Key result
In vitro aptamers bind HCV mRNA hairpins with 70 nM affinity via selective loop interactions.
Why the study?
High-affinity RNA motifs recognizing hepatitis C virus mRNA hairpins at the 3' and 5' ends were not previously identified.
Effect estimate: Kd of 70 nM
Apical loop-internal loop interaction could constitute a new recognition motif allowing specific intra- or intermolecular RNA-RNA association.
May enable specific RNA aptamer design; leaves open in vivo efficacy and clinical translation.
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.
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Aldaz-Carroll et al. (2002) studied Hepatitis C virus mRNA. In vitro selection of oligoribonucleotides (aptamers) was evaluated on Complex formation and binding affinity (Kd) (Kd of 70 nM). In vitro selection identified aptamers that form complexes with Hepatitis C virus mRNA hairpins with a Kd of 70 nM via selective apical loop-internal loop interactions.
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