High-Resolution Molecular Discrimination by RNA

TLDR

RNA aptamers with high affinity for theophylline were selected from an oligonucleotide library. The selected RNA binds theophylline with a 0.1 µM dissociation constant—10,000 times tighter than for caffeine—exhibits a ligand‑induced conformational change, and its specificity is defined by structural features revealed by related compound studies, demonstrating RNA’s capacity for extreme ligand discrimination.

Abstract

Species of RNA that bind with high affinity and specificity to the bronchodilator theophylline were identified by selection from an oligonucleotide library. One RNA molecule binds to theophylline with a dissociation constant Kd of 0.1 μM. This binding affinity is 10,000-fold greater than the RNA molecule's affinity for caffeine, which differs from theophylline only by a methyl group at nitrogen atom N-7. Analysis by nuclear magnetic resonance indicates that this RNA molecule undergoes a significant change in its conformation or dynamics upon theophylline binding. Binding studies of compounds chemically related to theophylline have revealed structural features required for the observed binding specificity. These results demonstrate the ability of RNA molecules to exhibit an extremely high degree of ligand recognition and discrimination.