Apical loop-internal loop interactions: a new RNA-RNA recognition motif identified through in vitro selection against RNA hairpins of the hepatitis C virus mRNA.
We performed in vitro selection of oligoribonucleotides in order to identify high-affinity motifs recognizing RNA hairpins located at the 3' end (SL1) and at the 5' end (domain IV of the internal ribosome entry site) of the hepatitis C virus mRNA. We selected aptamers constituted by an internal loop complementary to the SL1 apical loop, flanked by G-C-rich double-stranded regions, able to form complexes with a K(d) of 70 nM, at 37 degrees C under ionic conditions close to intracellular ones. The complex involves selective apical loop (SL1)-internal loop (aptamer) interactions. Similar structurally organized aptamers were independently identified against domain IV and were shown to also give rise to such complexes. Apical loop-internal loop interaction could constitute a new recognition motif allowing specific intra- or intermolecular RNA-RNA association.
Aldaz-Carroll
Lydia
L
INSERM U386, Université Victor Segalen, 146 rue Léo-Saignat, 33076 Bordeaux, France.
Tallet
Béatrice
B
Dausse
Eric
E
Yurchenko
Ludmila
L
Toulmé
Jean-Jacques
JJ
D001483:Base Sequence; D024202:Electrophoretic Mobility Shift Assay; D016174:Hepacivirus / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020038:RNA, Spliced Leader / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012260:Ribonucleases / Q000378:metabolism
D009843:Oligoribonucleotides; D012333:RNA, Messenger; D020038:RNA, Spliced Leader; D012367:RNA, Viral; D012260:Ribonucleases