A Novel Solid-Phase Assembly for Identifying Potent and Selective RNA Ligands

Nathan W. Luedtke and Yitzhak Tor


Replication of the human immunodeficiency virus (HIV-1) requires an ordered pattern of viral gene expression. This process is dependent upon the association of Rev, an essential viral regulatory protein, with its respective RNA binding site, the Rev-response-element (RRE). Small molecules that specifically bind the RRE and preclude or competitively displace the Rev protein are therefore promising antiviral candidates. New approaches that allow the rapid determination of both the RNA affinity and specificity of small molecules will assist in the discovery of new lead compounds and advance the understanding of RNA recognition. To this end, we report the assembly of an immobilized RNA-protein complex and demonstrate its application to the discovery and characterization of new RNA binders. We have developed an assay that identifies small molecules that specifically interfere with Rev-RRE binding. To examine the versatility of the assembly-based assay the competitive binding of polycyclic aromatic amidines to the RRE has also been examined. This family of ligands is more potent than aminoglycosides. Their previously reported trend in RRE affinity is again accurately reproduced. A tenfold increase in IC50 values in the presence of competing DNA indicates that these compounds also have a relatively high affinity for double-stranded DNA. This result clearly illustrates how the observed potency of an inhibitor is influenced by its selectivity.  Both selectivity and affinity are crucial for the design and evaluation of new RNA-protein inhibitors.

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