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About Us

 

In recent years a revolution has occurred in the basic sciences, which exploits novel single molecule detection and manipulation tools to track and analyze biomolecules in unprecedented detail. The goal of UM’s Single Molecule Analysis in Real-Time (SMART) Center is to develop a university-wide initiative in the emerging area of single molecule technology, including single molecule spectroscopy (SMS) and imaging (SMI), laser tweezers (LT), and atomic force microscopy (AFM), to bring basic scientists, engineers, and clinical researchers together to apply this technology to the most relevant questions in medicine and nanotechnology. This initiative will thus build on the momentum established by the State’s creation of the Michigan Lifescience Corridor (MLSC) Core Technology Alliance for single molecule spectroscopy at Michigan.

 

Nils G. Walter
SMART Center Director
Professor of Chemistry

930 N. University Avenue
Ann Arbor, MI 48109

Phone: (734)-615-2060

Email: nwalter@umich.edu

Damon Hoff
SMART Center Manager

3080 Chemistry Building
930 N. University Avenue
Ann Arbor, MI 48109

Phone: (734)-763-5449

Email: hoffj@umich.edu

 


Associated Faculty

 

Nils Walter (Chair, Steering Committee) – Chemistry

Julie Biteen – Chemistry

Theodore Goodson – Chemistry

Raoul Kopelman – Chemistry

Nicholas Kotov – Chemical Engineering

Jens-Christian Meiners – Physics, Biophysics

Joel Swanson – Microbiology and Immunology

Sarah Veatch – Biophysics

Kristen Verhey – Cell & Developmental Biology

 

Publications

 

