Dissection of the Proposed Base Triple in Human Immunodeficiency Virus TAR RNA Indicates the Importance of the Hoogsteen Interaction

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Abstract
A single arginine residue within the RNA-binding domain of the human immunodeficiency virus Tat protein makes a critical sequence-specific contact to TAR RNA. Arginine as the free amino acid also binds specifically to TAR and induces a change in RNA conformation similar to that induced by Tat peptides. NMR and biochemical studies have suggested that the arginine-binding site is stabilized by a base triple interaction between a bulged U and an A·U base pair in the adjacent stem. In this study, we have used chemical modification and mutagenesis experiments to examine the relative contributions of the Watson−Crick and Hoogsteen base-pairing partners of the proposed U-A·U base triple. We show that the Hoogsteen interaction is critical for arginine binding whereas the Watson−Crick interaction can be eliminated or replaced by other base−base interactions. The results are consistent with biochemical studies of the Tat−TAR interaction and support the base triple model for the structure of TAR.