XIAOWEI contact ZHUANG

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Exploring the folding landscape of a structured RNA
    Rick Russell
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:155-60. 2002
  2. pmc A single-molecule assay for telomerase structure-function analysis
    John Y Wu
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Nucleic Acids Res 38:e16. 2010
  3. pmc Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution
    Bo Huang
    Howard Hughes Medical Institute, Harvard University, 12 Oxford St Cambridge, Massachusetts 02138, USA
    Nat Methods 5:1047-52. 2008
  4. pmc Dynamics of nucleosome remodelling by individual ACF complexes
    Timothy R Blosser
    Howard Hughes Medical Institute, Massachusetts 02138, USA
    Nature 462:1022-7. 2009
  5. pmc Dual function of CD81 in influenza virus uncoating and budding
    Jiang He
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
    PLoS Pathog 9:e1003701. 2013
  6. pmc Dissecting the cell entry pathway of dengue virus by single-particle tracking in living cells
    Hilde M van der Schaar
    Department of Medical Microbiology, Molecular Virology Section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
    PLoS Pathog 4:e1000244. 2008
  7. pmc Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription
    Shixin Liu
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Struct Mol Biol 17:1453-60. 2010
  8. pmc Fast, three-dimensional super-resolution imaging of live cells
    Sara A Jones
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 8:499-508. 2011
  9. pmc Photoswitching mechanism of cyanine dyes
    Graham T Dempsey
    Graduate Program in Biophysics, School of Engineering and Applied Sciences, Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    J Am Chem Soc 131:18192-3. 2009
  10. pmc Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging
    Graham T Dempsey
    Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 8:1027-36. 2011

