STRUCTURE OF HIV-1 TAB RNA IN THE ABSENCE OF LIGANDS REVEALS A NOVEL CONFORMATION OF THE TRINUCLEOTIDE BULGE

Efficient transcription from the human immuno-deficiency virus (HIV) p romoter depends on binding of the viral regulatory protein Tat to a ci s-acting RNA regulatory element, TAR, Tat binds at a trinucleotide bul ge located near the apex of the TAR stem-loop structure, An essential feature of Tat-TAR interaction is that the protein induces a conformat ional change in TAR that repositions the functional groups on the base s and the phosphate backbone that are critical for specific intermolec ular recognition of TAR RNA. We have previously determined a high reso lution structure for the bound form of TAR RNA using heteronuclear NMR , Here, we describe a high resolution structure of the free TAR RNA ba sed on 871 experimentally determined restraints. In the free TAR RNA, bulged residues U23 and C24 are stacked within the helix, while U25 is looped out, This creates a major distortion of the phosphate backbone between C24 and G26. In contrast, in the bound TAR RNA, each of the t hree residues from the bulge are looped out of the helix and U23 is dr awn into proximity with G26 through contacts with an arginine residue that is inserted between the two bases, Thus, TAR RNA undergoes a tran sition from a structure with an open and accessible major groove to a much more tightly packed structure that is folded around basic side ch ains emanating from the Tat protein.