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.

Associated Faculty

Nils Walter (Chair, Steering Committee) – Chemistry

Julie Biteen – Chemistry

Theodore Goodson – 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. Chen, C., V. Piano, A. Alex, S. J. Y. Han, P. J. Huis In 't Veld, B. Roy, D. Fergle, A. Musacchio and A. P. Joglekar (2023). "The structural flexibility of MAD1 facilitates the assembly of the Mitotic Checkpoint Complex." Nat Commun 14(1): 1529. Full text in pdf format.
   
2. Hsu, Y. Y., A. M. Resto Irizarry, J. Fu and A. P. Liu (2023). "Mechanosensitive Channel-Based Optical Membrane Tension Reporter." ACS Sens 8(1): 12-18. Full text in pdf format.
   
3. Ziegler, C. A. and P. L. Freddolino (2023). "Escherichia coli Leucine-Responsive Regulatory Protein Bridges DNA In Vivo and Tunably Dissociates in the Presence of Exogenous Leucine." mBio 14(2): e0269022. Full text in pdf format.
   
4. Blanchard, A. T., Z. Li, E. C. Duran, C. E. Scull, J. D. Hoff, K. R. Wright, V. Pan and N. G. Walter (2022). "Ultra-photostable DNA FluoroCubes: Mechanism of Photostability and Compatibility with FRET and Dark Quenching." Nano Lett 22(15): 6235-6244. Full text in pdf format.
   
5. Farrell, E., M. Aliabouzar, C. Quesada, B. M. Baker, R. T. Franceschi, A. J. Putnam and M. L. Fabiilli (2022). "Spatiotemporal control of myofibroblast activation in acoustically-responsive scaffolds via ultrasound-induced matrix stiffening." Acta Biomater 138: 133-143. Full text in pdf format.
   
6. Humphries, B. A., M. Aliabouzar, C. Quesada, A. Bevoor, K. K. Y. Ho, A. Farfel, J. M. Buschhaus, S. Rajendran, M. L. Fabiilli and G. D. Luker (2022). "Ultrasound-Induced Mechanical Compaction in Acoustically Responsive Scaffolds Promotes Spatiotemporally Modulated Signaling in Triple Negative Breast Cancer." Adv Healthc Mater 11(10): e2101672. Full text in pdf format.
   
7. Nelson, M.M., Hoff, J.D., Zeese, M.L., Corfas, G. (2021) Poly (ADP-Ribose) Polymerase 1 Regulates Cajal–Retzius Cell Development and Neural Precursor Cell Adhesion. Frontiers in Cell and Developmental Biology. Full text in pdf format.
8. Kukreja, A.A., Kavuri, S., Joglekar, A.P. (2020) Microtubule Attachment and Centromeric Tension Shape the Protein Architecture of the Human Kinetochore. Current Biology. Full text in pdf format.
9. Dumbrepatil, A.B., Ghosh, S., Zegalia, K.A., Malec, P.A., Hoff, J.D., Kennedy, R.T., Marsh, E.N.G. (2019) Viperin interacts with the kinase IRAK1 and the E3 ubiquitin ligase TRAF6, coupling innate immune signaling to antiviral ribonucleotide synthesis. Journal of Biological Chemistry. Full text in pdf format.
10. Pitchiaya, S., Mourao, M.D.A., Jalihal, A.P., Xiao, L., Jiang, X., Chinnaiyan, A.M., Schnell, S., Walter, N.G. (2019) Dynamic Recruitment of Single RNAs to ProcessingBodies Depends on RNA Functionality. Molecular Cell.  Full text in pdf format.
11. Sladojevic N., Stamatovic S.M., Johnson A.M., Choi J., Hu A., Dithmer S., Blasig I.E., Keep R.F., Andjelkovic A.V. (2019)  Claudin-1-Dependent Destabilization of the Blood-Brain Barrier in Chronic Stroke. Journal of Neuroscience.  Full text in pdf format.
    
