^1H NMR studies of the high-affinity Rev binding site of the Rev responsive element of HIV-1 mRNA: base pairing in the core binding element
^lH NMR studies of a 30-nucleotide RNA oligonucleotide (RBE3), which contains a highaffinity binding site for Rev of the HIV-1 Rev responsive element (RRE), two derivatives of RBE3 (RBE3AA and RBE3-A), and the complex of RBE3 with peptides derived from the RNA binding domain of HIV-1 Rev, are presented. The high-affinity binding site of the RRE consists of an asymmetric internal loop and surrounding Watson-Crick base pairs. In the wild-type RRE, one of the stems is closed by a loop; this is replaced in REB3 by the stable UUCG tetraloop. NOE data suggest that the internal loop of the free RNA contains structural features that have been predicted on the basis of in vitro selection experiments [Bartel, D. P., et al. (1991) Cell 67, 529-5361, The structural features include a G_(syn)-G_(anti) base pair, a G_(anti),-A_(anti) base pair, and a looped out U. When the Rev peptide is bound to the RNA, the base pairs in the internal loop appear to be stabilized, although the RNA chemical shifts indicate that the RNA conformation undergoes some changes when bound by Rev peptide.
© 1994 American Chemical Society. Published in print 10 May 1994. This work was supported by NIH Grant PO1 GM 39558 and NSF Presidential Young Investigator Award DMB 89-58280 with matching funds from AmGen Inc., DuPont/Merck Pharmaceuticals, Monsanto Co., and Sterling Drug Inc. (J.F.), by NIH Predoctoral Training Grant GM 07185 (R.D.P.),and by Hoechst AG (D.P.B. and J.W.S.).