Francis S Collins Collegiate Professor of Chemistry, Biophysics, and Biological Chemistry
About
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 disease intervention approaches. Our group's goal is to understand the mechanistic 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 enzymes, 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 ncRNAs for gene therapy and as novel biosensors and biomarkers, 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. Using single-molecule fluorescence techniques to observe in unprecedented detail fluctuations of single ncRNA molecules between functionally active and inactive conformations.
2. 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.
3. Utilizing single molecule fluorescence imaging 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.
4. 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.
5. Utilizing super-resolution fluorescence imaging techniques in nanotechnology to follow and optimize autonomously moving engineered "molecular spiders" and the functionality of other RNA and DNA nanodevices.
Awards
Jean Dreyfus Boissevain Lecturer 2015, Trinity University, San Antonio, TX 2015
Harold R. Johnson Diversity Service Award, University of Michigan 2015
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 Darmstadt Insitute of Technology 1992
Fellowships
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
Other Positions
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
Representative Publications
Semlow, D.R., Blanco, M.R., Walter, N.G. and Staley, J. (2016) Spliceosomal DEAH-box ATPases remodel pre-mRNA to activate alternative splice sites. Cell 164, 985-998.
Rinaldi, A.J., Lund, P.E., Blanco, M.R. and Walter, N.G. (2016) The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts. Nat. Commun. 7, 8976.
Blanco, M.R., Martin, J.S., Kahlscheuer, M.L., Krishnan, R., Abelson, J., Laederach, A. and Walter, N.G. (2015) Single molecule cluster analysis dissects splicing pathway conformational dynamics. Nat. Methods 12, 1077-1084.
Johnson-Buck, A., Su, X., Giraldez, M.D., Zhao, M., Tewari, M. and Walter, N.G. (2015) Kinetic fingerprinting to identify and count single nucleic acids. Nat. Biotechnol. 33, 730-732.
Walter, N.G. (2015) Going viral: riding the RNA wave to discovery. RNA 21, 756–757.
Fu, J., Yang, Y., Johnson-Buck, A., Liu, M., Liu, Y., Walter, N.G., Woodbury, N.W. and Yan, H. (2014) Multi-enzyme complexes on DNA scaffolds capable of substrate channeling with an artificial swinging arm. Nat. Nanotechnol. 9, 531-536.
Pitchiaya, S., Custer, T.C., Heinicke, L.A. and Walter, N.G. (2014) Single molecule fluorescence approaches shed light on intracellular RNAs. Chem. Rev. 114, 3224-3265.
Krishnan, R., Blanco, M.R., Kahlscheuer, M.L., Abelson, J., Guthrie, C. and Walter, N.G. (2013) Biased Brownian ratcheting leads to pre-mRNA remodeling and capture prior to first-step splicing. Nat. Struct. Mol. Biol. 20, 1450-1457.
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.
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.
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, 40-47.
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) 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, 475-489. Editorial comments in Nat. Methods 5 (2008) 457.
Walter, N.G. (2007) Ribozyme catalysis revisited: Is water involved? Mol. Cell 28, 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, 10066-10071.
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, 1473-1476.
Research Areas(s)
- Analytical Chemistry
- Bioanalytical Chemistry
- Bioinorganic Chemistry
- Biophysical Chemistry
- Chemical Biology
- Energy Science
- Nano Chemistry
- Optics and Imaging
- Organic Chemistry
- Physical Chemistry
- RNA BioChemistry
- Sensor Science
- Surface Chemistry
- Sustainable Chemistry
- Ultrafast Dynamics
Other Research Interests
- Single-Molecule Fluorescence Spectroscopy and Microscopy
- Folding and Function of Non-Coding RNA
- Live-Cell Imaging
- Biophysical Chemistry of Nucleic Acids
- DNA Nanotechnology and Smart Materials
