Issue 7, 2009
From the journal:

Organic & Biomolecular Chemistry

8-Aza-7-deazaguanine nucleosides and oligonucleotides with octadiynyl side chains: synthesis, functionalization by the azide-alkyne ‘click’ reaction and nucleobase specific fluorescence quenching of coumarindye conjugates†

Frank Seela,*ab   Hai Xiong,ab   Peter Leonarda  and  Simone Budowa  

* Corresponding authors

a Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, Münster, Germany
E-mail: Frank.Seela@uni-osnabrueck.de, Seela@uni-muenster.de
Web: www.seela.net
Fax: +49 (0)251-53406-857
Tel: +49 (0)251-53406-500

b Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastraße 7, Osnabrück, Germany

Abstract

Oligonucleotides incorporating 7-(octa-1,7-diynyl) derivatives of 8-aza-7-deaza-2′-deoxyguanosine (2d) were prepared by solid-phase synthesis. The side chain of 2d was introduced by the Sonogashira cross coupling reaction and phosphoramidites (3a, 3b) were synthesized. Duplexes containing 2d are more stabilized compared to those incorporating the non-functionalized 8-aza-7-deaza-2′-deoxyguanosine (2a) demonstrating that these side chains have steric freedom in duplex DNA. Nucleoside 2d as well as 2d-containing oligonucleotides were conjugated to the non-fluorescent 3-azido-7-hydroxycoumarin 15 by the Huisgen-Meldal-Sharpless ‘click’ reaction. Pyrazolo[3,4-d]pyrimidine nucleoside conjugate 16 shows a much higher fluorescence intensity than that of the corresponding pyrrolo[2,3-d]pyrimidine derivative 17. The quenching in the dye conjugate 17 was found to be stronger on the stage of monomeric conjugates than in single-stranded or duplex DNA. Nucleobase-dye contact complexes are suggested which are more favourable in the monomeric state than in the DNA chain when the nucleobase is part of the stack. The side chains with the bulky dye conjugates are well accommodated in DNA duplexes thereby forming hybrids which are slightly more stable than canonical DNA.

Graphical abstract: 8-Aza-7-deazaguanine nucleosides and oligonucleotides with octadiynyl side chains: synthesis, functionalization by the azide-alkyne ‘click’ reaction and nucleobase specific fluorescence quenching of coumarin dye conjugates

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Article information

DOI
https://doi.org/10.1039/B822041G
Article type
Paper
Submitted
09 Dec 2008
Accepted
15 Jan 2009
First published
02 Mar 2009

Org. Biomol. Chem., 2009,7, 1374-1387

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8-Aza-7-deazaguanine nucleosides and oligonucleotides with octadiynyl side chains: synthesis, functionalization by the azide-alkyne ‘click’ reaction and nucleobase specific fluorescence quenching of coumarin dye conjugates

F. Seela, H. Xiong, P. Leonard and S. Budow, Org. Biomol. Chem., 2009, 7, 1374 DOI: 10.1039/B822041G

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