Collaborators

Detail Information

Publications39

  1. pmc Exploring the folding landscape of a structured RNA
    Rick Russell
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:155-60. 2002
    ..Together these results provide an unprecedented view of the topology of an RNA folding landscape and the RNA structural features that underlie this multidimensional landscape...
  2. pmc A single-molecule assay for telomerase structure-function analysis
    John Y Wu
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Nucleic Acids Res 38:e16. 2010
    ..Using this assay, we have identified an active conformation of telomerase among a heterogeneous population of enzymes with distinct structures...
  3. pmc Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution
    Bo Huang
    Howard Hughes Medical Institute, Harvard University, 12 Oxford St Cambridge, Massachusetts 02138, USA
    Nat Methods 5:1047-52. 2008
    ..The 3D STORM images resolved mitochondrial morphologies as well as mitochondria-microtubule contacts that were obscured in conventional fluorescence images...
  4. pmc Dynamics of nucleosome remodelling by individual ACF complexes
    Timothy R Blosser
    Howard Hughes Medical Institute, Massachusetts 02138, USA
    Nature 462:1022-7. 2009
    ..At equilibrium, a continuously bound ACF complex can move the nucleosome back-and-forth many times before dissociation, indicating that ACF is a highly processive and bidirectional nucleosome translocase...
  5. pmc Dual function of CD81 in influenza virus uncoating and budding
    Jiang He
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
    PLoS Pathog 9:e1003701. 2013
    ..In filamentous virus, CD81 was distributed at multiple sites along the viral filament. Taken together, these results demonstrate important roles of CD81 in both entry and budding stages of the influenza infection cycle. ..
  6. pmc Dissecting the cell entry pathway of dengue virus by single-particle tracking in living cells
    Hilde M van der Schaar
    Department of Medical Microbiology, Molecular Virology Section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
    PLoS Pathog 4:e1000244. 2008
    ..Fusion of the viral membrane with the endosomal membrane was primarily detected in late endosomal compartments...
  7. pmc Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription
    Shixin Liu
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Struct Mol Biol 17:1453-60. 2010
    ..These results highlight the important role of the structural dynamics of the initiation complex in directing transitions between early reverse transcription phases...
  8. pmc Fast, three-dimensional super-resolution imaging of live cells
    Sara A Jones
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 8:499-508. 2011
    ..These imaging capabilities open a new window for characterizing cellular structures in living cells at the ultrastructural level...
  9. pmc Photoswitching mechanism of cyanine dyes
    Graham T Dempsey
    Graduate Program in Biophysics, School of Engineering and Applied Sciences, Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    J Am Chem Soc 131:18192-3. 2009
    ..Mass spectrometry suggests that the photoconversion product is a thiol-cyanine adduct in which covalent attachment of the thiol to the polymethine bridge disrupts the original conjugated pi-electron system of the dye...
  10. pmc Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging
    Graham T Dempsey
    Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 8:1027-36. 2011
    ..Our evaluation identified several photoswitchable dyes with good to excellent performance in four independent spectral ranges, with which we demonstrated low-cross-talk, four-color super-resolution imaging...
  11. pmc Multicolor super-resolution fluorescence imaging via multi-parameter fluorophore detection
    Mark Bates
    School of Engineering and Applied Sciences, Graduate Program in Biophysics, Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, 02138, USA
    Chemphyschem 13:99-107. 2012
    ..The combination of multiple fluorescence detection parameters for improved fluorophore discrimination promises to substantially enhance our ability to visualize multiple cellular targets with sub-diffraction-limit resolution...
  12. pmc Ultrabright photoactivatable fluorophores created by reductive caging
    Joshua C Vaughan
    Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 9:1181-4. 2012
    ..Upon photoactivation, these probes can provide 10(4)-10(6) photons per localization and allow imaging of fixed samples with resolutions of several nanometers. This strategy can be applied to many fluorophores across the visible spectrum...
  13. pmc Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton
    Ke Xu
    Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 9:185-8. 2012
    ..We observed two vertically separated layers of actin networks with distinct structural organizations in sheet-like cell protrusions...
  14. ncbi request reprint Single-molecule folding
    Xiaowei Zhuang
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Curr Opin Struct Biol 13:88-97. 2003
    ..Recent applications of these two techniques to the protein and RNA folding problems have led to exciting new results...
  15. ncbi request reprint Molecular biology. Unraveling DNA condensation with optical tweezers
    Xiaowei Zhuang
    Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
    Science 305:188-90. 2004
  16. ncbi request reprint Single-molecule RNA science
    Xiaowei Zhuang
    Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
    Annu Rev Biophys Biomol Struct 34:399-414. 2005
    ....
  17. pmc Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting"
    Shixin Liu
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 104:12634-9. 2007
    ..These results underscore the kinetic interdependence of reversible steps on an enzymatic reaction pathway and demonstrate a potentially general route to dissect them...
  18. pmc Luminescent and Raman active silver nanoparticles with polycrystalline structure
    Jie Zheng
    Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
    J Am Chem Soc 130:10472-3. 2008
    ..The number of photons emitted from these nanoparticles exceeded that from quantum dots or dye molecules by approximately 2 or 5 orders of magnitude, respectively...
  19. pmc Super-resolution fluorescence microscopy
    Bo Huang
    Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
    Annu Rev Biochem 78:993-1016. 2009
    ..It is anticipated that super-resolution fluorescence microscopy will become a widely used tool for cell and tissue imaging to provide previously unobserved details of biological structures and processes...
  20. ncbi request reprint Correlating structural dynamics and function in single ribozyme molecules
    Xiaowei Zhuang
    Department of Physics, Stanford University, Stanford, CA 94305, USA
    Science 296:1473-6. 2002
    ..The complex structural dynamics quantitatively explain the heterogeneous cleavage kinetics common to many catalytic RNAs. The intimate coupling of structural dynamics and function is likely a general phenomenon for RNA...
  21. pmc Two distinct binding modes of a protein cofactor with its target RNA
    Gregory Bokinsky
    Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
    J Mol Biol 361:771-84. 2006
    ..The non-specific interaction potentially increases the local concentration of CBP2 and the number of conformational states accessible to the RNA, which may promote the formation of specific RNA-protein interactions...
  22. pmc Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein
    Michael D Stone
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nature 446:458-61. 2007
    ..These results identify the RNA folding pathway during telomerase biogenesis and define the mechanism of action for an essential telomerase holoenzyme protein...
  23. pmc Single-molecule transition-state analysis of RNA folding
    Gregory Bokinsky
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 100:9302-7. 2003
    ..Such a compact transition state without well formed tertiary contacts may be a general property of elementary RNA folding reactions...
  24. pmc Dynamic binding orientations direct activity of HIV reverse transcriptase
    Elio A Abbondanzieri
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nature 453:184-9. 2008
    ..These results indicate that the activities of reverse transcriptase are determined by its binding orientation on substrates...
  25. pmc Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates
    Shixin Liu
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Science 322:1092-7. 2008
    ..These long-range translocation activities facilitate multiple stages of the reverse transcription pathway, including normal DNA polymerization and strand displacement synthesis...
  26. ncbi request reprint Single-molecule RNA folding
    Gregory Bokinsky
    Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
    Acc Chem Res 38:566-73. 2005
    ....
  27. pmc Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy
    Bo Huang
    Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
    Science 319:810-3. 2008
    ..This development allowed us to resolve the 3D morphology of nanoscopic cellular structures...
  28. pmc Super-resolution microscopy by nanoscale localization of photo-switchable fluorescent probes
    Mark Bates
    School of Engineering and Applied Sciences, Cambridge, MA 02138, United States, USA
    Curr Opin Chem Biol 12:505-14. 2008
    ....
  29. pmc Short-range spectroscopic ruler based on a single-molecule optical switch
    Mark Bates
    Division of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
    Phys Rev Lett 94:108101. 2005
    ..This enables the switch to act as a ruler with the capability to probe distances difficult to access by other spectroscopic methods, thus presenting a new tool for the study of biomolecules at the single-molecule level...
  30. pmc Imaging poliovirus entry in live cells
    Boerries Brandenburg
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
    PLoS Biol 5:e183. 2007
    ..We expect this imaging assay to be broadly applicable to the investigation of entry mechanisms for nonenveloped viruses...
  31. pmc Multicolor super-resolution imaging with photo-switchable fluorescent probes
    Mark Bates
    School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
    Science 317:1749-53. 2007
    ..Using this approach, we demonstrate multicolor imaging of DNA model samples and mammalian cells with 20- to 30-nanometer resolution. This technique will facilitate direct visualization of molecular interactions at the nanometer scale...
  32. pmc Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)
    Michael J Rust
    Department of Physics, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nat Methods 3:793-5. 2006
    ..The fluorophore positions obtained from a series of imaging cycles were used to reconstruct the overall image. We demonstrated an imaging resolution of 20 nm. This technique can, in principle, reach molecular-scale resolution...
  33. pmc Using single-particle tracking to study nuclear trafficking of viral genes
    Hazen P Babcock
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Biophys J 87:2749-58. 2004
    ..We expect this single-particle tracking approach to find broad application in investigations of genetic trafficking...
  34. pmc Electrical detection of single viruses
    Fernando Patolsky
    Department of Chemistry and Chemical Biology, Division of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 101:14017-22. 2004
    ..The possibility of large-scale integration of these nanowire devices suggests potential for simultaneous detection of a large number of distinct viral threats at the single virus level...
  35. pmc Assembly of endocytic machinery around individual influenza viruses during viral entry
    Michael J Rust
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nat Struct Mol Biol 11:567-73. 2004
    ..CCP formation at these sites is much faster than elsewhere on the cell surface, suggesting a virus-induced CCP formation mechanism that may be commonly exploited by many other types of viruses...
  36. pmc Visualizing infection of individual influenza viruses
    Melike Lakadamyali
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 100:9280-5. 2003
    ..This finding suggests a previously undescribed scenario of the endocytic pathway toward late endosomes: endosome maturation, including initial acidification, largely occurs in the perinuclear region...
  37. pmc Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance
    David Rueda
    Department of Chemistry, University of Michigan, Ann Arbor, 48109, USA
    Proc Natl Acad Sci U S A 101:10066-71. 2004
    ..Our findings also have broad implications for applications such as the action of drugs and ligands distal to the active site or the engineering of allostery into RNA...
  38. ncbi request reprint Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA
    Laura E Bartley
    Department of Biochemistry, B400 Beckman Center, Stanford University, Stanford, CA 94305 5307, USA
    J Mol Biol 328:1011-26. 2003
    ..The results described here, combined with previous work, provide an in-depth view of an RNA tertiary structure formation event and suggest that large, highly structured RNAs may have local regions that are misordered...

