title: Characterisation of antibody-binding RNAs selected from structurally constrained libraries.
abstract: Constrained RNA libraries of limited sequence complexity were constructed and used to select RNA molecules binding to the antigen binding site of an anti-ferritin antibody. The sequences required as primer-binding sites for the selection cycle were designed to form a predictable secondary structure, which greatly facilitated the characterisation of the secondary structures of the selected RNAs. RNA-antibody interactions were studied by real-time interaction analysis to study the dynamic aspects of binding and by circular dichroism spectroscopy to search for conformational changes upon binding. The selected RNAs were analysed with a binding site sequestering assay and were shown to compete with ferritin for binding to the antigen-binding site. The experiments described here indicate that the introduction of strong structural constraints does not have to interfere with the ability to select tightly and specifically binding RNA-molecules.
authors.affiliation: Istituto di Ricerche di Biologia Molecolare, Roma, Italy.
authors.forename: J
authors.initials: J
authors.lastname: Hamm
mesh_terms: D000906:Antibodies / Q000276:immunology / Q000378:metabolism*; D001483:Base Sequence; D001666:Binding Sites, Antibody; D001667:Binding, Competitive; D017931:DNA Primers; D005293:Ferritins / Q000276:immunology* / Q000378:metabolism; D015723:Gene Library; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D013329:Structure-Activity Relationship
chemical_list: D000906:Antibodies; D017931:DNA Primers; D012313:RNA; D005293:Ferritins