RNA aptamer binding theophylline with 10,000-fold selectivity over caffeine
The theophylline RNA aptamer is a 32-nucleotide RNA selected in vitro for high-affinity binding to the bronchodilator theophylline. It binds its ligand with a dissociation constant near 0.1 µM while discriminating against caffeine, which differs only by a single methyl group at N-7, by roughly 10,000-fold, among the highest levels of small-molecule discrimination achieved by a nucleic acid. The binding pocket is formed by two interacting internal loops that assemble a sandwich of three base triples, locking the ligand in place through an interlocking network of hydrogen bonds and stacking interactions, together with an adenosine platform and a reversed sugar. Because ligand binding drives a large and well-defined conformational change, the aptamer has become the default small-molecule sensing module for engineered riboswitches, and has been used to place translation initiation, transcription and splicing under the control of an inexpensive, cell-permeable ligand in both bacterial and eukaryotic systems.
Applications:
1) Jenison, R.D., Gill, S.C., Pardi, A., & Polisky, B. (1994). High-resolution molecular discrimination by RNA. Science, 263(5152), 1425-1429
2) Zimmermann, G.R., Jenison, R.D., Wick, C.L., Simorre, J.P., & Pardi, A. (1997). Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nature Structural Biology, 4(8), 644-649
3) Suess, B., Fink, B., Berens, C., Stentz, R., & Hillen, W. (2004). A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Research, 32(4), 1610-1614
4) Suess, B. (2005). Engineered riboswitches control gene expression by small molecules. Biochemical Society Transactions, 33(Pt 3), 474-476
5) RCSB PDB structure file: 1EHT
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