  1.  Michelini, F., Pitchiaya, S., Vitelli, V., Sharma, S., Gioia, U., Wang, Y., Cabrini, M., Iannelli, F., Pessina, F., Matti, V., Francia, S., Shivashankar, G.V., Walter, N.G., and d’Adda di Fagagna, F. DNA break-induced transcription of non-coding RNA is required for DNA damage response, Nat. Cell Biol. In review
  2. Pitchiaya, S., Heinicke, L.A., Park, J.I., Cameron, E., and Walter, N.G., Resolving sub-cellular miRNA trafficking and turnover at single-molecule resolution, Cell Reports.  In review
  3. Rinaldi, A.J., Lund, P.E., Blanco, M.R., Walter, N.G. (2016) The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts, Nature Communications.  Full text in pdf format.
  4. Shankar, S., Pitchiaya, S., Malik, R., Kothari, V., Hosono, Y.,   Yocum, A.K., Gundlapalli, H., White, Y., Firestone, A., Cao, X.H.,  Dhanasekaran, S.M., Stuckey, J.A.,  Bollag, G.,  Shannon, K.,  Walter, N.G.,  Kumar-Sinha, C., Chinnaiyan, A.M. (2016) KRAS Engages AGO2 to Enhance Cellular Transformation, Cell Reports. Full text in pdf format
  5. Hariadi, R.F., Sommese, R., and Sivaramakrishnan, S. (2015) Tuning myosin-driven sorting on cellular actin networks, eLife. Full text in pdf format.
  6. Johnson-Buck, A., Su, X., Giraldez, M. D., Zhao, M., Tewari, M., Walter, N. G., (2015) Kinetic fingerprinting to identify and count single nucleic acids, Nature Biotechnology.  Full text in pdf format.
  7. Bartke, R.M., Cameron, E.L., Cristie-David, A.S., Custer, T.C., Denies, M.S., Daher, M., Dhakal, S., Ghosh, S., Heinicke, L.A., Hoff, J.D., Hou, Q., Kahlscheuer, M.L., Karslake, J., Krieger, A.G., Li, J., Li, X., Lund, P.E., Vo, N.N., Park, J., Pitchiaya, S., Rai, V., Smith, D.J., Suddala, K.C., Wang, J., Widom, J.R., Walter, N.G. (2015) Meeting Report: SMART Timing—Principles of Single Molecule Techniques Course at the University of Michigan 2014, Biopolymers
  8. Dougherty, C.A., Vaidyanathan, S., Orr, B.G., Banaszak Holl, M.M. (2015) Fluorophore:Dendrimer Ratio Impacts Cellular Uptake and Intracellular Fluorescence Lifetime, Bioconjugate Chemistry
  9. Bahng, J.H., Yeom, B., Wang, Y., Tung, S.O., Hoff, J.D., Kotov, N. (2015) Anomalous dispersions of ‘hedgehog’ particles. Nature 517
  10. Nyati, S., Schinske-Sebolt, K., Pitchiaya, S., Chekhovskiy, K., Chator, A., Chaudhry, N., Dosch, J., Van Dort, M.E., Varambally, S., Kumar-Sinha, C., Nyati, M.K., Ray, D., Walter, N.G., Yu, H., Ross, B.D. and Rehemtulla, A. (2015) The kinase activity of the Ser/Thr kinase BUB1 promotes TGF-b signaling. Sci. Signal. 8, ra1.​  Full text in pdf format.
  11. Hariadi, R.F., Cale, M., Sivaramakrishnan, S. (2014) Myosin lever arm directs collective motion on cellular actin network, PNAS 111(11).  Full text in pdf format.
  12. Sripathi, K.N., Tay, W.W., Banas, P., Otyepka, M., Sponer, J., Walter, N.G. (2014) Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape, RNA 20(7).  Full text in pdf format.
  13. Chang, C., Althaus, J.C., Carruthers, C.J.L, Sutton, M.A., Steel, D.G., Gafni, A. (2013) Synergistic Interactions between Alzheimer’s Aβ40 and Aβ42 on the Surface of Primary Neurons Revealed by Single Molecule Microscopy, PLoS One 8(12).  Available online.
  14. Johnson, R.D., Schauerte, J.A., Chang, C., Wisser, K.C., Althaus, J.C., Carruthers, C.J.L., Sutton, M.A., Steel D.G., Gafni, A. Single-Molecule Imaging Reveals Aβ42:Aβ40 Ratio-Dependent Oligomer Growth on Neuronal Processes  Biophys J. 104 (4) p. 894-903. Full text in pdf format.
  15. Michelotti, N., de Silva, C., Johnson-Buck, A.E., Manzo, A.J., Walter, N.G. (2010) A bird’s eye view: tracking slow nanometer-scale movements of single molecular nano-assemblies. Methods Enzymol. 475, p. 121-148. Full text in pdf format.
  16. Blanco, M., Walter, N.G. (2010) Analysis of complex single-molecule FRET time trajectories. Methods Enzymol. 472, p. 154-176. Full text in pdf format.
  17. Lund, K., Manzo, A.J., Dabby, N., Michelotti, N., Johnson-Buck, A., Nangreave, J., Taylor, S., Pei, Stojanovic, M.N., Walter, N.G., Winfree, E., and Yan, H. (2010) Molecular robots guided by prescriptive landscapes. Nature 465, p. 206-210. Full text in pdf format. Supplement in pdf format. See reference on the cover. Highlighted in Nature News and Views.
