Selection and characterization of an RNA decoy for transcription factor NF-kappa B

Despite their chemical similarity, DNA and RNA sequences typically adopt very different structures within cells and are recognized by different proteins. However, a few interesting examples of proteins with dual specificity for DNA and RNA have previously been noted. These observations raise the possibility that RNA surrogates might be identified for many transcription factors that normally bind DNA. As an initial test of this novel concept, we used in vitro selection to isolate a small RNA aptamer that binds with nanomolar affinity to human transcription factor NF-kappa B, a key regulator of inflammation, HIV-1 gene expression, and apoptosis. Selected RNAs contain a 31-nucleotide core domain that was shown by mutation and deletion analyses to be necessary and sufficient for NF-kappa B binding. Neither DNA nor 2'-O-methyl RNA analogues of the aptamer bound NF-kappa B. The results of competition experiments demonstrate that binding of the RNA aptamer blocks the ability of NF-kappa B to bind duplex DNA. Expression of this aptamer structure within heterologous nuclear RNA transcripts may provide a new strategy to inhibit NF-kappa B function in vivo. Aptamers that inhibit transcription factors might be useful in a variety of applications.