12. Wang, X., Sun, M., Ferguson, S.A., Hoff, J.D., Qin, Y., Bailey, R.C., Meyerhoff, M.E. (2019) Ionophore-Based Biphasic Chemical Sensing in Droplet Microfluidics. Angewandte Chemie. Full text in pdf format.
13. Hopkins, T., Swanson, S.D., Hoff, J.D., Potter, N., Ukani, R., Kopelman, R. (2018) Ultracompact Nanotheranostic PEG Platform for Cancer Applications. Applied Bio Materials.  Full text in pdf format.
14.  Tiwari, V., Matutes, Y.A., Gardiner, A.T., Jansen, T.L.C., Cogdell, R.J., Ogilvie, J.P. (2018)  Spatially-resolved fluorescence-detected two-dimensional electronic spectroscopy probesvarying excitonic structure in photosynthetic bacteria. Nature Communications.
15. Barnaba, C., Ravula, T., Medina-Meza, I. G., Im, S-C., Anantharamaiah, G. M., Waskell, L., Ramamoorthy, A. (2018) Lipid-exchange in nanodiscs discloses membrane boundaries of cytochrome-P450 reductase. Chemical Communications.  Full text in pdf format.
16. Barnaba, C., Sahoo, B. R., Ravula, T., Medina-Meza, I.G., Im, S-C., Anantharamaiah, G.M., Waskell, L., Ramamoorthy, A. (2018) Cytochrome-P450-Induced Ordering of Microsomal Membranes Modulates Affinity for Drugs. Angewandte Chemie.  Full text in pdf format.
    
17. Yang, G., Liu, C., Chen, S-H., Kassab, M.A., Hoff, J.D., Walter, N.G., Yu, X. (2018) Super-resolution imaging identifies PARP1 and the Ku complex acting as DNA double-strand break sensors. Nucleic Acid Research. Full text in pdf format.
    
18. Johnson, A.M., Roach, J.P., Hu, A., Stamatovic, S.M., Zochowski, M.R., Keep, R.F., Andjelkovoc, A.V. (2018) Connexin 43 gap junctions contribute to brainendothelial barrier hyperpermeability in familialcerebral cavernous malformations type III bymodulating tight junction structure. FASEB Journal. Full text in pdf format.
19. Hodges, C., Kafle, R.P., Hoff, J.D., Meiners, J-C. (2018) Fluorescence Correlation Spectroscopy with Photobleaching Correction in Slowly Diffusing Systems, Journal of Fluorescence. Full text in pdf format. 
20. Hosono, Y., Niknafs, Y.S., Prensner, J.R., Iyer, M.K., Dhanasekaran, S.M., Mehra, R., Pitchiaya, S., Tien, J., Escar-Wilke, J., Poliakov, A., Chu, S-C., Saleh, S., Sankar, K., Su, F., Guo, S., Qiao, Y., Freier, S., Bui, H-H., Cau, X., Malik, R., Johnson, T.M., Beer, D.G., Feng, F.Y., Zhou, W., Chinnaiyan, A.M. (2017) Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA. Cell. Full text in pdf format.
    
21. 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. (2017) DNA break-induced transcription of non-coding RNA is required for DNA damage response, Nat. Cell Biol. Full text in pdf format.
22. Pitchiaya, S., Heinicke, L.A., Park, J.I., Cameron, E., and Walter, N.G., (2017) Resolving sub-cellular miRNA trafficking and turnover at single-molecule resolution, Cell Reports.  Full text in pdf format.
    
23. 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.
24. 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.
25. Hariadi, R.F., Sommese, R., and Sivaramakrishnan, S. (2015) Tuning myosin-driven sorting on cellular actin networks, eLife. Full text in pdf format.
26. 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.
27. 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
28. 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
29. Bahng, J.H., Yeom, B., Wang, Y., Tung, S.O., Hoff, J.D., Kotov, N. (2015) Anomalous dispersions of ‘hedgehog’ particles. Nature 517
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. 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.
37. 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.
38. 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.
39. 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.
40. 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.
41. 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.
42. 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.
43. 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.
44. 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.
45. 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
46. 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.
47. 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.
48. 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.
49. Walter, N.G. (2007) Future of biomedical sciences: Single molecule microscopy. Biopolymers  85, p. 103-105. Full text in pdf format.
50. 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.
51. 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.
52. Walter, N.G. (2006) Michaelis-Menten is dead, long live Michaelis-Menten! Nature Chem. Biol.  2, p. 66-67. Full text in pdf format.
53. 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.
54. 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.
55. 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.
56. 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.