In a multi-way collaboration during the past year, we were the first to employ the ultrabright X-rays available from the free electron laser to perform a time-resolved binding study on an RNA. Our work on ligand binding by the adenine riboswitch captured, in atomic detail, the intermediates through which the RNA transits in order to achieve its ligand-bound, signaling conformation. This information will open the way to the structure-guided discovery and optimization of small molecules that target not the ground state of an RNA, but excited states. In this first study, ligand was simply diffused into the RNA nanocrystals employed for diffraction studies. Because of this, the time resolution of the experiment is of the order of several seconds. Future studies, utilizing photo-caged compounds, will allow time resolutions in the millisecond to microsecond range. For these studies, the ultrabright, femto-second resolution X-ray pulses available from the free electron laser will be essential.

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Budget End
Support Year
6
Fiscal Year
2017
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Indirect Cost
Name
U.S. National Heart Lung and Blood Inst
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Stagno, J R; Liu, Y; Bhandari, Y R et al. (2017) Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature 541:242-246
Baird, Nathan J; Inglese, James; Ferré-D'Amaré, Adrian R (2015) Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes. Nat Commun 6:8898
Baird, Nathan J; Ferré-D'Amaré, Adrian R (2014) Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). Methods Mol Biol 1103:211-25
Warner, Katherine Deigan; Homan, Philip; Weeks, Kevin M et al. (2014) Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem Biol 21:591-5
Posakony, Jeffrey J; Ferré-D'Amaré, Adrian R (2013) Glucosamine and glucosamine-6-phosphate derivatives: catalytic cofactor analogues for the glmS ribozyme. J Org Chem 78:4730-43
Ferre-D'Amare, Adrian R (2011) Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules. Philos Trans R Soc Lond B Biol Sci 366:2942-8
Deigan, Katherine E; Ferré-D'Amaré, Adrian R (2011) Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. Acc Chem Res 44:1329-38