title: Selection and characterization of peptides specifically binding to HIV-1 psi (psi) RNA.
abstract: The packaging of HIV genomic RNA is mediated by a specific interaction between a nucleocapsid (NC) protein and packaging signal (psi, psi) RNA sequence. However, this interaction can be inhibited by the presence of peptides or proteins that specifically bind to the psi sequence. The 125-base-long psi 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 psi RNA in a dose-dependent manner, plus it competed effectively with the NC protein as regards binding with the target RNA.
authors.affiliation: Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yong-In, Kyung-Gi Do 449-791, Republic of Korea.
authors.forename: Mi Young
authors.initials: MY
authors.lastname: Park
authors.forename: Jiyeon
authors.initials: J
authors.lastname: Kwon
authors.forename: Sangyoon
authors.initials: S
authors.lastname: Lee
authors.forename: Jichang
authors.initials: J
authors.lastname: You
authors.forename: Heejoon
authors.initials: H
authors.lastname: Myung
mesh_terms: D015683:Gene Products, gag / Q000737:chemistry*; D016679:Genome, Viral; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics*; D009690:Nucleic Acid Conformation; D019251:Nucleocapsid / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D010446:Peptide Fragments / Q000378:metabolism; D019151:Peptide Library; D011485:Protein Binding; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D019065:Virus Assembly
chemical_list: D015683:Gene Products, gag; D010446:Peptide Fragments; D019151:Peptide Library; D012367:RNA, Viral