  18. 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. 4, p. 504-512. Full text in pdf format. Supplement in pdf format. Highlighted as UM News Release on March 21, 2010.
  19. Kuszak, A., Pitchiaya, S., Anand, J.P., Mosbery, H.I., Walter, N.G., and Sunahara, R.K. (2009) Purification and functional reconstitution of monomeric Mu-Opioid receptors. Journal of Biological Chemistry vol. 284, number 39, p.26732-26741. Full text in pdf format. Supplement in pdf format.
  20. de Silva, C. and Walter, N.G. (2009) Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme. RNA 15, p. 76-84. Full text in pdf format.
  21. Walter, N.G. and Perumal, S. (2009) The small ribozymes: Common and diverse features observed through the FRET lens. In: Non-Protein Coding RNAs, p. 103-127 (N.G. Walter, S.A. Woodson and R.T. Batey, eds.), Springer Series in Biophysics volume 13, Springer Publishers, Berlin. Full text in pdf format.
  22. Walter, N.G. (2008) Single molecule detection, analysis, and manipulation. Encycl. Anal. Chem.   DOI 10.1002/9780470027318.a0213m.pub2, John Wiley & Sons, Ltd., online at http://www.mrw.interscience.wiley.com/eac/. Full text in pdf format.
  23. Ditzler, M.A., Rueda, D., Mo, J., Hakansson, 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. Full text in pdf format. Highlighted in Science and Technology of C&E News on March 1, 2010, see in pdf format.
  24. Pereira, M.J.B., Nikolova, E.N., Hiley, S.L, Jaikaran, D., Collins, R.A., and Walter, N.G. (2008) Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis. J. Mol. Biol. 382, p. 496-509. Full text in pdf format. Supplement in pdf format.
  25. Walter, N.G., Huang, C.-Y., Manzo, A.J., and Sobhy, M.A. (2008) Do-it-yourself guide: How to use the modern single-molecule toolkit. Nat. Methods 5, p. 475-489. Full text in pdf format. Editorial comments in Nat. Methods 5, p. 457
  26. Ditzler, M.A., Aleman, E.A., Rueda, D. and Walter, N.G.  (2007)  Focus on function: Single molecule RNA enzymology. Biopolymers 87, p. 302-316. Full text in pdf format.
  27. Liu, S., Bokinsky, G., Walter, N.G. and Zhuang, X. (2007)  Dissecting the multi-step reaction pathway of an RNA enzyme by single-molecule kinetic “fingerprinting”. Proc. Natl. Acad. Sci. USA 104, p. 12634-12639. Full text in pdf format.
  28. Walter, N.G., Meiners, J-C, Meyhofer, E., Neubig, R.R., Sunahara, R.K., Perkins, N.C., Steel, D.G., and Swanson, J.A. (2007) Under the microscope: Single molecule symposium at the University of Michigan, 2006. Biopolymers  85, p. 106-114. Full text in pdf format.
  29. Walter, N.G. (2007) Future of biomedical sciences: Single molecule microscopy. Biopolymers  85, p. 103-105. Full text in pdf format.
  30. Rhodes, M.M., Reblova, K., Sponer, J., and Walter, N.G. (2006) Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proc. Natl. Acad. Sci. USA  103, p. 13381-13385. Full text in pdf format. Supplement in pdf format. Highlighted as UM News Release on August 21, 2006.
  31. Lambert, M.N., Vocker, E., Blumberg S., Redemann, S., Gajraj, A., Meiners, J., and Walter, N.G. (2006) Mg2+ induced compaction of single RNA molecules monitored by tethered particle microscopy. Biophys. J.  90, p. 3672-3685. Full text in pdf format.
  32. Walter, N.G. (2006) Michaelis-Menten is dead, long live Michaelis-Menten! Nature Chem. Biol.  2, p. 66-67. Full text in pdf format.
  33. Rueda, D. and Walter, N.G. (2005) Single molecule fluorescence control for nanotechnology. J. Nanosci. Nanotechnol.  5, p. 1990-2000. Full text in pdf format.
  34. 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. Full text in pdf format. Supplement in pdf format. Highlighted as UM News Release on June 29, 2004.
  35. Bokinsky, G., Rueda, D., Misra, V.K., Rhodes, M.M., Gordus, A., Babcock, H.P., Walter, N.G., and Zhuang, X. (2003) Single-molecule transition-state analysis of RNA folding. Proc. Natl. Acad. Sci. USA 100, p. 9302-9307. Full text in pdf format. Highlighted in Science Concentrates of C&E News on July 21, 2003, see in pdf format.
  36. Zhuang, X., Kim, H., Pereira, M.J.B., Babcock, H.P., Walter, N.G., and Chu, S. (2002) Correlating structural dynamics and function in single ribozyme molecules. Science 296, p. 1473-1476. Full text in pdf format. Supplement in pdf format.