The variability of the peptide-binding specificity of RNA

Variants of the HIV Rev-response element (RRE) that bind to HIV Rev peptide or to RSG-1.2, a selected RRE-binding peptide, were selected using an in vivo assay system for RNA-polypeptide interactions. The selected RRE variants could be classified into three groups based on their specificity towards the Rev and RSG-1.2 peptide. The class I RRE variants showed specificities similar to wild-type RRE, while class II variants specifically bound RSG-1.2 peptide, and class III variants bound specifically to the Rev peptide. Examination of the class II and class III RNAs revealed distinct nucleotide and structural requirements in the upper stem region, and suggested that single nucleotide changes may dramatically alter the peptide-binding specificity of the RRE.