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Catalytic RNAs

Gene regulatory RNAs

RNA in signal transduction

RNA-protein interactions

RNA analogs of GFP

Small molecule recognition by RNA

RNA folding and dynamics

Molecular evolution



Ferré-D'Amaré Lab Research > Gene regulatory RNAs

Non-coding RNAs play diverse roles in the control of the flow of genetic information, cellular homeostasis and adaptation, and virulence. Riboswitches are non-coding mRNA domains that directly bind to cognate ligands and modulate transcription, translation or splicing. Riboswitches have been discovered in archaea, bacteria and eukarya. We have studied bacterial riboswitches that respond to the intracellular concentration of a variety of metabolites such as vitamin B1, glucosamine-6-phosphate, and preQ1, that respond to starvation for specific amino acids, and that sense the concentration of molecules responsible for intracellular signaling (second messengers) such as c-di-AMP, c-di-GMP, and ZMP. Riboswitches control essential metabolic and signaling pathways in pathogenic bacteria, and represent attractive targets for the development of novel antibiotics. Moreover, our studies have led to the discovery of general principles for the function of non-coding RNAs, including mechanisms for RNA:RNA recognition and the use of quaternary and pseudo-quaternary structure for specificity, cooperativity and allostery.

• Jones, C.P. & Ferré-D'Amaré, A.R. Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains. Nature Struct. Mol. Biol. 22, 679-685 (2015). [abstract]

• Jones, C.P., & Ferré-D'Amaré, A.R. RNA quaternary structure and global symmetry. Trends Biochem. Sci. 40, 211-220 (2015). [abstract]

• Zhang, J. & Ferré-D'Amaré, A.R. Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature 500, 363-366 (2013) [abstract]

• Zhang, J., Lau, M. & Ferré-D'Amaré, A.R. Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry 49, 9123-9131 (2010). [abstract]

• Klein, D.J., Edwards, T.E. & Ferré-D'Amaré, A.R. Cocrystal structure of a class-I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nature Struct. Mol. Biol. 16, 343-344 (2009). [abstract]