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Nucleic Acids Research, 2000, Vol. 28, No. 15 2977-2985
© 2000 Oxford University Press

4-amino-1H-benzo[g]quinazoline-2-one: a fluorescent analog of cytosine to probe protonation sites in triplex forming oligonucleotides

Frédéric Godde, Jean-Jacques Toulmé and Serge Moreau*

INSERM U-386, IFR Pathologies Infectieuses, 146 rue Léo Saignat, Université Victor Segalen, 33076 Bordeaux Cedex, France

We developed a new fluorescent analog of cytosine, the 4-amino-1H-benzo[g]quinazoline-2-one, which constitute a probe sensitive to pH. The 2'-O-Me ribonucleoside derivative of this heterocycle was synthesized and exhibited a fluorescence emission centered at 456 nm, characterized by four major excitation maxima (250, 300, 320 and 370 nm) and a fluorescence quantum yield of {Phi} = 0.62 at pH 7.1. The fluorescence emission maximum shifted from 456 to 492 nm when pH was decreased from 7.1 to 2.1. The pKa (4) was close to that of cytosine (4.17). When introduced in triplex forming oligonucleotides this new nucleoside can be used to reveal the protonation state of triplets in triple-stranded structures. Complex formation was detected by a significant quenching of fluorescence emission (~88%) and the N-3 protonation of the quinazoline ring by a shift of the emission maximum from 485 to 465 nm. Using this probe we unambiguously showed that triplex formation of the pyrimidine motif does not require the protonation of all 4-amino-2-one pyrimidine rings.

* To whom correspondence should be addressed. Tel: +33 05 5757 1016; Fax: +33 05 5757 1015; Email: serge.moreau@bordeaux.inserm.fr


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