Zhuang Research Lab
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last updated 02/07/14

Research Summary

The Zhuang research lab works on the forefront of single-molecule biology and bioimaging, developing and applying advanced optical imaging techniques to study the behavior of individual biological molecules and molecular assemblies in vitro and in live cells. Students and postdoctoral fellows in the Zhuang lab apply their diverse backgrounds in chemistry, physics, biology, and engineering to develop new imaging probes and methods and applying these tools to study a variety of interesting biological systems. Our current research is focused on three major directions: (1) Developing super-resolution optical microscopy that allows cell and tissue imaging with nanoscopic scale resolution and applying this technology to cell biology and neurobiology, (2) investigating how biomolecules function, especially how proteins and nucleic acids interact, using single-molecule fluorescence imaging and spectroscopy; (3) Investigating how viruses and cells interact using imaging techniques with high spatiotemporal resolution.

Nanoscopic Optical Imaging

Single-molecule biology: Nucleic Acid - Protein Interactions

Single-virus tracking: Virus-cell Interactions

Storm Image

Nanoscopic Optical Imaging

Optical microscopy is one of the most widely used imaging methods in biomedical research. Several advantages make light microscopy a particularly powerful tool for cell, tissue and animal imaging. These include the exquisite molecular specificity, the relatively fast time resolution and the non-invasive imaging nature. However, the spatial resolution of far-field optical microscopy, classically limited by the diffraction of light to a few hundred nanometers, is substantially larger than typical molecular length scales in cells. This limit leaves many biological problems beyond the reach of light microscopy. To overcome this limit, we have developed a new form of super- resolution light microscopy, stochastic optical reconstruction microscopy (STORM). STORM uses photo-switchable fluorescent probes to temporally separate the otherwise spatially overlapping images of individual molecules, allowing the construction of high-resolution images. Using this concept, we have achieved three-dimensional, multicolor fluorescence imaging of molecular complexes, cells, and tissues with ~10-20 nm resolutions. We have demonstrated live-cell STORM imaging with sub-second time resolution. We hope to advance STORM capabilities to ultimately enable real-time imaging of cells and tissues with resolution at the true molecular length scale. This new form of fluorescence microscopy allows molecular interactions in cells and cell-cell interactions in tissues to be imaged at the nanometer scale. We are applying this new technology to problems in cell biology and neurobiology.

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Nature Method of the Year (2008)

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STORM Workshop (August 2010, April 2012)

Workshop Information

Selected recent publications:

  1. K. Xu, G. Zhong, X. Zhuang, "Actin, spectrin and associated proteins form a periodic cytoskeleton structure in axons", Science 339, 452-456 (2013)
  2. J. Vaughan, S. Jia, X. Zhuang, "Ultra-bright Photoactivatable Fluorophores Created by Reductive Caging", Nature Methods 9, 1181-1184 (2012)
  3. S-H. Shim, C. Xia, G. Zhong, H.P. Babcock, J.C. Vaughan, B. Huang, X. Wang, C. Xu, G-Q. Bi, X. Zhuang "Super-resolution Fluorescence Imaging of Organelles in Live Cells with Photoswitchable Membrane Probes", Proc. Natl. Acad. Sci. 109, 13978-13983 (2012)
  4. W. Wang, G. Li, C. Chen, X. Xie, X. Zhuang, "Chromosome Organization by a Nucleoid Associated Protein", Science 333, 1445-1449 (2011)
  5. B. Huang, H. Babcock, X. Zhuang, "Breaking the diffraction barrier: Super-resolution imaging of cells", Cell 143, 1047-1058 (2010)
  6. B. Huang, W. Wang, M. Bates, X. Zhuang, "Three-dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy", Science 319, 810-813 (2008)
  7. M. Bates, B. Huang, G. T. Dempsey, X. Zhuang, "Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes", Science 317, 1749-1753 (2007)
  8. M. J. Rust, M. Bates, X. Zhuang, "Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)", Nature Methods 3, 793-795 (2006)

Single Molecule Image

Single-Molecule biology:

