Modification of DNA with octadiynyl side chains: synthesis, base pairing, and formation of fluorescent coumarin dye conjugates of four nucleobases by the alkyne--azide "click" reaction.
Oligonucleotides incorporating 5-(octa-1,7-diynyl)-2'-deoxycytidine 1a, 5-(octa-1,7-diynyl)-2'-deoxyuridine 2a and 7-deaza-7-(octa-1,7-diynyl)-2'-deoxyguanosine 3a, 7-deaza-7-(octa-1,7-diynyl)-2'-deoxyadenosine 4a were prepared. For this, the phosphoramidites 7, 10, and 13 were synthesized and employed in solid-phase oligonucleotide synthesis. The octa-1,7-diynyl nucleosides 1a- 4a were obtained from their corresponding iodo derivatives using the palladium-assisted Sonogashira cross-coupling reaction. The Tm values demonstrated that DNA duplexes containing octa-1,7-diynyl nucleosides show a positive influence on the DNA duplex stability when they are introduced at the 5-position of pyrimidines or at the 7-position of 7-deazapurines. The terminal alkyne residue of oligonucleotides were selectively conjugated to the azide residue of the nonfluorescent 3-azido-7-hydroxycoumarin ( 38) using the protocol of copper(I)-catalyzed [3 + 2] Huisgen--Sharpless--Meldal cycloaddition "click chemistry" resulting in the formation of strongly fluorescent 1,2,3-triazole conjugates. The fluorescence properties of oligonucleotides with covalently linked coumarin--nucleobase assemblies were investigated. Among the four modified bases, the 7-deazapurines show stronger fluorescence quenching than that of pyrimidines.
Seela
Frank
F
Laboratory for Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany. Frank.Seela@uni-osnabrueck.de
Sirivolu
Venkata Ramana
VR
Chittepu
Padmaja
P
D000480:Alkynes / Q000737:chemistry*; D000818:Animals; D001386:Azides / Q000737:chemistry*; D020029:Base Pairing; D003374:Coumarins / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D003853:Deoxyribonucleosides / Q000737:chemistry; D005456:Fluorescent Dyes / Q000737:chemistry*; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry; D009943:Organophosphorus Compounds / Q000737:chemistry; D010727:Phosphoric Diester Hydrolases / Q000378:metabolism; D012910:Snake Venoms / Q000201:enzymology
D000480:Alkynes; D001386:Azides; D003374:Coumarins; D003853:Deoxyribonucleosides; D005456:Fluorescent Dyes; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; D012910:Snake Venoms; C434331:phosphoramidite; D004247:DNA; C030123:coumarin; D010727:Phosphoric Diester Hydrolases