Libraries of multifunctional RNA conjugates for the selection of new RNA catalysts.

An in vitro selection system was developed for the selection of RNA molecules catalyzing bimolecular reactions between small reactants. The system is based on the direct selection protocol and involves libraries of multifunctional RNA conjugates rather than unmodified RNA transcripts. For the preparation of RNA conjugate libraries, a dinucleotide analog has been designed and synthesized containing a poly(ethylene glycol) linker with an embedded photocleavage site and a terminal attachment site for coupling potential reactants. Reactants are first coupled to the dinucleotide analog by activated ester chemistry and then ligated to the 3'-ends of enzymatically prepared RNA pool molecules, giving libraries of complex conjugates. Species that become attached to biotin on incubation with a biotinylated partner are isolated using streptavidin-derivatized matrices and then subjected to a photocleavage step. Selective cleavage of the linker releases only those RNA species in which reaction has taken place at the linker-coupled reactant, while products with the biotin attached to internal positions of the RNA part remain immobilized. Efficient photocleavage is achieved by laser irradiation at 355 nm, and the released RNAs are intact and amplifiable by reverse transcription. All steps are shown to be compatible with the overall selection procedure, as was shown by performing a model selection cycle. Besides allowing a broader scope of reaction types to be selected for, the strategy relieves the RNA from the requirement to possess substrate properties as well as catalytic activity, and the use of a cleavable linker will suppress the selection of catalysts for side reactions.