Selection and characterization of peptides specifically binding to HIV-1 psi (ψ) RNA

The packaging of HIV genomic RNA is mediated by a specific interaction between a nucleocapsid (NC) protein and packaging signal (psi, ψ) RNA sequence. However, this interaction can be inhibited by the presence of peptides or proteins that specifically bind to the ψ sequence. The 125-base-long ψ RNA comprises a specific secondary structure that can be recognized by certain peptide sequences. Accordingly, the current study presents a method for selecting such peptides from a phage-displayed peptide library and characterization of resulting peptides in vitro. The RNA was covalently immobilized in a Covalink module using a carbodiimide condensation reaction at its 5′-end, leaving the proper secondary structure exposed and readily accessible. A phage display random peptide library was then screened against the RNA structure, and after five rounds of biopanning, enriched peptide sequences and conserved amino acid frames appeared. One of the enriched peptides was tested and shown to bind to ψ RNA in a dose-dependent manner, plus it competed effectively with the NC protein as regards binding with the target RNA.