Anti-Brownian Traps for Studies on Single Molecules

Methods in Enzymology

Volumn 475, Issue C, 2010, Pages 149-174

  Fields, Alexander P ^a   Cohen, Adam E ^b,c  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIMETICONE; NUCLEIC ACID; PLATINUM; FLUORESCENT DYE; MOLECULAR PROBE;

ADSORPTION; AQUEOUS SOLUTION; BOOK; CATALYSIS; CONFOCAL MICROSCOPY; DESORPTION; ELECTRIC FIELD; ELECTRODE; ELECTROOSMOSIS; ELECTROPHORESIS; FEEDBACK SYSTEM; HYDRODYNAMICS; IN VITRO STUDY; IN VIVO STUDY; INFRARED RADIATION; LASER; LIPID VESICLE; MAGNETIC FIELD; MICROFLUIDICS; MOLECULE; OPTICAL TWEEZERS; PHOTON; PRIORITY JOURNAL; ROOM TEMPERATURE; SPECTROSCOPY; SYSTEMATIC REVIEW; VISCOSITY; ALGORITHM; CHEMISTRY; MOLECULAR PROBE; SPECTROFLUOROMETRY;

ALGORITHMS; FLUORESCENT DYES; LASERS; MICROFLUIDICS; MICROSCOPY, CONFOCAL; MOLECULAR PROBES; SPECTROMETRY, FLUORESCENCE;

EID: 77954591428     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(10)75007-2     Document Type: Chapter

References (64)

