title: 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.
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]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 and the fluorescence properties of nucleosides, oligonucleotides and their coumarin conjugates were studied.
authors.affiliation: Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 4814, Münster, Germany. Frank.Seela@uni-osnabrueck.de
authors.forename: Frank
authors.initials: F
authors.lastname: Seela
authors.forename: Venkata Ramana
authors.initials: VR
authors.lastname: Sirivolu
mesh_terms: D000480:Alkynes / Q000737:chemistry*; D001386:Azides / Q000737:chemistry*; D020029:Base Pairing; D002384:Catalysis; D020650:Combinatorial Chemistry Techniques; D003300:Copper / Q000737:chemistry; D003374:Coumarins / Q000737:chemistry*; D003500:Cyclization; D004247:DNA / Q000737:chemistry; D003853:Deoxyribonucleosides / Q000737:chemistry; D005456:Fluorescent Dyes / Q000737:chemistry*; D008968:Molecular Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry; D013237:Stereoisomerism; D013997:Time Factors
chemical_list: D000480:Alkynes; D001386:Azides; D003374:Coumarins; D003853:Deoxyribonucleosides; D005456:Fluorescent Dyes; D009841:Oligonucleotides; D003300:Copper; D004247:DNA