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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 > RNA folding and dynamics

Biological functions of RNA such as small molecule recognition and catalysis require that RNAs fold into complex three-dimensional structures that are specified by their sequences. Moreover, different moieties of these folded structures sample a variety of conformations at diverse timescales. Crystallographic studies elucidate the folded conformations of RNAs, and can indirectly provide information on dynamics. For instance, comparison of structures of the domains of the hairpin ribozyme free and docked demonstrated that this RNA undergoes dramatic rearrangements upon assembly. Yet, its active site is remarkably rigid once assembled. Structural, biochemical and in vitro evolution studies of flexizyme suggest that this artificial ribozyme takes advantage of flexibility to achieve higher substrate specificity through induced fit. Examination of riboswitches bound to diverse ligands indicates that the conformation and stability of these gene-regulatory RNAs are modulated by the small molecules. Direct examination of folding and flexibility by small-angle X-ray scattering confirms this.

• Baird, N.J., & Ferré-D'Amaré, A.R. Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 19, 167-176 (2013). [abstract]

• Baird, N.J. & Ferré-D'Amaré, A.R. Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis. RNA 16, 598-609 (2010). [abstract]

• Xiao, H., Murakami, H., Suga, H. & Ferré-D'Amaré, A.R. Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 454, 358-361 (2008). [abstract]

• Klein, D.J., Been, M.D. & Ferré-D'Amaré, A.R. Essential role of an active-site guanine in glmS ribozyme catalysis. J. Am. Chem. Soc. 129, 14858-14859 (2007). [abstract]

• Rupert, P.B. & Ferré-D’Amaré, A.R. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410, 780-786 (2001). [abstract]