1. Abbondanzieri E.A., Bokinsky G., Rausch J.W., Zhang J.X., Le Grice S.F.J., Zhuang X. Dynamic binding orientations direct activity of HIV reverse transcriptase. Nature 2008, 453:184-189.
2. Armani M., Chaudhary S., Probst R., Walker S., Shapiro B. Control of microfluidic systems: Two examples, results, and challenges. Int. J. Robust Nonlinear Control 2005, 15:785.
3. Armani M., Chaudhary S., Probst R., Shapiro B. Using feedback control of microflows to independently steer multiple particles. J. Microelectromech. Syst. 2006, 15:945-956.
4. Arnold S., Hessel N. Photoemission from single electrodynamically levitated microparticles. Rev. Sci. Instrum. 1985, 56:2066.
5. Berg H.C. How to track bacteria. Rev. Sci. Instrum. 1971, 42:868.
6. Berg H.C. Random Walks in Biology 1993, Princeton University Press, Princeton, NJ.
7. Berglund A.J., Mabuchi H. Feedback controller design for tracking a single fluorescent molecule. Appl. Phys. B 2004, 78:653-659.
8. Berglund A.J., Mabuchi H. Tracking-FCS: Fluorescence correlation spectroscopy of individual particles. Opt. Express 2005, 13:8069-8082.
9. Berglund A.J., Mabuchi H. Performance bounds on single-particle tracking by fluorescence modulation. Appl. Phys. B 2006, 83:127-133.
10. Berglund A.J., McHale K., Mabuchi H. Feedback localization of freely diffusing fluorescent particles near the optical shot-noise limit. Opt. Lett. 2007, 32:145-147.
11. Boukobza E., Sonnenfeld A., Haran G. Immobilization in surface-tethered lipid vesicles as a new tool for single biomolecule spectroscopy. J. Phys. Chem. B 2001, 105:12165-12170.
12. Brocchieri L., Karlin S. Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res. 2005, 33:3390.
13. Brune D., Kim S. Predicting protein diffusion coefficients. Proc. Natl. Acad. Sci. USA 1993, 90:3835-3839.
14. Bustamante C., Bryant Z., Smith S.B. Ten years of tension: Single-molecule DNA mechanics. Nature 2003, 421:423-427.
15. Cai L., Friedman N., Xie X.S. Stochastic protein expression in individual cells at the single molecule level. Nature 2006, 440:358-362.
16. Cang H., Wong C.M., Xu C.S., Rizvi A.H., Yang H. Confocal three dimensional tracking of a single nanoparticle with concurrent spectroscopic readouts. Appl. Phys. Lett. 2006, 88:223901.
17. Cang H., Xu C.S., Montiel D., Yang H. Guiding a confocal microscope by single fluorescent nanoparticles. Opt. Lett. 2007, 32:2729-2731.
18. Cang H., Xu C.S., Yang H. Progress in single-molecule tracking spectroscopy. Chem. Phys. Lett. 2008, 457:285-291.
19. Chaudhary S., Shapiro B. Arbitrary steering of multiple particles independently in an electro-osmotically driven microfluidic system. IEEE Trans. Control Syst. Technol. 2006, 14:669-680.
20. Chen Y., Müller J.D., So P.T.C., Gratton E. The photon counting histogram in fluorescence fluctuation spectroscopy. Biophys. J. 1999, 77:553-567.
21. Cisse I., Okumus B., Joo C., Ha T. Fueling protein DNA interactions inside porous nanocontainers. Proc. Natl. Acad. Sci. USA 2007, 104:12646.
22. Cohen A.E. Control of nanoparticles with arbitrary two-dimensional force fields. Phys. Rev. Lett. 2005, 94:118102.
23. Cohen A.E., Moerner W.E. An all-glass microfluidic cell for the ABEL trap: Fabrication and modeling. Proc. SPIE 2005, 5930:191-198.
24. Cohen A.E., Moerner W.E. The anti-Brownian electrophoretic trap (ABEL Trap): Fabrication and software. Proc. SPIE 2005, 5699:296.
25. Cohen A.E., Moerner W.E. Method for trapping and manipulating nanoscale objects in solution. Appl. Phys. Lett. 2005, 86:093109.
26. Cohen A.E., Moerner W.E. Suppressing Brownian motion of individual biomolecules in solution. Proc. Natl. Acad. Sci. USA 2006, 103:4362-4365.
27. Cohen A.E., Moerner W.E. Internal mechanical response of a polymer in solution. Phys. Rev. Lett. 2007, 98:116001.
28. Cohen A.E., Moerner W.E. Principal-components analysis of shape fluctuations of single DNA molecules. Proc. Natl. Acad. Sci. USA 2007, 104:12622.
29. Cohen A.E., Moerner W.E. Controlling Brownian motion of single protein molecules and single fluorophores in aqueous buffer. Opt. Express 2008, 16:6941-6956.
30. Davis L., Sikorski Z., Robinson W., Shen G., Li X., Canfield B., Lescano I., Bomar B., Hofmeister W., Germann J., King J., White Y., Terekhov A. Maximum-likelihood position sensing and actively controlled electrokinetic transport for single-molecule trapping. Proc. SPIE 2008, 6862:68620P.
31. Dertinger T., Pacheco V., von der Hocht I., Hartmann R., Gregor I., Enderlein J. Two-focus fluorescence correlation spectroscopy: A new tool for accurate and absolute diffusion measurements. ChemPhysChem 2007, 8:433-443.
32. Dickson R.M., Norris D.J., Moerner W.E. Simultaneous imaging of individual molecules aligned both parallel and perpendicular to the optic axis. Phys. Rev. Lett. 1998, 81:5322-5325.
33. Einstein A. On the movement of small particles suspended in stationary liquids required by the molecular-kinetic theory of heat. Ann. Phys. 1905, 17:549-560.
34. Enderlein J. Tracking of fluorescent molecules diffusing within membranes. Appl. Phys. B 2000, 71:773-777.
