CHARACTERIZATION OF ANTIBODY-BINDING RNAS SELECTED FROM STRUCTURALLY CONSTRAINED LIBRARIES

Constrained RNA libraries of limited sequence complexity were construc ted and used to select RNA molecules binding to the antigen binding si te of an anti-ferritin antibody. The sequences required as primer-bind ing 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 interacti ons were studied by real-time interaction analysis to study the dynami c aspects of binding and by circular dichroism spectroscopy to search for conformational changes upon binding. The selected RNAs were analys ed with a binding site sequestering assay and were shown to compete wi th ferritin for binding to the antigen-binding site. The experiments d escribed here indicate that the introduction of strong structural cons traints does not have to interfere with the ability to select tightly and specifically binding RNA-molecules.