title: Structural characterization of a 2'F-RNA aptamer that binds a HIV-1 SU glycoprotein, gp120.
abstract: Here we describe the isolation of specific 2'F-substituted RNA ligands for the SU glycoprotein, gp120, of HIV-1 strain HXB2. These aptamers bind the target protein with an affinity of the order of 10(-7) M. Binding was specific to SU glycoprotein and directed to a non-neutralizing epitope that was not shared with the related strain, HIV-1(BaL). The structure of one aptamer was defined by a combination of deletion analysis and enzymatic probing studies, revealing a 42 nt minimal element comprising a three-helix junction that retained the binding affinity of the parental sequence. Interestingly, binding to SU glycoprotein was accompanied by structural changes in the aptamer that stabilized the weakest of the 3 helices.
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
authors.forename: N
authors.initials: N
authors.lastname: Sayer
authors.forename: J
authors.initials: J
authors.lastname: Ibrahim
authors.forename: K
authors.initials: K
authors.lastname: Turner
authors.forename: A
authors.initials: A
authors.lastname: Tahiri-Alaoui
authors.forename: W
authors.initials: W
authors.lastname: James
mesh_terms: D000818:Animals; D019380:Anti-HIV Agents / Q000737:chemistry* / Q000378:metabolism* / Q000494:pharmacology; D001483:Base Sequence; D001665:Binding Sites; D006224:Cricetinae; D018983:DNA Footprinting; D015699:HIV Envelope Protein gp120 / Q000378:metabolism*; D015497:HIV-1; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry* / Q000378:metabolism* / Q000494:pharmacology; D012313:RNA / Q000737:chemistry; D016415:Sequence Alignment; D014407:Tumor Cells, Cultured
chemical_list: D019380:Anti-HIV Agents; D015699:HIV Envelope Protein gp120; D009843:Oligoribonucleotides; D012313:RNA