35. Gore J., Bryant Z., Stone M.D., Nollmann M.N., Cozzarelli N.R., Bustamante C. Mechanochemical analysis of DNA gyrase using rotor bead tracking. Nature 2006, 439:100-104.
36. Gosse C., Croquette V. Magnetic tweezers: Micromanipulation and force measurement at the molecular level. Biophys. J. 2002, 82:3314-3329.
37. Ha T. Single-molecule fluorescence methods for the study of nucleic acids. Curr. Opin. Struct. Biol. 2001, 11:287-292.
38. Ha T., Ting A.Y., Liang J., Caldwell W.B., Deniz A.A., Chemla D.S., Schultz P.G., Weiss S. Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism. Proc. Natl. Acad. Sci. USA 1999, 96:893.
39. Ha T., Zhuang X., Kim H.D., Orr J.W., Williamson J.R., Chu S. Ligand-induced conformational changes observed in single RNA molecules. Proc. Natl. Acad. Sci. USA 1999, 96:9077.
40. Hamilton J.D. Time Series Analysis 1994, Princeton University Press, Princeton, NJ.
41. Jiang Y., Wang Q., Cohen A.E., Douglas N., Frydman J., Moerner W.E. Hardware-based anti-Brownian electrokinetic trap (ABEL Trap) for single molecules: Control loop simulations and application to ATP binding stoichiometry in multi-subunit enzymes. Proc. SPIE 2008, 7038:703807.
42. Katsura S., Yamaguchi A., Inami H., Matsuura S., Hirano K., Mizuno A. Indirect micromanipulation of single molecules in water-in-oil emulsion. Electrophoresis 2001, 22:289-293.
43. Kim S.Y., Semyonov A.N., Twieg R.J., Horwich A.L., Frydman J., Moerner W.E. Probing the sequence of conformationally induced polarity changes in the molecular chaperonin GroEL with fluorescence spectroscopy. J. Phys. Chem. B 2005, 109:24517-24525.
44. Kim S.Y., Gitai Z., Kinkhabwala A., Shapiro L., Moerner W.E. Single molecules of the bacterial actin MreB undergo directed treadmilling motion in Caulobacter crescentus. Proc. Natl. Acad. Sci. USA 2006, 103:10929-10934.
45. Lessard G.A., Goodwin P.M., Werner J.H. Three-dimensional tracking of individual quantum dots. Appl. Phys. Lett. 2007, 91:224106.
46. Levi V., Gratton E. Chromatin dynamics during interphase explored by single-particle tracking. Chromosome Res. 2008, 16:439-449.
47. Levi V., Ruan Q., Kis-Petikova K., Gratton E. Scanning FCS, a novel method for three-dimensional particle tracking. Biochem. Soc. Trans. 2003, 31:997-1000.
48. Levi V., Ruan Q., Gratton E. 3-D particle tracking in a two-photon microscope: Application to the study of molecular dynamics in cells. Biophys. J. 2005, 88:2919-2928.
49. Li X., Hofmeister W., Shen G., Davis L., Daniel C. Fabrication and characterization of nanofluidics device using fused silica for single protein molecule detection. Medical Device Materials IV (Proceedings of the Materials and Processes for Medical Devices Conference 2007) 2008, 145-150. ASM International, Materials Park, OH. J. Gilbert (Ed.).
50. Lipman E.A., Schuler B., Bakajin O., Eaton W.A. Single-molecule measurement of protein folding kinetics. Science 2003, 301:1233.
51. Lu H.P., Xun L., Xie X.S. Single-molecule enzymatic dynamics. Science 1998, 282:1877-1882.
52. Lu P.J., Sims P.A., Oki H., Macarthur J.B., Weitz D.A. Target-locking acquisition with real-time confocal (TARC) microscopy. Opt. Express 2007, 15:8702-8712.
53. McHale K., Berglund A.J., Mabuchi H. Quantum dot photon statistics measured by three-dimensional particle tracking. Nano Lett. 2007, 7:3535-3539.
54. Meseth U., Wohland T., Rigler R., Vogel H. Resolution of fluorescence correlation measurements. Biophys. J. 1999, 76:1619-1631.
55. Mills R. Self-diffusion in normal and heavy water in the range 1-45°. J. Phys. Chem. 1973, 77:685-688.
56. Plenert M.L., Shear J.B. Microsecond electrophoresis. Proc. Natl. Acad. Sci. USA 2003, 100:3853-3857.
57. Svoboda K., Schmidt C.F., Schnapp B.J., Block S.M. Direct observation of Kinesin stepping by optical trapping interferometry. Nature 1993, 365:721-727.
58. Toussaint K.C., Liu M., Pelton M., Pesic J., Guffey M.J., Guyot-Sionnest P., Scherer N.F. Plasmon resonance-based optical trapping of single and multiple Au nanoparticles. Opt. Express 2007, 15:12017-12029.
59. Tyn M.T., Gusek T.W. Prediction of diffusion coefficients of proteins. Biotechnol. Bioeng. 1990, 35:327-338.
60. Valentine M.T., Guydosh N.R., Gutiérrez-Medina B., Fehr A.N., Andreasson J.O., Block S.M. Precision steering of an optical trap by electro-optic deflection. Opt. Lett. 2008, 33:599-601.
61. Voldman J., Braff R.A., Toner M., Gray M.L., Schmidt M.A. Holding forces of single-particle dielectrophoretic traps. Biophys. J. 2001, 80:531-541.
62. Wang H.Y., Foote R.S., Jacobson S.C., Schneibel J.H., Ramsey J.M. Low temperature bonding for microfabrication of chemical analysis devices. Sens. Actuators B 1997, 45:199-207.
63. Wen J.D., Lancaster L., Hodges C., Zeri A.C., Yoshimura S.H., Noller H.F., Bustamante C., Tinoco I. Following translation by single ribosomes one codon at a time. Nature 2008, 452:598-603.
64. Xu C.S., Cang H., Montiel D., Yang H. Rapid and quantitative sizing of nanoparticles using three-dimensional single-particle tracking. J. Phys. Chem. C 2007, 111:32-35.