Schematic representation of aminoglycoside-arginine conjugate (AAC) binding sites on TAR RNA

[From: A. Litovchick, A. G. Evdokimov, and A. Lapidot, "Aminoglycoside-Arginine Conjugates That Bind TAR RNA: Synthesis, Characterization, and Antiviral Activity", Biochemistry 39, 2838-2852 (2000). ]

The NMR average structure of TAR RNA complex with arginine amide was obtained from the Protein Data Bank, access code 1arj. Only the nucleic acid chain is presented.

• Nucleotides highlighted in red represent high-affinity binding sites for AAC and Tat peptide. Binding of AAC to this site is not inhibited by excess tRNA.
• Nucleotides highlighted in blue represent low-affinity binding sites for AAC and aminoglycosides (e.g., neomycin B). Binding of AAC to this site is inhibited by a 10-fold excess of tRNA.
• Nucleotides highlighted in yellow represent sites of major conformational changes induced by AAC binding to TAR. These positions are cleaved by RNase A in the TAR-AAC complex, but are not cleaved in the absence of AAC.
• Small green balls represent proposed Mg²⁺ and Ca²⁺ binding sites.
• The big yellow ball represents the UO₂ ²⁺ binding site.

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