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Nucleic Acids Research, 2002, Vol. 30, No. 6 1333-1337
© 2002 Oxford University Press

Binding of oligonucleotides to a viral hairpin forming RNA triplexes with parallel G*G•C triplets

Pedro Carmona* and Marina Molina1

Instituto de Estructura de la Materia (CSIC), Serrano 121, 28006 Madrid, Spain and 1Departamento de Química Orgánica I, Escuela Universitaria de Optica, Arcos de Jalón s/n, 28037 Madrid, Spain

Infrared and UV spectroscopies have been used to study the assembly of a hairpin nucleotide sequence (nucleotides 3–30) of the 5' non-coding region of the hepatitis C virus RNA (5'-GGCGGGGAUUAUCCCCGCUGUGAGGCGG-3') with a RNA 20mer ligand (5'-CCGCCUCACAAAGGUGGGGU-3') in the presence of magnesium ion and spermidine. The resulting complex involves two helical structural domains: the first one is an intermolecular duplex stem at the bottom of the target hairpin and the second one is a parallel triplex generated by the intramolecular hairpin duplex and the ligand. Infrared spectroscopy shows that N-type sugars are exclusively present in the complex. This is the first case of formation of a RNA parallel triplex with purine motif and shows that this type of targeting RNA strands to viral RNA duplexes can be used as an alternative to antisense oligonucleotides or ribozymes.

* To whom correspondence should be addressed. Tel: +34 91 5616800; Fax: +34 91 5645557; Email: p.carmona{at}iem.cfmac.csic.es


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