Dissection of the proposed base triple in human immunodeficiency virus TAR RNA indicates the importance of the Hoogsteen interaction.
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 x 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 x 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.
Tao
J
J
Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, USA.
Chen
L
L
Frankel
A D
AD
D001120:Arginine / Q000378:metabolism; D001665:Binding Sites; D015696:Gene Products, tat / Q000378:metabolism*; D016325:HIV Long Terminal Repeat; D015497:HIV-1; D006834:Hydrazines / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D008956:Models, Chemical; D016296:Mutagenesis; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification; D012260:Ribonucleases / Q000378:metabolism; D054322:tat Gene Products, Human Immunodeficiency Virus
D015696:Gene Products, tat; D006834:Hydrazines; D012367:RNA, Viral; D054322:tat Gene Products, Human Immunodeficiency Virus; C029424:hydrazine; D001120:Arginine; D012260:Ribonucleases