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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 > Methods

New methods drive progress in the experimental sciences. In addition to the development of techniques for the synthesis and characterization of biological molecules, we have a long-standing interest in methods to enable the preparation of highly-ordered crystals of nucleic acids, proteins, and their complexes. These are key to their structure determination by X-ray crystallography. Important advances include domain elucidation by mass spectrometry, construct engineering to improve crystallizability, and pre-crystallization analysis of monodispersity. Another area of biomedical research where we have contributed new methods is in the analysis of in vitro selection experiments.

• Lau, M.W. & Ferré-D'Amaré, A.R. In vitro evolution of coenzyme-independent variants from the glmS ribozyme structural scaffold. Methods (2016). [abstract]

• Baird, N.J., Inglese, J., & Ferré-D'Amaré, A.R. Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes. Nature Comm. 6, 8898 (2015). [abstract]

• Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C. & Ferré-D'Amaré, A.R. Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem. Biol. 21, 591-595 (2014). [abstract]

• Zhang, J., & Ferré-D'Amaré, A.R. Dramatic improvement of crystals of large RNAs by cation replacement and dehydration. Structure 22, 1363-1371 (2014). [abstract]

• Pitt, J.N., Rajapakse, I., & Ferré-D'Amaré, A.R. SEWAL: an open-source platform for next-generation sequence analysis and visualization. Nucleic Acids Res. 38, 7908-7915 (2010). [abstract]