Nucleic Acid - Protein Interactions

We explore single-molecule fluorescence imaging and spectroscopy techniques to study complex biomolecular systems. An area of special interest to us is the interactions of proteins with nucleic acids. Many essential cellular reactions, such as DNA replication, transcription, messenger RNA editing, and protein synthesis, involve DNA-protein or RNA-protein complexes. Understanding nucleic acid-protein interactions is thus crucial for deciphering the molecular mechanisms underlying many important biological processes. Using single-molecule fluorescence imaging and spectroscopy methods, we directly visualize the assembly and function of these molecular complexes in real time. These experiments allow us to observe transient states and multiple kinetic paths that are difficult to detect by classical ensemble experiments, to probe the dynamic interactions between DNA, RNA and proteins, and to determine the relationship between the structural dynamics and function for these molecular complexes. From these quantitative data, we aim to formulate in-depth mechanistic understanding of these biomolecular processes. Using this approach, we have studied the assembly process, catalytic cycle, and structure-function relationship of several nucleic acid-interacting enzymes, including ribozymes, telomerase, HIV reverse transcriptase and chromatin remodeling enzymes, with the focus currently on chromatin remodeling.

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Selected recent publications:

  1. S. Deindl, W.L. Hwang, S.K. Hota, T.R. Blosser, P. Prasad, B. Bartholomew, X. Zhuang, "ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps", Cell 152, 442-452 (2013)
  2. S. Liu, B.T. Harada, J.T. Miller, S.F.J. Le Grice, X. Zhuang, "Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription", Nature Struct. Mol. Biol. 17, 1453-1460 (2010)
  3. T. Blosser, J. Yang, M. Stone, G. Narlikar, X. Zhuang, "Dynamics of Nucleosome Remodeling by Individual ACF Complexes", Nature 462, 1022-1027 (2009)
  4. S. Liu, E. Abbondanzieri, J. W. Rausch, S. F. J. Le Grice, X. Zhuang, "Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates", Science 322, 1092-1097 (2008)
  5. E. Abbondanzieri, G. Bokinsky, J. W. Rausch, J. X. Zhang, S. F. J. Le Grice, X. Zhuang, "Dynamic binding orientations direct activity of HIV reverse transcriptase", Nature 453, 184-189 (2008)
  6. M. D. Stone, M. Mihalusova, C. M. O'Connor, R. Prathapam, K. Collins, X. Zhuang, "Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein", Nature 446, 458-461 (2007)

Virus Image

Single-virus tracking:

Our research in this direction focuses on virus-cell interactions and related cellular trafficking pathways. Viruses must deliver their genome into cells to initiate infection. This entry process is a subject of fundamental importance as well as a therapeutic target for viral disease treatment. However, understanding viral entry mechanisms is challenging because of the involvement of multiple entry pathways and multiple steps in the pathway, each featuring interactions of the viruses with different cellular structures. What could be a better way to study viral trafficking than to take a ride with the virus particle on its journey into the cell? To realize this goal, we have developed real-time imaging methods to track individual virus particles in live cells. This approach allows us to follow the fate of individual viruses, to dissect the infection pathways into microscopic steps, and to determine the molecular mechanism of each step. By combining this approach with other biochemical methods, we have studied the entry mechanisms of influenza virus, poliovirus, dengue virus and non-viral gene delivery vectors. Our research also extends to the post entry trafficking, assembly and budding mechanisms of viruses.

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Selected recent publications:

  1. C. Chen, X. Zhuang, "Epsin1 is a cargo specific adaptor for the clathrin-mediated endocytosis of influenza virus", Proc. Natl. Acad. Sci. USA 105, 11790-11795 (2008)
  2. B. Brandenburg, L. Y. Lee, M. Lakadamyali, M. J. Rust, X. Zhuang, J. M. Hogle, "Imaging poliovirus entry in live cells", PLoS Biol. 5, e183, 1543-1555 (2007)
  3. B. Brandenburg, X. Zhuang, "Virus trafficking - learning from single-virus tracking", Nat. Rev. Microbiology 5, 197-208 (2007)
  4. M. Lakadamyali, M. J. Rust, X. Zhuang, "Ligands for clathrin-mediated endocytosis are differentially sorted into distinct populations of early endosomes", Cell 124, 997-1009 (2006)
  5. M. J. Rust, M. Lakadamyali, F. Zhang, X. Zhuang, "Assembly of endocytic machinery around individual influenza viruses during viral entry", Nature Struct. Mol. Biol. 11 , 567-573 (2004)