title: Binding of oligonucleotides to a viral hairpin forming RNA triplexes with parallel G*G*C triplets.
abstract: 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.
authors.affiliation: Instituto de Estructura de la Materia (CSIC), Serrano 121, 28006 Madrid, Spain. p.carmona@iem.cfmac.csic.es
authors.forename: Pedro
authors.initials: P
authors.lastname: Carmona
authors.forename: Marina
authors.initials: M
authors.lastname: Molina
mesh_terms: D001483:Base Sequence; D024202:Electrophoretic Mobility Shift Assay; D006526:Hepatitis C / Q000235:genetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009843:Oligoribonucleotides / Q000737:chemistry* / Q000378:metabolism*; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism*; D013055:Spectrophotometry, Infrared; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
chemical_list: D009843:Oligoribonucleotides; D012367:RNA, Viral