HIV-1 TAR RNA recognition by an unnatural biopolymer

A tat-derived oligocarbamate containing the basic-arginine-rich region of full length Tat protein has been derived by solid phase peptide synthesis methods. After HPLC purification and characterization by mass spectrometry, the oligocarbamate was tested for TAR RNA binding. The tat-derived oligocarbamate binded well with TAR RNA. To compare the RNA-binding affinities of the oligocarbamate to natural peptide, a tat-derived peptide containing the RNA-binding domain of Tat protein was synthesized. Dissociation constants of the Tat peptide-RNA complexes were determined from multiple sets of experiments under the same conditions used for oligocarbamate-TAR RNA complexes. Overall, the results show that a small tat-derived oligocarbamate binds TAR RNA specifically and interacts in the widened major groove of TAR RNA.