Zhuang Research Lab
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last updated 01/23/09
 

Publications

  1. H.M. van der Schaar, M.J. Rust, C. Chen, H. van der Ende-Metselaar, J. Wilschut, X. Zhuang, J.M. Smit, "Dissecting the Cell Entry Pathway of Dengue Virus by Single-Particle Tracking in Living Cells", PLOS Pathogens 4, e1000244 (2008)
  2. B. Huang, S.A. Jones, B. Brandenburg, X. Zhuang, "Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution", Nature Methods 5, 1047-1052 (2008)
  3. 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)
  4. M. Bates, B. Huang, X. Zhuang, "Super-resolution microscopy by nanoscale localization of photo-switchable fluorescent probes", Curr. Opin. Chem. Biol. 12, 505-514 (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. 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)
  7. J. Zheng, Y. Ding, B. Tian, Z. Wang, X. Zhuang, "Luminescent and Raman active silver nanoparticles with polycrystalline structure", J. Am. Chem. Soc. 130, 10472-10473 (2008)
  8. B. Huang, W. Wang, M. Bates, X. Zhuang, "Three-dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy", Science 319, 810-813 (2008)
  9. M. Bates, B. Huang, G. T. Dempsey, X. Zhuang, "Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes", Science 317, 1749-1753 (2007)
  10. S. Liu, G. Bokinsky, N. G. Walter, X. Zhuang, "Dissecting the multi-step reaction pathway of an RNA enzyme by single-molecule kinetic fingerprinting", Proc. Natl. Acad. Sci. USA 104, 12634-12639 (2007)
  11. 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)
  12. 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)
  13. B. Brandenburg, X. Zhuang, "Virus trafficking - learning from single-virus tracking", Nat. Rev. Microbiology 5, 197-208 (2007)
  14. Y. Zhou, X. Zhuang, "Kinetic analysis of sequential multi-step reactions", J. Phys. Chem. B 111, 13600-13610, (2007)
  15. H. M. van der Shaar, M. J. Rust, B. Waarts, H. van der Ende Metselaar, R. J. Kuhn, J. Wilschut, X. Zhuang, J. M. Smit, "Characterization of the early events in Dengue virus cell entry by biochemical assays and single-virus tracking", J. Virol. 81, 12019-12028 (2007)
  16. C. K. Payne, S. Jones, C. Chen, X. Zhuang, "Internalization and trafficking of cell surface proteoglycans and proteoglycan binding ligands", Traffic 8, 389-401 (2007)
  17. Y. Zhou, X. Zhuang, "Robust reconstruction of the rate constant distribution using the phase function method", Biophysical Journal 91, 4045-4053 (2006)
  18. M. J. Rust, M. Bates, X. Zhuang, "Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)", Nature Methods 3, 793-795 (2006)
  19. G. Bokinsky, L. G. Nivon, S. Liu, G. Chai, M. Hong, K. M. Weeks, X. Zhuang, "Two distinct binding modes of a protein cofactor with its target RNA", J. Mol. Biol. 361, 771-784 (2006)
  20. 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)
  21. G. Bokinsky, X. Zhuang, "Single-molecule RNA folding", Acc. Chem. Res. 38, 566-573 (2005)
  22. X. Zhuang, "Single-molecule RNA Science", Annu. Rev. Biophys. Biomol. Struct. 34, 399-414 (2005)
  23. M. Bates, T. R. Blosser, X. Zhuang, "Short-range spectroscopic ruler based on a single-molecule optical switch", Phys. Rev. Lett. 94, 108101 (2005)
  24. X. Zhuang, "Unraveling DNA condensation by optical tweezers", Science 305 , 188-190 (2004)
  25. 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)
  26. M. Lakadamyali, M. J. Rust, X. Zhuang, "Endocytosis of influenza viruses", Micro. Infection 6, 929-936 (2004)
  27. F. Patolsky, G. Zheng, O. Hayden, M. Lakadamyali, X. Zhuang, C. M. Lieber, "Electrical detection of single viruses", Proc. Natl. Acad. Sci. USA 101, 14017-14022 (2004)
  28. H. P. Babcock, C. Chen, X. Zhuang, "Using single particle-tracking to study nuclear trafficking of viral genes", Biophys. J. 87, 2749-2758 (2004)
  29. D. Rueda, G. Bokinsky, M. M. Rhodes, M. J. Rust, X. Zhuang, N. G. Walter, "Single-molecule enzymology of RNA: Essential functional groups impact catalysis from a distance", Proc. Natl. Acad. Sci. USA 101, 10066-10071 (2004)
  30. M. Lakadamyali, M. J. Rust, H P. Babcock, X. Zhuang, "Visualizing infection of individual influenza viruses", Proc. Natl. Acad. Sci. USA 100, 9280-9285 (2003)
