We report here the in-cell NMR-spectroscopic observation of the binding of the cognate ligand 2'-deoxyguanosine to the aptamer domain of the bacterial 2'-deoxyguanosine-sensing riboswitch in eukaryotic cells, namely Xenopus laevis oocytes and in human HeLa cells. The riboswitch is sufficiently stable in both cell types to allow for detection of binding of the ligand to the riboswitch. Most importantly, we show that the binding mode established by in vitro characterization of this prokaryotic riboswitch is maintained in eukaryotic cellular environment. Our data also bring important methodological insights: Thus far, in-cell NMR studies on RNA in mammalian cells have been limited to investigations of short (<15 nt) RNA fragments that were extensively modified by protecting groups to limit their degradation in the intracellular space. Here, we show that the in-cell NMR setup can be adjusted for characterization of much larger (≈70 nt) functional and chemically non-modified RNA.

Center for Biomolecular Magnetic Resonance Institute for Organic Chemistry and Chemical Biology Goethe University Max von Laue Str 7 60438 Frankfurt M Germany

Center for Biomolecular Magnetic Resonance Institute of Biophysical Chemistry Goethe University Max von Laue Str 9 60438 Frankfurt M Germany

Central European Institute of Technology Masaryk University Kamenice 753 5 625 00 Brno Czech Republic

Institute of Biophysics Czech Academy of Sciences Kralovopolska 135 612 65 Brno Czech Republic

National Centre for Biomolecular Research Masaryk University Kamenice 5 625 00 Brno Czech Republic

Present address Center for Molecular Medicine Cologne Robert Koch Str 21 50931 Cologne Germany

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