faculty

Associate Professor of Chemistry
Ph.D., Max-Planck-Institute; Technical University of Darmstadt

Chemical Biology; Folding and Function of RNA Enzymes; Single-Molecule Fluorescence Spectroscopy; Biophysical Chemistry of Nucleic Acids

Phone: (734) 615-2060
E-mail: nwalter@umich.edu
FAX: (734) 647-4865

Research Group
UM Single Molecule Analysis
MiRNA

Our group's goal is to understand the fundamental nature of catalysis by a novel class of ribonucleic acid (RNA) enzymes (ribozymes). The enzymes we study range from small RNA catalysts, such as the hammerhead and hepatitis delta virus ribozymes with potential use in human gene therapy and relevance to human disease, to large RNA-protein complexes, such as the ribosome, the cellular protein synthesis machinery. In particular, we employ fluorescence techniques to study the enzymology of these ribozymes, in bulk solution, in live cells, and at the single-molecule level. Applications include the identification and optimization of ribozymes for gene therapy and as novel biosensors, as well as the characterization of antiviral and antibiotic drugs that target pathogenic RNA function.

Our research by its very nature is highly interdisciplinary, engaging students with a diverse background and providing a broad education. The molecules we study are extremely dynamic over time scales of microseconds to hours. To understand these dynamics we combine state-of-the-art chemical and molecular biology and biophysical approaches. An outline of several projects is given below.

• In NIH funded work on the ribozyme from the human pathogen hepatitis delta virus (HDV) we have discovered by fluorescence resonance energy transfer (FRET) and other fluorescence techniques an essential conformational change that impacts the rate of catalysis by this RNA.
• We have been able to follow in real time, by fluorescence resonance energy transfer (FRET), the switching of the "switch helix" of 16S ribosomal RNA between two alternate conformations that are linked to fidelity in protein biosynthesis.
• Using single-molecule FRET techniques, we have observed in unprecedented detail fluctuations of single hairpin ribozyme molecules between catalytically active and inactive conformations.
• We have generated a biosensor for high-throughput screening of the broncho-dilator drug theophylline, by directly monitoring the cleavage activity of a theophylline controlled hammerhead ribozyme by FRET.
• As a model system for gene regulation we have directly observed the degradation of RNA in cell extracts and live cells.

For more information, please see our group webpage at http://www.umich.edu/~rnapeopl/

AWARDS

• 2004 Camille Dreyfus Teacher-Scholar Award
• 2002 Dow Corning Assistant Professorship - University of Michigan
• Otto-Hahn medal 1995 for Outstanding Researchers of the Max-Planck Society
• Feodor-Lynen Postdoctoral Research Fellowship from the Alexander von Humboldt Foundation
• Kekule Ph.D. Scholarship from the Stiftung Stipendienfonds des Verbandes der Chemischen Industrie
• Anton Keller Prize for best Chemistry Diploma of the Year at the Technical University of Darmstadt
• Study Scholarship from the Studienstiftung des Deutschen Volkes

REPRESENTATIVE PUBLICATIONS

1. Tinsley, R.A. and Walter, N.G. (2006) Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation. RNA 12, p. 522-529.
   
2. Rueda, D., Bokinsky, G., Rhodes, M.M., Rust, M.J., Zhuang X., and Walter, N.G. (2004) Single-molecule enzymology of RNA: Essential functional groups impact catalysis from a distance. Proc. Natl. Acad. Sci. USA 101, p. 10066-10071.
   
3. Krasovska, M.V., Sefcikova, J., Spackova, N., Sponer, J., and Walter, N.G. (2005) Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. J. Mol. Biol. 351, p. 731-748.
   
4. G Bokinsky, D Rueda, VK Misra, A Gordus, MM Rhodes, HP Babcock, NG Walter, X Zhuang. "Single-molecule transition-state analysis of RNA folding" Proc. Natl. Acad. Sci. USA 2003, 100, 9302.
   
5. X Zhuang, H Kim, MJB Pereira, HP Babcock, NG Walter, S Chu. "Coupling of structural dynamics and function in single ribozyme molecules" Science 2002, 296, 1473.