Publications

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