonucleotides containing 3 and related derivatives was studied. Oligonucleotides with terminal triple bonded nucleosides such as 3 are more stabilizing than those lacking a side chain with terminal unsaturation; open-chain derivatives (4) are even more efficient. The click reaction was also performed on oligonucleotides containing the pyrdC-derivative 3 and the fluorescence properties of nucleosides, oligonucleotides and their coumarin conjugates were studied.

Graphical abstract: Pyrrolo-dC oligonucleotides bearing alkynyl side chains with terminal triple bonds: synthesis, base pairing and fluorescent dye conjugates prepared by the azide–alkyne “click” reaction

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Publication details

The article was received on 17 Dec 2007, accepted on 01 Feb 2008 and first published on 26 Mar 2008


Article type: Paper
DOI: 10.1039/B719459E
Citation: Org. Biomol. Chem., 2008,6, 1674-1687
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    Pyrrolo-dC oligonucleotides bearing alkynyl side chains with terminal triple bonds: synthesis, base pairing and fluorescent dye conjugates prepared by the azidealkyne “click” reaction

    F. Seela and V. R. Sirivolu, Org. Biomol. Chem., 2008, 6, 1674
    DOI: 10.1039/B719459E

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