DC 6: Characterization of riboswitch-ligand interactions using NMR spectroscopy and other biophysical methods

PhD project description:

The PhD candidate will conduct RNA preparation suitable for fragment screening for the SAM-I/IV riboswitch using NMR at the Schwalbe group. Complementary fragment screening will be conducted by GCI at Malvern. To guide fragment optimization, a second-site screening at Saverna will be conducted. Further, virtual screening hits and newly synthesized compounds from the ITN consortium will be analysed. For selected ligands, more extensive NMR characterisations will be conducted. Specifically, binding sites will be structurally characterised using isotope-labelled riboswitch samples for resonance assignment as well as NOE-filter experiments. In favourable cases, the structure of the ligand-riboswitch complex will be determined. The NMR focused characterisation will be cross validated by other biophysical technologies including CD spectroscopy and SAXS. In addition, the PhD candidate will contribute to the development of in vitro transcription assays for all riboswitches and the 5’-UTR of ompA using previously established methods to determine the activities of compounds discovered in the ITN consortium.