Methodological development and application on RNA structure and dynamics

  • Posted on: 28 July 2020
  • By: liuk

Refining RNA solution structures with solvent PRE

Covalent conjugation of a paramagnetic probe is difficult for RNAs. Thus,we refine RNA solution structures using lable-free solvent PRE method which simply with the addition of an inert paramagnetic cosolute. The structure calculated by sPRE is in good agreement with the known structure.
Reference: Biophys. Rep, 2019,5:244-253

Conjoined use of EM and NMR in RNA structure refinement

Hence structural characterization of large RNAs can be difficult for NMR alone. Electron microscopy (EM) provides global shape information of macromolecules at nanometer resolution, which should be complementary to NMR for RNA structure determination, Reference: Plos One, 2015,10, e0120445.

Investigate the hierarchical conformational dynamics of preQ1 RNA riboswitches

We characterize the conformational dynamics of preQ1 riboswitches from mesophilic and thermophilic bacterial species at various temperatures. With the integrative use of small-angle X-ray scattering, NMR, and molecular dynamics simulations, we model the ensemble-structures of the preQ1 riboswitch aptamers without or with a ligand bound. We show that the preQ1 riboswitch is sufficiently dynamic and fluctuating among multiple folding intermediates only near the physiological temperature of the microorganism. We find the hierarchical folding dynamics of the RNA involves the docking of 3′-tail to form a second RNA helix and the helical stacking to form an H-type pseudoknot structure.
Reference: J Mol Biol, 2020, doi:10.1016/j.jmb.2020.06.002

The mechanism of METTL3-METTL14 N6-methyladenosine methyltransferase recognizing different RNA

We have obtained the solution structure of the zinc finger domain of METTL3, which comprise two tandem CCCH-type zinc fingers. Significantly, we have shown that the ZFD is responsible for specific binding towards m6A RNA substrate and forfulfilling the methyltransferase activity of METTL3-METTL14 heterodimer.
Reference: Protein & Cell, 2019,10:272-284

We obtained selectively isotope labeled SAM through an enzyme-catalyzed reaction. Using the NMR signal change of the methyl group on the SAM, the RNA methylation process can be studied in real time.