Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B

finding of human immunodeficiency virus type 1 (HIV-I) transactivator (Tat) protein to Tat-responsive RNA (TAR) is essential for viral replication and is considered a promising starting point for the design of anti-HIV drugs. NMR spectroscopy indicated that the aminoglycosides neomycin B and ribosta mycin bind to TAR and that neomycin is able to inhibit Tat binding to TAR. The solution structure of the neomycin-bound TAR has been determined by NMR spectroscopy. Chemical shift mapping and intermolecular nuclear Overhauser effects define the binding region of the aminoglycosides on TAR and give s trong evidence for minor groove binding. Based on 15 nuclear Overhauser eff ect-derived intermolecular distance restraints, a model structure of the TA R-neomycin complex was calculated. Neomycin is bound in a binding pocket fo rmed by the minor groove of the lower stem and the uridine-rich bulge of TA R, which adopts a conformation different from those known. The neamine core of the aminoglycoside (rings I and II) is covered with the bulge, explaini ng the inhibition of Tat by an allosteric mechanism. Neomycin reduces the v olume of the major groove in which Tat is bound and thus impedes essential protein-RNA contacts.