title: In vitro selection of RNAs that bind to the human immunodeficiency virus type-1 gag polyprotein.
abstract: RNA ligands that bind to the human immunodeficiency virus type-1 (HIV-1) gag polyprotein with 10(-9) M affinity were isolated from a complex pool of RNAs using an in vitro selection method. The ligands bind to two different regions within gag, either to the matrix protein or to the nucleocapsid protein. Binding of a matrix ligand to gag did not interfere with the binding of a nucleocapsid ligand, and binding of a nucleocapsid ligand to gag did not interfere with the binding of a matrix ligand. However, binding of a nucleocapsid ligand to gag did interfere with binding of an RNA containing the HIV-1 RNA packaging element (psi), even though the sequence of the nucleocapsid ligand is not similar topsi. The minimal sequences required for the ligands to bind to matrix or nucleocapsid were determined. Minimal nucleocapsid ligands are predicted to form a stem-loop structure that has a self-complementary sequence at one end. Minimal matrix ligands are predicted to form a different stem-loop structure that has a CAARU loop sequence. The properties of these RNA ligands may provide tools for studying RNA interactions with matrix and nucleocapsid, and a novel method for inhibiting HIV replication.
authors.affiliation: NeXstar Pharmaceuticals, Inc., 2860 Wilderness Place, Boulder, CO 80301, USA. mlochrie@nexstar.com
authors.forename: M A
authors.initials: MA
authors.lastname: Lochrie
authors.forename: S
authors.initials: S
authors.lastname: Waugh
authors.forename: D G
authors.initials: DG
authors.lastname: Pratt
authors.forename: J
authors.initials: J
authors.lastname: Clever
authors.forename: T G
authors.initials: TG
authors.lastname: Parslow
authors.forename: B
authors.initials: B
authors.lastname: Polisky
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D002213:Capsid / Q000235:genetics / Q000378:metabolism; D036022:Capsid Proteins; D015683:Gene Products, gag / Q000235:genetics / Q000378:metabolism*; D015497:HIV-1 / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008024:Ligands; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D019251:Nucleocapsid / Q000378:metabolism; D019590:Nucleocapsid Proteins; D011498:Protein Precursors / Q000235:genetics / Q000378:metabolism; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D012313:RNA / Q000378:metabolism*; D011993:Recombinant Fusion Proteins / Q000235:genetics / Q000378:metabolism; D013329:Structure-Activity Relationship; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus
chemical_list: D036022:Capsid Proteins; D015683:Gene Products, gag; D008024:Ligands; C071884:NCP7 protein, Human immunodeficiency virus 1; D019590:Nucleocapsid Proteins; D011498:Protein Precursors; D011506:Proteins; D011993:Recombinant Fusion Proteins; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus; C060295:p15 gag protein, Human immunodeficiency virus 1; C059767:p55 gag precursor protein, Human immunodeficiency virus 1; D012313:RNA