BINDING OF NEOMYCIN TO THE TAR ELEMENT OF HIV-1 RNA INDUCES DISSOCIATION OF TAT PROTEIN BY AN ALLOSTERIC MECHANISM

Neomycin inhibits the binding of Tat-derived peptides to the trans-act ivating region (TAR) of HIV-1 RNA. Kinetic studies reveal that neomyci n acts as a noncompetitive inhibitor that can bind to the Tat-TAR comp lex and increase the rate constant (k(off)) for dissociation of the pe ptide from the RNA. Neomycin effects a conformational change in the st ructure of TAR that can be detected by circular dichroism spectroscopy , The increase in ellipticity measured at 265 nm upon binding of the a minoglycoside is opposite to the decrease seen when Tar peptides bind to the RNA. Thus, the structural transition induced by neomycin is app arently incompatible with the binding of Tat and underlies the inhibit ory action of the antibiotic. The binding site for neomycin on TAR was identified in ribonuclease protection experiments and is located in t he stem immediately below the three-nucleotide bulge that serves as th e primary identity element for Tat. Apparent protection of residues in the bulge by neomycin may represent additional contacts to the aminog lycoside, but more likely result from changes in the structure of this region when the ligand binds to the RNA. Binding assays using variant s of TAR in which inosine residues were substituted for guanosine resi dues support the results from the ribonuclease protection experiments. Inosine substitutions in the lower stem, but not the upper stem, decr ease the binding constant for neomycin by approximately 100-fold. Neit her of these variants affected the binding affinity of Tar peptide. In addition, these latter experiments suggest that the aminoglycoside ma y be located in the minor groove of the stem. This mode of association may be a critical aspect of neomycin's ability to bind to the Tat-TAR complex and could serve as a guide for the design of other drugs that bind to specific RNA targets as noncompetitive inhibitors.