Research Grants8

  1. Cellular Entry of Influenza by Single-particle Imaging
    Xiaowei Zhuang; Fiscal Year: 2007
    ..These techniques can also be applied to other molecular and cellular biological systems. ..
  2. Cellular Entry of Influenza by Single-particle Imaging
    Xiaowei Zhuang; Fiscal Year: 2004
    ..These techniques can also be applied to other molecular and cellular biological systems. ..
  3. Cellular Entry of Influenza by Single-particle Imaging
    Xiaowei Zhuang; Fiscal Year: 2005
    ..These techniques can also be applied to other molecular and cellular biological systems. ..
  4. Cellular Entry of Influenza by Single-particle Imaging
    Xiaowei Zhuang; Fiscal Year: 2006
    ..These techniques can also be applied to other molecular and cellular biological systems. ..
  5. Cellular Entry of Influenza by Single-particle Imaging
    Xiaowei Zhuang; Fiscal Year: 2007
    ..These techniques can also be applied to other molecular and cellular biological systems. ..
  6. Dynamic cellular architecture of bacteria by system-wide super-resolution imaging
    XIAOWEI contact ZHUANG; Fiscal Year: 2010
    ..The new high-sensitivity, high-resolution imaging techniques and proteomic analysis tools developed here will also have broad applications to other areas of biomedical research. ..
  7. Super-resolution studies of the entry mechanisms of influenza viruses
    Xiaowei Zhuang; Fiscal Year: 2011
    ..Furthermore, the super-resolution imaging approach developed here will have broad applications in many areas of biomedical research. ..