NMR spectroscopy revealed that upon arginine binding, the HIV-1 TAR RNA bulge changes conformation to form a base-triple interaction stabilizing hydrogen bonding.
The study demonstrates that specificity in the arginine-TAR interaction is largely derived from the RNA structure, providing structural insights into HIV-1 viral protein binding.
The messenger RNAs of human immunodeficiency virus-1 (HIV-1) have an RNA hairpin structure, TAR, at their 5' ends that contains a six-nucleotide loop and a three-nucleotide bulge. The conformations of TAR RNA and of TAR with an arginine analog specifically bound at the binding site for the viral protein, Tat, were characterized by nuclear magnetic resonance (NMR) spectroscopy. Upon arginine binding, the bulge changes conformation, and essential nucleotides for binding, U23 and A27.U38, form a base-triple interaction that stabilizes arginine hydrogen bonding to G26 and phosphates. Specificity in the arginine-TAR interaction appears to be derived largely from the structure of the RNA.
Puglisi et al. (1992) studied HIV-1. Arginine analog vs. Unbound TAR RNA was evaluated on Conformational changes. NMR spectroscopy revealed that upon arginine binding, the HIV-1 TAR RNA bulge changes conformation to form a base-triple interaction stabilizing hydrogen bonding.