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Nucleic Acids Research, 2002, Vol. 30, No. 23 5276-5283
© 2002 Oxford University Press

G-quartets assembly within a G-rich DNA flap. A possible event at the center of the HIV-1 genome

Sébastien Lyonnais, Candide Hounsou1, Marie-Paule Teulade-Fichou1, Josette Jeusset, Eric Le Cam and Gilles Mirambeau*

Laboratoire de Microscopie Moléculaire et Cellulaire, CNRS UMR 8126, Institut Gustave Roussy, 94805 Villejuif, France and 1 Laboratoire de Chimie des Interactions Moléculaires, Collège de France, UPR 285, 11 Place Marcelin Berthelot, 75005 Paris, France

*To whom correspondence should be addressed. Tel: +33 1 42114880; Fax: +33 1 42115494; Email: mirambe{at}igr.fr

Stretches of guanines can associate in vitro through Hoogsteen hydrogen bonding to form four-stranded structures. In the HIV-1 central DNA flap, generated by reverse transcriptase at the end of retrotranscription, both the two 99 nt-long overlapping (+) strands contain two adjacent tracts of guanines. This study demonstrates that oligonucleotides containing these G-clusters form highly stable G-quadruplexes of various structures in vitro, whose formation was controlled by an easy and reversible protocol using sodium hydroxide. Among these sequences, a G'2 hairpin dimer was the most stable structure adopted by the 5'-tail of the (+) downstream strand. Since the two (+) strands of the HIV-1 central DNA flap hold these G-clusters, and based on the properties of reverse branch migration in DNA flaps, constructions using HIV-1 sequences were assembled to mimic small DNA flaps where the G-clusters are neighbors. G-quartets were successfully probed in such flaps. They were induced by potassium and by a dibenzophenanthroline derivative already known to stabilize them. Such results suggest some function(s) for G-quartets associated with a DNA flap in the HIV-1 pre-integration steps, and argue for their transient formation during the processing of G-rich DNA flaps at the time of replication and/or repair.


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