We have published a preliminary model of the HIV TAR RNA in complex with argininamide. However, several features of this RNA are poorly resolved. The wild-type TAR RNA has a three nucleotide bulge (UCU) that is critical for formation of the correct structure such that the HIV tat protein can bind. A naturally occurring TAR variant has a two nucleotide (UU) bulge, and we have prepared this RNA for structural characterization. It binds to argininamide somewhat more tightly than the UCU bulge TAR, and we observe several new inter- and intramolecular NOEs in the bulge region. After collecting a huge number of 2D-, 3D-, and 4D- data sets on 13C-labeled RNA, and 15N-labeled RNA, we have obtained a large number of distance constraints. There are over 700 NOEs that define the structure of this 30 nucleotide RNA, including 20 intermolecular NOEs to the argininamide ligand. Preliminary structure calculations reveal a geometry consistent with the preliminary picture, but a considerably higher resolution will result from these studies. Structure calculations are in progress.
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