Publications

Gu, Chan; Zhang, Jun; Yang, Y. Isaac; Chen, Xi; Ge, Hao; Sun, Yujie; Su, Xiaodong; Yang, Lijiang; Xie, Sunney; Gao, Yi Qin "DNA Structural Correlation in Short and Long Ranges," J. Phys. Chem. B 119(44), 13980-13990 DOI: 10.1021/acs.jpcb.5b06217 (2015)
Chong, Shasha; Chen, Chongyi; Ge, Hao; Xie, X. Sunney "Mechanism of Transcriptional Bursting in Bacteria," Cell 158(2), 314-326 DOI: 10.1016/j.cell.2014.05.038 (2014)
Xie, X. S. "Enzyme Kinetics, Past and Present," Science 342(6165), 1457-1459 DOI: 10.1126/science.1248859 (2013)
Kim, S.; Brostromer, E.; Xing, D.; Jin, J.; Chong, S.; Ge, H.; Wang, S.; Gu, C.; Yang, L.; Gao, Y. Q.; Su, X.-d.; Sun, Y.; Xie, X. S. "Probing Allostery Through DNA," Science 339(6121), 816-819 DOI: 10.1126/science.1229223 (2013)
Min, Wei; Jiang, Liang; Xie, X. Sunney "Complex Kinetics of Fluctuating Enzymes: Phase Diagram Characterization of a Minimal Kinetic Scheme," Chemistry - An Asian Journal 5(5), 1129-1138 DOI: 10.1002/asia.200900627 (2010)
Kim, Sangjin; Schroeder, Charles M.; Xie, X. Sunney "Single-Molecule Study of DNA Polymerization Activity of HIV-1 Reverse Transcriptase on DNA Templates," Journal of Molecular Biology 395(5), 995-1006 DOI: 10.1016/j.jmb.2009.11.072 (2010)
Blainey, Paul C; Luo, Guobin; Kou, S C; Mangel, Walter F; Verdine, Gregory L; Bagchi, Biman; Xie, X Sunney "Nonspecifically bound proteins spin while diffusing along DNA," Nature Structural & Molecular Biology 16(12), 1224-1229 DOI: 10.1038/nsmb.1716 (2009)
Min, Wei; Xie, X. Sunney; Bagchi, Biman "Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state," J. Chem. Phys. 131(6), 065104 DOI: 10.1063/1.3207274 (2009)
Li, J. J.; Chu, Y.; Lee, B. Y.-H.; Xie, X. S. "Enzymatic signal amplification of molecular beacons for sensitive DNA detection," Nucleic Acids Research 36(6), e36-e36 DOI: 10.1093/nar/gkn033 (2008)
Bagchi, Biman; Blainey, Paul C.; Xie, X. Sunney " Diffusion Constant of a Nonspecifically Bound Protein Undergoing Curvilinear Motion along DNA," J. Phys. Chem. B 112(19), 6282-6284 DOI: 10.1021/jp077568f (2008)
Min, Wei; Xie, X. Sunney; Bagchi, Biman " Two-Dimensional Reaction Free Energy Surfaces of Catalytic Reaction: Effects of Protein Conformational Dynamics on Enzyme Catalysis † ," J. Phys. Chem. B 112(2), 454-466 DOI: 10.1021/jp076533c (2008)
Luo, G.; Wang, M.; Konigsberg, W. H.; Xie, X. S. "Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase," Proceedings of the National Academy of Sciences 104(31), 12610-12615 DOI: 10.1073/pnas.0700920104 (2007)
Kim, Sangjin; Blainey, Paul C; Schroeder, Charles M; Xie, X Sunney "Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA," Nature Methods 4, 397-399 DOI: 10.1038/nmeth1037 (2007)
Min, Wei; Gopich, Irina V.; English, Brian P.; Kou, S. C.; Xie, X. Sunney; Szabo, Attila "When Does the Michaelis−Menten Equation Hold for Fluctuating Enzymes?," J. Phys. Chem. B 110(41), 20093-20097 DOI: 10.1021/jp065187g (2006)
Qian, Hong; Sunney Xie, X. "Generalized Haldane equation and fluctuation theorem in the steady-state cycle kinetics of single enzymes," Phys. Rev. E 74(1) DOI: 10.1103/physreve.74.010902 (2006)
