In vivo recognition of an RNA aptamer by its transcription factor target

In vitro-selected RNA aptamers are potential inhibitors of disease-related macromolecules. Our laboratory previously isolated an RNA aptamer that specifically binds to the human transcription factor NF-kappaB. This RNA aptamer competitively inhibits DNA binding by NF-kappaB in vitro. In the study presented here, this aptamer was tested for binding to the p50 homodimer form of NF-kappaB (p50(2)) in eukaryotic cells using a yeast three-hybrid system. We show that the alpha-p50 RNA aptamer selectively binds recombinant p50(2) expressed in yeast, demonstrating in vivo recognition of an in vitro-selected RNA aptamer by its protein target. This result suggests that RNA decoys might be used to inhibit the function of DNA-binding proteins in vivo.