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DNP-Enhanced Magic Angle Spinning Solid-State NMR Spectroscopy to Determine RNA-Ligand Interactions
Alexey Sudakov1, Johanna Becker-Baldus2, Konstantin S Mineev1
1Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Str. 7, Frankfurt 60438, Germany.
Journal of the American Chemical Society
|December 30, 2025
Summary
Magic angle spinning solid-state NMR with dynamic nuclear polarization (MAS-DNP) reveals molecular recognition in large RNA-ligand complexes. Selective labeling is key for structural insights into riboswitches and drug development.
Area of Science:
- Biochemistry
- Structural Biology
- Chemical Biology
Background:
- RNA-ligand interactions are crucial for riboswitch regulation.
- Understanding these interactions aids in developing RNA-targeting drugs.
- Solid-state NMR is a powerful tool for studying biomolecular structures.
Purpose of the Study:
- To determine the molecular recognition of a ligand-RNA riboswitch complex using MAS-DNP.
- To benchmark labeling strategies for large RNA molecules in MAS-DNP studies.
- To explore the application of MAS-DNP for structural analysis of RNA-ligand complexes.
Main Methods:
- Magic Angle Spinning Solid-State Nuclear Magnetic Resonance (MAS-DNP) spectroscopy.
- Chemoenzymatic and solid-phase chemical synthesis of labeled RNA.
- Preparation of RNA-ligand complexes with cognate metabolites.
- 2D 13C,15N-TEDOR experiments for structural determination.
Main Results:
- MAS-DNP successfully studied a 2'deoxyguanosine-sensing riboswitch from Mesoplasma florum.
- Nucleotide- and ligand-selective labeling were essential to overcome signal overlap in large RNAs.
- Site-specific and atom-specific labeling enabled structure determination of the ligand-binding pocket.
Conclusions:
- MAS-DNP is a viable method for investigating large RNA-ligand complexes.
- Optimized labeling strategies are critical for successful MAS-DNP studies of complex RNA systems.
- This approach advances structural studies of riboswitches and facilitates RNA-targeted drug discovery.
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