Laboratory of Nucleic Acids

The Laboratory of Nucleic Acids studies RNA molecules in their many guises. Led by Dr. Adrian R. Ferr-D'Amare, the lab employs fundamental biophysical approaches to understanding the function of non-coding RNAs, and seeks to leverage this knowledge for the development of new therapeutics and biotechnological tools.

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Methods

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]

Featured Publications

Real-time monitoring of single ZTP riboswitches reveals a complex and kinetically controlled decision landscape.

Authors: Hua B, Jones CP, Mitra J, Murray PJ, Rosenthal R, Ferré-D'Amaré AR, Ha T.
Nat Commun. 2020 Sep 10;11(1):4531
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Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design.

Authors: Tran B, Pichling P, Tenney L, Connelly CM, Moon MH, Ferré-D'Amaré AR, Schneekloth JS Jr, Jones CP.
Cell Chem Biol. 2020 Aug 10;S2451-9456(20):30294-4
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Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair.

Authors: Trachman RJ 3rd, Cojocaru R, Wu D, Piszczek G, Ryckelynck M, Unrau PJ, Ferré-D'Amaré AR.
Structure. 2020 Jul 07;28(7):776-785
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Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers.

Authors: Trachman RJ, Ferré-D'Amaré AR.
Q Rev Biophys. 2019 Aug 19;52:e8
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Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence.

Authors: Sjekloća L, Ferré-D'Amaré AR.
Cell Chem Biol. 2019 Aug 15;26(8):1374-1386
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Meet the Team

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Adrian Ferré-D'Amaré, Ph.D.

Senior Investigator

Adrian R. Ferré-D'Amaré graduated from the Instituto Tecnológico y de Estudios Superiores de Monterrey in Mexico in 1990 with a B.S. in chemistry. He earned a Ph.D. in molecular biophysics from The Rockefeller University in 1995. He was a Jane Coffin Childs postdoctoral fellow at Yale University from 1995 to 1999. Dr. Ferré-D'Amaré was a Member of the Fred Hutchinson Cancer Research Center and an Affiliate Professor of Biochemistry at the University of Washington, Seattle, from 1999 to 2011. He was also an Investigator of the Howard Hughes Medical Institute (HHMI) from 2008 to 2011. He resigned from HHMI and joined the NHLBI in 2011 as a Senior Investigator and Chief of the Laboratory of RNA Biophysics and Cellular Physiology. Dr. Ferré-D'Amaré was a Rita Allen Foundation Scholar from 2001 to 2004, received the Eli Lilly and Company Research Award from the American Society for Microbiology in 2004 and was a Distinguished Young Scholar in Medical Research of the W.M. Keck Foundation from 2003 to 2008. Dr. Ferré-D'Amaré has authored or coauthored more than 100 papers. He is on the editorial board of the journal RNA and has served on many review panels for the National Institutes of Health, the National Science Foundation, as well as foreign and international scientific organizations.

michael

Michael Banco, Ph.D.

Postdoctoral Fellow
robert

Robert Trachman III, Ph.D.

Postdoctoral Fellow
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Luiz Passalacqua

Postdoctoral Fellow
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Patrick Pichling, Ph.D.

Postdoctoral Fellow
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Emily Roney

Postbaccalaureate FEllow
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