Determinants of apical loop-internal loop RNA-RNA interactions involving the HCV IRES.
Domain II of the hepatitis C virus internal ribosome entry site is a major RNA structure involved in the viral mRNA translation. It comprises four different structural domains. We performed in vitro selection against the apical loop of the domain II and we identified RNA aptamers folding as an imperfect hairpin with an internal loop of interacting with the apical loop of the domain II. This RNA-RNA interaction creates apical loop-internal loop complex. The aptamer binds the target with an apparent K(d) of 35nM. In this study, the main structural elements of the target and the aptamer involved in the formation of the complex are characterized by mutation, deletion, and RNase probing analysis. We demonstrate that a complementary loop flanked by G,C rich upper and lower stems are crucial for such RNA-RNA interactions.
Da Rocha Gomes
Sonia
S
INSERM U386, IFR 66, Université Victor Segalen Bordeaux 2, France and Institut Européen de Chimie et Biologie, Pessac, France.
Dausse
Eric
E
Toulmé
Jean-Jacques
JJ
D001483:Base Sequence; D001665:Binding Sites; D016174:Hepacivirus / Q000235:genetics*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D012260:Ribonucleases; D012270:Ribosomes / Q000821:virology
D012333:RNA, Messenger; D012367:RNA, Viral; D012260:Ribonucleases