title: Selection and characterization of anti-NF-kappaB p65 RNA aptamers.
abstract: NF-kappaB transcription factors include a group of five mammalian proteins that form hetero- or homodimers and regulate hundreds of target genes involved in acute inflammation, HIV-1 transcription activation, and resistance to cancer therapy. We previously used in vitro selection to develop a small RNA aptamer (anti-p50) that binds the DNA-binding domain of NF-kappaB p50(2) with low nanomolar affinity but does not bind NF-kappaB p65(2). Here, we report the in vitro selection of anti-NF-kappaB p65 RNA aptamers using parallel in vitro selections with either a fully randomized RNA library or a degenerate RNA library based on the primary sequence of the 31-nucleotide anti-p50 RNA aptamer. We report the characterization of these aptamers with respect to NF-kappaB target specificity, affinity, minimal sequence requirements, secondary structure, and competition with DNA kappaB sites. These results expand opportunities for artificial inhibition of NF-kappaB transcription factor dimers containing p65 subunits.
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.
authors.forename: Susan E
authors.initials: SE
authors.lastname: Wurster
authors.forename: L James
authors.initials: LJ
authors.lastname: Maher
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000302:isolation & purification / Q000494:pharmacology; D001483:Base Sequence; D019281:Dimerization; D006801:Humans; D008024:Ligands; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D012313:RNA / Q000737:chemistry* / Q000302:isolation & purification / Q000494:pharmacology; D016415:Sequence Alignment; D051996:Transcription Factor RelA / Q000037:antagonists & inhibitors* / Q000737:chemistry
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D051996:Transcription Factor RelA; D012313:RNA