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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.

Original publication

DOI

10.1016/S0006-291X(02)00308-X

Type

Journal article

Journal

Biochem Biophys Res Commun

Publication Date

10/05/2002

Volume

293

Pages

924 - 931

Keywords

Animals, Anti-HIV Agents, Base Sequence, Binding Sites, Cricetinae, DNA Footprinting, HIV Envelope Protein gp120, HIV-1, Kinetics, Molecular Sequence Data, Nucleic Acid Conformation, Oligoribonucleotides, RNA, Sequence Alignment, Tumor Cells, Cultured