Structure-inhibition analysis of RNA aptamers that bind to HCV IRES | Zendy

Koji Kikuchi | Zendy; Tadashi Umehara | Zendy; K. Fukuda | Zendy; Jae Yeon Hwang | Zendy; Atsushi Kuno | Zendy; Takema Hasegawa | Zendy; Shin-Ichi Nishikawa | Zendy

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Structure-inhibition analysis of RNA aptamers that bind to HCV IRES

Author(s) -

Koji Kikuchi,

Tadashi Umehara,

K. Fukuda,

Jae Yeon Hwang,

Atsushi Kuno,

Takema Hasegawa,

Shin-Ichi Nishikawa

Publication year - 2003

Publication title -

nucleic acids symposium series

Language(s) - English

Resource type - Journals

eISSN - 1746-8272

pISSN - 0261-3166

DOI - 10.1093/nass/3.1.291

Subject(s) - internal ribosome entry site , aptamer , rna , ribosome , systematic evolution of ligands by exponential enrichment , biotinylation , rnase p , biology , oligonucleotide , untranslated region , microbiology and biotechnology , translation (biology) , virology , computational biology , chemistry , genetics , messenger rna , dna , gene

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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