RNA Recognition by an Isolated a Helix

A 17 amino acid peptide containing the arginine-rich region of the HIV Rev protein binds specifically to Rev response element (RRE) RNA. Even though it is highly charged, the peptide forms an a helix in solution, but only when its Nand Ctermini are modified to provide favorable electrostatic interactions with the helix macrodipole. Binding aff inlty for IIB RNA (the primary binding site within the RRE) increases with a helix content, whereas nonspecific binding affinity is independent of helix content. Binding of mutant peptides demonstrates that one threonine, one asparagine, and four arginine side chains are important for sequence-specific recognition. Transactlvation of the HIV LTR using Tat-Rev peptide hybrids and the RRE 118 site indicates that the peptide adopts an a-helical conformation in vivo. The results suggest that interactions with the RNA backbone may help to orient the a helix in the major groove of RNA.