Luo, Guobin; Andricioaei, Ioan; Xie, X. Sunney; Karplus, Martin "Dynamic Distance Disorder in Proteins Is Caused by Trapping," J. Phys. Chem. B 110(19), 9363-9367 DOI: 10.1021/jp057497p (2006)
Blainey, P. C.; van Oijen, A. M.; Banerjee, A.; Verdine, G. L.; Xie, X. S. "A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA," Proceedings of the National Academy of Sciences 103(15), 5752-5757 DOI: 10.1073/pnas.0509723103 (2006)
Lee, Jong-Bong; Hite, Richard K.; Hamdan, Samir M.; Sunney Xie, X.; Richardson, Charles C.; van Oijen, Antoine M. "DNA primase acts as a molecular brake in DNA replication," Nature 439(7076), 621-624 DOI: 10.1038/nature04317 (2006)
Min, Wei; Xie, X. Sunney "Kramers model with a power-law friction kernel: Dispersed kinetics and dynamic disorder of biochemical reactions," Phys. Rev. E 73(1) DOI: 10.1103/physreve.73.010902 (2006)
English, Brian P; Min, Wei; van Oijen, Antoine M; Lee, Kang Taek; Luo, Guobin; Sun, Hongye; Cherayil, Binny J; Kou, S C; Xie, X Sunney "Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited," Nat Chem Biol 2(2), 87-94 DOI: 10.1038/nchembio759 (2006)
Nan, Xiaolin; Sims, Peter A.; Chen, Peng; Xie, X. Sunney "Observation of Individual Microtubule Motor Steps in Living Cells with Endocytosed Quantum Dots," J. Phys. Chem. B 109(51), 24220-24224 DOI: 10.1021/jp056360w (2005)
Min, Wei; Jiang, Liang; Yu, Ji; Kou, S. C.; Qian, Hong; Xie, X. Sunney "Nonequilibrium Steady State of a Nanometric Biochemical System: Determining the Thermodynamic Driving Force from Single Enzyme Turnover Time Traces," Nano Lett. 5(12), 2373-2378 DOI: 10.1021/nl0521773 (2005)
Min, Wei; English, Brian P.; Luo, Guobin; Cherayil, Binny J.; Kou, S. C.; Xie, X. Sunney "Fluctuating Enzymes: Lessons from Single-Molecule Studies," Acc. Chem. Res. 38(12), 923-931 DOI: 10.1021/ar040133f (2005)
Debnath, Pallavi; Min, Wei; Xie, X. Sunney; Cherayil, Binny J. "Multiple time scale dynamics of distance fluctuations in a semiflexible polymer: A one-dimensional generalized Langevin equation treatment," J. Chem. Phys. 123(20), 204903 DOI: 10.1063/1.2109809 (2005)
Kou, S. C.; Sunney Xie, X.; Liu, Jun S. "Bayesian analysis of single-molecule experimental data (with discussion)," Journal of the Royal Statistical Society: Series C (Applied Statistics) 54(3), 469-506 DOI: 10.1111/j.1467-9876.2005.00509.x (2005)
Min, Wei; Luo, Guobin; Cherayil, Binny J.; Kou, S. C.; Xie, X. Sunney "Observation of a Power-Law Memory Kernel for Fluctuations within a Single Protein Molecule," Physical Review Letters 94(19) DOI: 10.1103/physrevlett.94.198302 (2005)
Kou, S. C.; Xie, X. Sunney "Generalized Langevin Equation with Fractional Gaussian Noise: Subdiffusion within a Single Protein Molecule," Physical Review Letters 93(18) DOI: 10.1103/physrevlett.93.180603 (2004)
Cotlet, M.; Masuo, S.; Luo, G.; Hofkens, J.; Van der Auweraer, M.; Verhoeven, J.; Mullen, K.; Xie, X. S.; De Schryver, F. "Probing conformational dynamics in single donor-acceptor synthetic molecules by means of photoinduced reversible electron transfer," Proceedings of the National Academy of Sciences 101(40), 14343-14348 DOI: 10.1073/pnas.0406119101 (2004)
Louie, Tai Man; Xie, X. Sunney; Xun, Luying " Coordinated Production and Utilization of FADH 2 by NAD(P)H−Flavin Oxidoreductase and 4-Hydroxyphenylacetate 3-Monooxygenase † ," Biochemistry 42(24), 7509-7517 DOI: 10.1021/bi034092r (2003)
