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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 analogs of GFP

Tens of thousands of small and large non-coding RNAs have been identified in the human transcriptome, and new molecular tools are urgently needed to analyze their synthesis and turnover, transport and localization. While green fluorescent protein (GFP) and its many derivatives can be used to tag cellular RNAs, such an approach suffers from the large size of the tag (often many times larger than the RNA of interest), cryptic localization signals in the protein, slow maturation of the intrinsic chromophre of the protein, and high background fluorescence due to unbound protein. Fluorescent RNA analogs of GFP offer a fundamentally different and promising approach to the in vivo analysis of non-coding RNAs. Our crystallographic characterization of Spinach, an in vitro selected RNA that when bound to its exogenous chromophore is brighter than GFP and can be used to visualize RNAs in live cells, revealed an unprecedented structure built around a G-quadruplex. We are employing structure-guided engineering approaches to optimize Spinach as well as other fluorescent RNAs that are analogs of, among others, yellow and red fluorescent proteins (YFP and RFP).

• Warner, K.D., Chen, M.C., Song, W., Strack, R.L., Thorn, A., Jaffrey, S.R., & Ferré-D'Amaré, A.R. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nature Struct. Mol. Biol. 21, 658-663 (2014). [abstract]

• Warner, K.D., Sjekloca, L., Song, W., Filonov, G.S., Jaffrey, S.R., & Ferré-D'Amaré, A.R. A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nature Chem. Biol. 13, 1195-1201 (2017).[abstract]

• Trachman, R.J. III, Demeshkina, N.A., Lau, M.W.L., Panchapakesan, S.S.S., Jeng, S.C.Y., Unrau, P.J., & Ferré-D'Amaré, A.R. Structural basis for high-affinity fluorophore binding and activation by RNA Mango. Nature Chem. Biol. 13, 807-813 (2017). [abstract]

• Trachman, R.J. III, Truong, L., & Ferré-D'Amaré, A.R. Structural principles of fluorescent RNA aptamers. Trends Pharacol. Sci. 38, 928-939 (2017). [abstract]