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Arthur PARDI
Office Phone: 303 492 6263
E-mail: Arthur.Pardi@colorado.edu
FAX: 303 492 5894
Lab: Cristol Chemistry 223, 241
Lab Phone: 303 492 8085, 303 492 4503
Group Website: http://www.colorado.edu/chemistry/pardilab/
Ph.D.: University of California at Berkeley, 1980
Postdoctoral Fellow: NATO Fellow, 1982-83
Solution Structures of RNAs and Proteins
Professor Pardi's primary research interests are in the area of biophysical chemistry and NMR spectroscopy. High-resolution multi-dimensional NMR experiments are used to probe the structure and dynamics of biomolecules in solution. A long-range goal is to understand the relationship between the structures (and dynamics) of these molecules and their biological functions.
A major area of interest is structural studies of RNA enzymes (ribozymes). RNA has been shown to be the biological catalyst for a number of important reactions. The hammerhead ribozyme is one of the most biochemically studied systems and has been shown to efficiently and catalytically cleave specific sites in target RNAs. In Professor Pardi's lab, multi-dimensional NMR experiments are being used to probe the structure of the hammerhead ribozyme in solution.
The primary structural data derived from the NMR experiments are proton-proton internuclear distances. This distance information is used to determine the secondary and tertiary structure of the hammerhead RNA domain. The structural information is then combined with kinetic, mechanistic, and biochemical properties of these ribozymes to aid in the design of optimal RNA cleavage reagents. The Pardi lab has developed methods for generating NMR quantities of isotopically (13C and/or 15N) labeled RNAs. The use of isotopic labels makes it possible to increase the dimensionality of the NMR experiments. The Pardi lab reported the first applications of two-and three-dimensional heteronuclear NMR to structural studies of nucleic acids. These techniques enormously facilitate the resonance assignment and structural analysis of RNA. The tremendous increase in resolution in these experiments allows detailed structure determinations of much larger RNAs than were previously possible. The Pardi group is continuing to develop new NMR techniques for structural studies of isotopically labeled RNA. These techniques are being applied to a variety of biologically important RNA systems including: a lead-dependent ribozyme, a family of naturally-occurring and unusually stable hairpins containing tetranucleotide loops, tRNA precursors, and in vitro selected RNAs.
The structure and function of several in vitro selected RNAs are being studied that show high affinity and specificity for proteins or small molecule ligands. The three-dimensional structure of a RNA that has high affinity and specificity for theophylline is being determined. Theophylline is widely used in the treatment of asthma and this in vitro selected RNA shows an extremely high level of discrimination between binding of theophylline and the structurally similar molecule, caffeine. The RNA being studied has 10-100 fold better discrimination between these two small molecules than the best available monoclonal antibody. The structural studies are being complemented with thermodynamic and chemical probing studies to better understand the structural features that give rise to the high affinity and specificity of this theophylline-binding RNA.
An RNA that binds with high affinity and specificity to the basic fibroblast growth factor (bFGF) is also being studied. bFGF has been implicated in tumor proliferation and this RNA represents a potent inhibitor for bFGF binding to its receptor. The NMR structural studies of this protein-RNA complex are being complemented with chemical and enzymatic probing of the RNA to identify the residues involved in protein-RNA recognition.
Selected Publications
L. Mueller, P. Legault, and A. Pard, "Improved RNA Structure Determination by Detection of NOE Contacts to Exchange-broadened Amino Protons", J. Amer. Chem. Soc., 117, 11043-8 (1995).
F.M. Jucker and A. Pardi, "Solution Structure of the CUUG Hairpin Loop : A Novel RNA Tetraloop Motif", Biochemistry, 34, 14416-27 (1995).
P. Legault and A. Pardi, "In Situ Probing of Adenine Protonation in RNA by 13C NMR", J. Am. Chem. Soc. 116, 8390-1 (1994). F.M. Jucker and A. Pardi, "GNRA Tetraloops Make a U-turn," RNA 1, 219-22 (1995).
R.D. Jenison, S.C. Gill, A. Pardi, and B. Polisky, "High-resolution Molecular Discrimination by RNA," Science 263, 1425-9 (1994).
E.P. Nikonowicz and A. Pardi, "An Efficient Procedure for Assignment of the Proton, Carbon and Nitrogen Resonances in 13 C/15 N Labeled Nucleic Acids," J. Mol. Biol., 232, 1141-56 (1993).
H.A. Heus and A. Pardi, "Structural Features that Give rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops," Science, 253, 191-4 (1991).
H.A. Heus and A. Pardi, "Nuclear Magnetic Resonance Studies of the Hammerhead Ribozyme Domain. Secondary Structure Formation and Magnesium ion Dependence," J. Mol. Biol., 217, 113-24 (1991).
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