12 - Catalysis of Organic Reactions by RNA—Strategies for the Selection of Catalytic RNAs

Abstract

This chapter introduces the strategies for the selection of catalytic ribonucleic acid (RNAs). Systematic evolution of ligands by exponential enrichment (SELEX) is a powerful methodology for the identification of RNA or deoxyribonucleic acid (DNA) molecules with specific binding properties or catalytic activities. The most successful technique for the isolation of catalytically active species among the huge number of random sequences is direct selection. In this process, the catalytic properties of the desired molecule can be directly exploited for their iterative enrichment. SELEX with linker-coupled reactants is an improvement of direct selection, designed to expand the chemistry of RNA catalysis, to bimolecular reactions involving two small non-oligonucleotide substrates. Thereby, one of the potential reactants is site-specifically attached to the RNA pool molecules via a long flexible polymeric linker, while the other reactant carries an affinity tag, such as biotin. After reaction, the products are linked to both the RNA and the affinity tag, allowing isolation and amplification of functional species. The incorporation of a cleavage site in the linker gives additional control of the reaction site.