  31. G. Bokinsky, D. Rueda, V. K. Misra, A. Gordus, M. M. Rhodes, H. P. Babcock, N. G. Walter, X. Zhuang, "Single-molecule transition-state analysis of RNA folding", Proc. Natl. Acad. Sci. USA 100 , 9302-9307 (2003)
  32. X. Zhuang and M. Rief, "Single-molecule folding", Curr. Opin. Struct. Biol. 13 , 88-97 (2003)
  33. L. E. Bartley, X. Zhuang, R. Das, S. Chu, D. Herschlag, "Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA", J. Mol. Biol. 328 , 1011-1026 (2003)
  34. X. Zhuang, H. Kim, M. Pereira, H. Babcock, N. Walter, S. Chu, "Correlating structural dynamics and function in single ribozyme molecules", Science 296 , 1473-1476 (2002)
  35. R. Russell, X. Zhuang, H. Babcock, I. S. Millett, S. Doniach, S. Chu, D. Herschlag, "Exploring the folding landscape of a structured RNA", Proc. Natl. Acad. Sci. USA 99 , 155-160 (2002)
  36. X. Zhuang, L. Bartley, H. Babcock, R. Russell, T. Ha, D. Herschlag, S. Chu, "A single-molecule study of RNA catalysis and folding", Science 288 , 2048-2051 (2000)
  37. X. Zhuang, T. Ha, H. Kim, T. Centner, S. Labeit, S. Chu, "Fluorescence quenching: a tool for single-molecule protein-folding study", Proc. Natl. Acad. Sci. USA 97 , 14241-14244 (2000)
  38. T. Ha, X. Zhuang, H. Kim, J. Orr, J. Williamson, S. Chu, "Ligand-induced conformational changes of single RNA molecules", Proc. Natl. Acad. Sci. USA 96 , 9077-9082 (1999)
  39. S.-C. Hong, M. Oh-e, X. Zhuang, Y. R. Shen, J. J. Ge, F. W. Harris, S. Z. D. Cheng, "Orientation of side chains and adsorbed liquid crystal molecules on a rubbed polyimide surface studied by optical harmonic generation", Phys. Rev. E 63 , 0517061-7 (2001)
  40. J. J. Ge, C. Y. Li, G.I. Xue, I. K. Mann, S. Z. D. Cheng, J. Z. Zhang, D. Zhang, S. Wang, F. W. Harris, S.-C. Hong, X. Zhuang, Y. R. Shen, "Rubbing-induced molecular reorientation on an alignment surface of an aromatic polyimide containing cyanobiphenyl side chains", J. Am. Chem. Soc. 123 , 5768-5776 (2001)
  41. X. Wei, X. Zhuang, D. Kim, S.-C. Hong, T. Goto, and Y. R. Shen, "Vibrational spectroscopy of rubbed polymer surfaces", Mole. Cryst. Liq. Cryst. 358 , 103-108 (2001)
  42. X. Wei, S. Hong, X. Zhuang, T. Goto, Y. R. Shen, "Nonlinear optical studies of liquid crystal alignment on a rubber polyvinyl alcohol surface", Phys. Rev. E 62 , 5160-5172, (2000)
  43. X. Wei, X. Zhuang, S. Hong, T. Goto, Y. R. Shen, "Sum-Frequency vibrational spectroscopic study of a rubbed polymer surface", Phys. Rev. Lett. 82 , 4256-4259 (1999)
  44. X. Zhuang, P. B. Miranda, D. Kim, Y. R. Shen, "Mapping molecular orientation and conformation at interfaces by surface nonlinear optics", Phys. Rev. B 59 , 12632-12640 (1999)
  45. T. Qian, X. Zhuang, Y. R. Shen, "Surface-monolayer-induced bulk alignment of liquid crystals: from nematic to smectic-a phase", Phys. Rev. E 59 , 1873-1879 (1999)
  46. X. Zhuang, R. Muenster, M. Jarasch, Y. R. Shen, "Dye-induced enhancement of optical nonlinearity in liquid crystals and ordinary liquids", Mole. Cryst. Liq. Cryst. 321 , 165-172 (1998)
  47. J. J. Ge, G.Xue, K. W. McCreight, S. Wang, F. W. Harris, S. Z. D. Cheng, X. Zhuang, S. Hong, Y. R. Shen, "Surface studies of polyimide thin films via surface enhanced Raman scattering and second harmonic generation", Macromol. Rapid Comm. 19 , 619-623 (1998)
  48. R. Muenster, M. Jarasch, X. Zhuang, Y. R. Shen, "Enhanced optical kerr effect of dye-doped isotropic liquid", Phys. Rev. Lett. 78 , 42-45 (1997)
  49. A. Le Calvez, S. Montant, E. Freysz, A. Ducasse, X. Zhuang, Y. R. Shen, "Ultrafast orientation dynamics of liquid crystals in smectic phase", Chem. Phys. Lett. 258 , 620-625 (1996)
  50. X. Zhuang and Y. R. Shen, "The application of nonlinear optics to the study of polymers at interfaces", Trends Polym. Sci. 4 , 258-264 (1996)
  51. X. Zhuang, H. S. Lackritz, and Y. R. Shen, "Photo-isomerization of polymer monolayers and multi-layers on water", Chem. Phys. Lett. 246 , 279-284 (1995)
  52. X. Zhuang, D. Wilk, L. Marrucci, and Y. R. Shen, "Orientation of amphiphilic molecules on polar substrates", Phys. Rev. Lett. 75 , 2144-2147 (1995)
  53. X. Zhuang, L. Marrucci, D. Johannsmann, and Y. R. Shen, "Dependence of liquid crystal bulk alignment on its surface monolayer", Mole. Cryst. Liq. Cryst. 262 , 35-43 (1995)
  54. X. Zhuang, L. Marrucci, and Y. R. Shen, "Surface-monolayer-induced bulk alignment of liquid crystals", Phys. Rev. Lett. 73 , 1513-1516 (1994)