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Updated: Aug 31, 2026

Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example
Published on: December 3, 2014
Structure-inhibition analysis of RNA aptamers that bind to HCV IRES
Kunio Kikuchi1, Takuya Umehara, Kotaro Fukuda
1Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba 305-8566, Japan.
Abstract:
The translation of HCV starts at the internal ribosomal entry site (IRES) within the 5' untranslated region and IRES is well-conserved in HCV strains. We developed a novel selection strategy using biotinylated oligonucleotide probe and obtained RNA aptamers that bind HCV IRES domain II and domain III-IV, respectively. Selected aptamers specifically bound to target sequence via RNA-RNA interactions. These aptamers inhibited IRES-depend translation in vitro. Especially, 3-07 aptamer, which bound domain IIId, showed strong inhibition. Structure/function relationship of these aptamers was analyzed by mutagenesis, RNase mapping and binding kinetics.
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