Pardi Lab Research

NMR Methods Development

As larger and more complex molecular systems are studied by solution NMR, there is a need to develop new methods and expand traditional methods currently being used in the study of smaller systems. We are applying novel data acquisition and processing techniques such as Filter Diagonalization Method (FDM) and G-matrix Fourier transform (GFT) to high-resolution high-dimensionality NMR studies of RNAs. These methods have the potential to accelerate the resonance assignments process which is currently the bottle-neck of high resolution structure studies of large RNAs. We are also exploring novel methods for the detection of residual dipolar couplings (RDCs) which assist in determining the correct global structure of an RNA.

Ribozymes

Ribozymes are catalytic RNAs that perform a variety of biochemical reactions including peptidyl transfer (the ribosome), self-splicing (the Group I Intron), tRNA maturation (RNase P RNA), translational regulation (glmS), and processing of replication intermediates of viroids and virus satellite RNAs. Our group specifically studies the hammerhead ribozyme, a self-cleaving and self-ligating RNA that is involved in rolling circle replication. We are interested in characterizing the kinetics of this cleavage reaction and of the reverse ligation reaction as well as the folding pathways involved. Of special interest is the catalytic mechanism. We are using a combined approach of kinetic assays, Fluorescence Resonance Energy Transfer (FRET) ensemble experiments, single molecule assays, and NMR structural studies that together may give us a complete picture of this ribozyme's function.