Dufresne, E. R.; Corwin, E. I.; Greenblatt, N. A.; Ashmore, J.; Wang, D. Y.; Dinsmore, A. D.; Cheng, J. X.; Xie, X. S.; Hutchinson, J. W.; Weitz, D. A. "Flow and Fracture in Drying Nanoparticle Suspensions," Physical Review Letters 91(22) DOI: 10.1103/physrevlett.91.224501 (2003)
Pautot, Sophie; Frisken, Barbara J.; Cheng, Ji-Xin; Xie, X. Sunney; Weitz, D. A. "Spontaneous Formation of Lipid Structures at Oil/Water/Lipid Interfaces," Langmuir 19(24), 10281-10287 DOI: 10.1021/la034532f (2003)
Yang, Haw; Luo, Guobin; Karnchanaphanurach, Pallop; Louie, Tai-Man; Rech, Ivan; Cova, Sergio; Xun, Luying; Xie, X. Sunney "Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer," Science 302(5643), 262-266 DOI: 10.1126/science.1086911 (2003)
van Oijen, Antoine M.; Blainey, Paul C.; Crampton, Donald J.; Richardson, Charles C.; Ellenberger, Tom; Xie, X. Sunney "Single-Molecule Kinetics of Exonuclease Reveal Base Dependence and Dynamic Disorder," Science 301(5637), 1235-1238 DOI: 10.1126/science.1084387 (2003)
Yang, Haw; Xie, X. Sunney "Probing single-molecule dynamics photon by photon," J. Chem. Phys 117, 10965 DOI: (2002)
Xie, X. Sunney "Single-molecule approach to dispersed kinetics and dynamic disorder: Probing conformational fluctuation and enzymatic dynamics," J. Chem. Phys 117, 11024 DOI: (2002)
Yang, Haw; Xie, X. Sunney "Probing Single Molecule Dynamics Photon by Photon," J. Chem. Phys 117, 10965 DOI: (2002)
Luoie, Tai Man; Yang, Haw; Karnchanaphanurach, Pallop; Xie, X. Sunney; Xun, Luying "FAD is a Preferred Substrate and an Inhibitor of Escherichia coli General NAD(P)H: flavin Oxidoreductase," J. Biol. Chem 277, 39450 DOI: (2002)
Yang, Haw; Xie, X. Sunney "Statistical Approaches for Probing Single-molecule Dynamics Photon-by-Photon," Chem. Phys 284, 423 DOI: (2002)
Xie, Sunney "Single-Molecule Approach to Enzymology," Single Mol. 2(4), 229-236 DOI: 10.1002/1438-5171(200112)2:4<229::aid-simo229>3.0.co;2-9 (2001)
Schenter, Gregory K.; Lu, H. Peter; Xie, X. Sunney "Statistical Analyses and Theoretical Models of Single-Molecule Enzymatic Dynamics," J. Phys. Chem. A 103(49), 10477-10488 DOI: (1999)
Zumbusch, Andreas; Holtom, Cary R.; Xie, X. Sunney "Three-Dimensional Vibrational Imaging by Coherent Anti-Stokes Raman Scattering," Physical Review Letters 82, 4142-4145 DOI: (1999)
Xie, X. Sunney; Lu, H. Peter "Single-Molecule Enzymology," J. Biol. Chem 274, 15967 DOI: (1999)
Schenter, Greg K; Lu, H. Peter; Xie, X. Sunney "Statistical Analysis and Theoretical Models of Single-Molecule Enzymatic Dynamics," J. Phys. Chem. A 103, 10477 DOI: (1999)
Bai, Chunli; Wang, Chen; Xie, X. Sunney; Wolynes, Peter, G "Single Molecule Physics and Chemistry," Proc. Natl. Acad. Sci. USA 96, 10477 DOI: (1999)
Lu, H. Peter; Xun, Luying; Xie, X. Sunney "Single Molecule Enzymatic Dynamics," Science 282, 1877 DOI: (1998)
Ying, Liming; Xie, X. Sunney "Fluorescence Spectroscopy, Excitation Dynamics and Photochemistry of Single Allophycocyanin Trimers," J. Phys. Chem. B 102, 10399 DOI: (1998)
Xie, X. Sunney; Trautman, Jay K "Optical studies of single molecules at room temperature," Ann. Rev. Phys. Chem 49, 441 DOI: (1998)