At the interface of Chemistry and Biology, a revolution has recently taken place that has uncovered a plethora of small non-coding (nc)RNAs in our bodies, which outnumber protein-coding genes by several-fold, dominate the expression patterns of all genes in all cells, and have inspired entirely new therapeutic intervention approaches. Our group's goal is to understand the structure-function relationships in these ncRNAs using single molecule tools and then utilize them for biomedical, bioanalytical and nanotechnological applications. The ncRNAs we study range from small RNA catalysts, such as the hammerhead, hairpin and hepatitis delta virus ribozymes with potential use in human gene therapy and relevance to human disease, to large RNA-protein complexes, such as RNA interference machinery involved in gene regulation and virus suppression. In particular, we employ fluorescence techniques to study in real-time the kinetic mechanisms of these ncRNAs, 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, molecular biological, and biophysical approaches. An outline of several exciting current projects is given below.
1. Developing a model system for understanding gene silencing by directly observing, using fluorescence techniques, the action of small interfering (si)RNAs and micro (mi)RNAs on pathogenic mRNAs in cell extracts and live cells.
2. Utilizing single molecule fluorescence imaging techniques to follow movement of the ribosome on a secondary structured mRNA, including riboswitch motifs that utilize an aptamer domain to recognize a specific ligand and effect downstream gene expression.
3. Utilizing super-resolution fluorescence imaging techniques in nanotechnology to follow autonomously moving engineered "molecular spiders".
4. Developing a non-biological mimic of the superb sensing and actuation efficiency and precision reached during RNA transcription.
5. Using single-molecule fluorescence techniques to observe in unprecedented detail fluctuations of single ribozyme molecules between catalytically active and inactive conformations.
6. Dissecting pre-mRNA splicing by fluorophore labeling individual RNA or protein components and following their fluorescence fluctuations during splicing in cell extracts by single molecule fluorescence microscopy.
Faculty Recognition Award 2013
Imes and Moore Faculty Award 2013
Alumnus of the Year Award, Sherbrooke RiboClub 2006
Camille Dreyfus Teacher-Scholar Award 2004
Otto-Hahn Award for Outstanding Researchers of the Max-Planck Society 1995
Anton Keller Prize for best Chemistry Diploma of the Year at the Technical University of Darmstadt
Election as AAAS Fellow, 2011
JILA Distinguished Visitor Fellowship (David Nesbitt group), 2006
Feodor-Lynen Postdoctoral Research Fellowship, Alexander von Humboldt Foundation
Kekule Ph.D. Scholarship from the Stiftung Stipendienfonds des Verbandes der Chemischen Industrie
Study Scholarship from the Studienstiftung des Deutschen Volkes
Alexander von Humboldt Foundation Visiting Scholar, 2012
ADVANCE Program for Executive Leadership, College of LS&A, University of Michigan, 2011
Buchanan Lecturer, Bowling Green State University, 2011
Chartered NIH Study Section Member, MSFB, 2009-2013
Visiting Scholar, Harvard University (Sunney Xie group), 2006
Dow Corning Assistant Professorship - University of Michigan, 2002
Johnson-Buck, A., Nangreave, J., Kim, D., Bathe, M., Yan, H. and Walter, N.G. (2013) Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards. Nano Lett.,13, 728-733.
Pitchiaya, S., Androsavich, J.R. and Walter, N.G. (2012) Intracellular single molecule microscopy reveals time and mRNA dependent microRNA assembly. EMBO rep. 13, 709-715.
Rawlings, R.A., Krishnan, V. and Walter, N.G. (2011) Viral RNAi suppressor reversibly binds siRNA to outcompete Dicer and RISC via multiple-turnover. J. Mol. Biol. 408, 262-276.
Lund, K., Manzo, A.J., Dabby, N., Michelotti, N., Johnson-Buck, A., Nangreave, J., Taylor, S., Pei, R., Stojanovic, M.N., Walter, N.G., Winfree, E. and Yan, H. (2010) Molecular robots guided by prescriptive landscapes. Nature 465, 206-210.
Abelson, J., Blanco, M., Ditzler, M.A., Fuller, F., Aravamudhan, P., Wood, M., Villa, T., Ryan, D.E., Pleiss, J.A., Maeder, C., Guthrie, C. and Walter, N.G. (2010) Conformational dynamics of single pre-mRNA molecules in spliceosome assembly. Nat. Struct. Mol. Biol. 17, 504-512.
Ditzler, M.A., Otyepka, M., Šponer, J. and Walter, N.G. (2010) Molecular dynamics and quantum mechanics of RNA: Conformational and chemical change we can believe in. Acc. Chem. Res. 40, p. 40-47.
Walter, N.G. (2009) The blessing and curse of RNA dynamics: past, present, and future. Methods 49, p. 85-86.
Ditzler, M.A., Rueda, D., Mo, J., Håkansson, K. and Walter, N.G. (2008) A rugged free energy landscape separates multiple functional RNA folds throughout denaturation. Nucleic Acids Res. 36, p. 7088-7099.
Al-Hashimi, H.M.* and Walter, N.G. (2008) RNA dynamics: it is about time. Curr. Opin. Struct. Biol. 18, 321-329. Editorial comments in Curr. Opin. Struct. Biol. 18 (2008) p. 279-281.
Walter, N.G., Huang, C., Manzo, A.J. & Sobhy, M.A. (2008). Do-it-yourself guide: How to use the modern single molecule toolkit. Nat. Methods 5, p. 475-489. Editorial comments in Nat. Methods 5 (2008) 457.
Walter, N.G. (2007) Ribozyme catalysis revisited: Is water involved? Mol. Cell 28, p. 923-929.
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. [Highlighted as UM News Release June 29, 2004]
Zhuang, X., Kim, H., Pereira, M.J.B., Babcock, H.P., Walter, N.G. and Chu, S. (2002) Coupling of structural dynamics and function in single ribozyme molecules. Science 296, p. 1473-1476.