INTERACTING RNA SPECIES IDENTIFIED BY COMBINATORIAL SELECTION

RNA molecules were selected from a random sequence library for their a bility to bind to an RNA stem-loop target. Oligonucleotides with exten sive Watson-Crick complementarity to the RNA ligand were selected agai nst by inclusion of a blocking oligodeoxynucleotide in the binding pha se of the selection protocol. After 18 generations of SELEX (systemati c evolution of ligands by exponential enrichment) a single RNA family was predominant in the binding population. The winning aptamer RNA bou nd the target RNA with an apparent K-d = 70 nM. Structural mapping and Fe(II)-EDTA protection indicated that the target RNA interacted with small unpaired loops in the aptamer structure. (C) 1997 Elsevier Scien ce Ltd.