RNA-binding proteins are involved in the regulation of many
aspects of eukaryotic gene expression. Targeted interference
with RNA–protein interactions could offer novel approaches
to modulation of expression profiles, alteration of developmental
pathways, and reversal of certain disease processes. Here we
investigate a decoy strategy for the study of the αCP subgroup
of KH-domain RNA-binding proteins. These poly(C)-binding proteins
have been implicated in a wide spectrum of posttranscriptional
controls. Three categories of RNA decoys to αCPs were studied:
poly(C) homopolymers, native mRNA-binding sites, and a
high-affinity structure selected from a combinatorial library.
Native chemistry was found to be essential for αCP decoy
action. Because αCP proteins are found in both the nucleus
and cytoplasm, decoy cassettes were incorporated within both
nuclear (U1 snRNA) and cytoplasmic (VA1 RNA) RNA frameworks.
Several sequences demonstrated optimal decoy properties when
assayed for protein-binding and decoy bioactivity in vitro.
A subset of these transcripts was shown to mediate targeted
inhibition of αCP-dependent translation when expressed in
either the nucleus or cytoplasm of transfected cells.
Significantly, these studies establish the feasibility of
developing RNA decoys that can selectively target biologic
functions of abundant and widely expressed RNA binding proteins.