1992-1995: Ph.D. with Nobel laureate Prof. Manfred Eigen, Max-Planck-Institute for Biophysical Chemistry, Göttingen; Dr. rer. nat. Thesis: Studies on Molecular in vitro Evolution using Non-Radioactive Detection of Nucleic Acids; Grade: Summa cum laude (highest possible); awarded an Otto-Hahn Medal 1995 of the Max-Planck-Society
1995: Postdoctoral Research Fellow with Nobel laureate Prof. Manfred Eigen, Max-Planck-Institute for Biophysical Chemistry, Göttingen; Subject: Applications of Fluorescence Correlation Spectroscopy
1996-1999: Postdoctoral Research Fellow with Prof. John M. Burke, University of Vermont; Subject: Biophysical Studies of the Hairpin Ribozyme
1999-2005: Assistant Professor of Chemistry, UM
2002-2005: Dow Corning Assistant Professor of Chemistry, UM
2005-2009: Associate Professor of Chemistry, UM
2009-present: Professor of Chemistry, UM
2010-present Founding Director, Single Molecule Analysis in Real-Time (SMART) Center, UM
2015-present Associate Director, Michigan Post-baccalaureate Research Education Program (PREP)
2015-present Co-Director, Microfluidics in Biomedical Sciences Training Program
2016-present Founding Co-Director, Center for RNA Biomedicine, UM
2016-present Professor of Biological Chemistry
2017-present Francis S. Collins Collegiate Professor of Chemistry, Biophysics, and Biological Chemistry, College of Literature, Science and the Arts
2018 Sabbatical Visitor, Chan Zuckerberg Biohub, San Francisco
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, and in live cells, primarily 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.
- 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.
- 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.
- Utilizing super-resolution fluorescence imaging techniques in nanotechnology to follow autonomously moving engineered "molecular spiders".
- Developing a non-biological mimic of the superb sensing and actuation efficiency and precision reached during RNA transcription.
- Using single-molecule fluorescence techniques to observe in unprecedented detail fluctuations of single ribozyme molecules between catalytically active and inactive conformations.
- 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.
Hayward, S.L., Lund, P.E., Kang, Q., Johnson-Buck, A.*, Tewari, T. and Walter,N.G. (2018) Ultra-specific and amplification-free quantification of mutant DNA by single-molecule kinetic fingerprinting. J. Am. Chem. Soc. 140, 11755-11762.
Li, J., Johnson-Buck, A., Yang, Y.R., Shih, W.M., Yan, H. and Walter, N.G. (2018) Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat. Nat. Nanotechnol. 13, 723-729.
Valero, J., Pal, N., Dhakal, S., Walter, N.G. and Famulok, M. (2018) A bio-hybrid DNA rotor/stator nanoengine that moves along predefined tracks. Nat. Nanotechnol. 13, 496-503.
Suddala, K.C., Cabello-Villegas, J.,Michnicka, M., Nikonowicz, E.P. and Walter,N.G. (2018) Hierarchical mechanism of amino acid sensing by the T-box riboswitch. Nat. Commun. 9, 1896.
Ray, S., Widom, J.R. and Walter, N.G. (2018) Life under the microscope: Single-molecule fluorescence highlights the RNA World. Chem. Rev. 118, 4120-4155.
Pitchiaya, S., Heinicke, L.A.,Park, J.I., Cameron, E.L. and Walter, N.G. (2017) Resolving sub-cellular miRNA trafficking and turnover at single-molecule resolution. Cell Rep. 19, 630-642.
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.
Zhao, Z., Fu*, J., Dhakal, S., Johnson-Buck, A., Liu, M., Zhang, T., Woodbury, N., Liu, Y., Walter, N.G. and Yan, H. (2016) Nano-caged enzymes with enhanced activity and stability. Nat. Commun. 7, 10619.
Suddala, K.C., Wang, J., Hou, Q. and Walter, N.G. (2015) Mg2+ shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection. J. Amer. Chem. Soc. 137, 14075-14083.
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.
Widom, J. R., Dhakal, S., Heinicke, L. A. and Walter, N.G. (2014) Single molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update. Arch. Toxicol. 88, 1965-1985.
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.
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, p. 709-715.
McDowell, S.E., Jun, J.M. and Walter, N.G. (2010) Loop-loop interactions enhance both structural dynamics and cleavage activity in single hammerhead ribozymes. RNA 16, p. 2414-2426.
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, p. 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, p. 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.
Al-Hashimi, H.M. and Walter, N.G. (2008) RNA dynamics: it is about time. Curr. Opin. Struct. Biol. 18, 321-329.
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.
Walter, N.G. (2007) Ribozyme catalysis revisited: Is water involved? Mol. Cell 28, p. 923-929.
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.