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PMID: 17664434 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

New directions in single-molecule imaging and analysis.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 104 ·No. 31 ·2007-07-31 ·Pages 12596-602

Moerner WE

Abstract

Optical imaging and analysis of single molecules continue to unfold as powerful ways to study the individual behavior of biological systems, unobscured by ensemble averaging. Current expansion of interest in this field is great, as evidenced by new meetings, journal special issues, and the large number of new investigators. Selected recent advances in biomolecular analysis are described, and two new research directions are summarized: superresolution imaging using single-molecule fluorescence and trapping of single molecules in solution by direct suppression of Brownian motion.

MeSH Terms
Biomedical Technology/instrumentation,methods DNA/analysis PubMed Solutions Time Factors
Chemicals
Solutions DNA
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Moerner W E
Department of Chemistry, Stanford University, Stanford, CA 94305, USA. wmoerner@stanford.edu
References (99)
99 references, click to expand
  1. Single-molecule folding.
    Curr Opin Struct Biol. 2003 Feb;13(1):88-97 PMID: 12581665
  2. Tracking kinesin-driven movements with nanometre-scale precision.
    Nature. 1988 Feb 4;331(6155):450-3 PMID: 3123999
  3. Superresolution by localization of quantum dots using blinking statistics.
    Opt Express. 2005 Sep 5;13(18):7052-62 PMID: 19498727
  4. Proposed method for molecular optical imaging.
    Opt Lett. 1995 Feb 1;20(3):237-9 PMID: 19859146
  5. Controlled bimolecular collisions allow sub-diffraction limited microscopy of lipid vesicles.
    Phys Chem Chem Phys. 2006 May 7;8(17):2077-82 PMID: 16633697
  6. Nonlinear optical chromophores as nanoscale emitters for single-molecule spectroscopy.
    Acc Chem Res. 2005 Jul;38(7):549-56 PMID: 16028889
  7. Shot-noise limited single-molecule FRET histograms: comparison between theory and experiments.
    J Phys Chem B. 2006 Nov 9;110(44):22103-24 PMID: 17078646
  8. Single-molecule fluorescence spectroscopy and microscopy of biomolecular motors.
    Annu Rev Phys Chem. 2004;55:79-96 PMID: 15117248
  9. Site-specific labeling of proteins with small molecules in live cells.
    Curr Opin Biotechnol. 2005 Feb;16(1):35-40 PMID: 15722013
  10. Feedback localization of freely diffusing fluorescent particles near the optical shot-noise limit.
    Opt Lett. 2007 Jan 15;32(2):145-7 PMID: 17186045
  11. Theory of single-molecule spectroscopy: beyond the ensemble average.
    Annu Rev Phys Chem. 2004;55:457-507 PMID: 15117260
  12. Single molecule kinetics. II. Numerical Bayesian approach.
    J Chem Phys. 2004 Oct 1;121(13):6373-9 PMID: 15446934
  13. Visualization and tracking of single protein molecules in the cell nucleus.
    Biophys J. 2001 Jun;80(6):2954-67 PMID: 11371468
  14. A revolution in optical manipulation.
    Nature. 2003 Aug 14;424(6950):810-6 PMID: 12917694
  15. Dynamics of single biomolecules in free solution.
    Annu Rev Phys Chem. 2004;55:97-126 PMID: 15117249
  16. An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein.
    Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12651-6 PMID: 12271129
  17. Fluorescence correlation spectroscopy. II. An experimental realization.
    Biopolymers. 1974 Jan;13(1):29-61 PMID: 4818131
  18. Internal mechanical response of a polymer in solution.
    Phys Rev Lett. 2007 Mar 16;98(11):116001 PMID: 17501066
  19. Stochastic protein expression in individual cells at the single molecule level.
    Nature. 2006 Mar 16;440(7082):358-62 PMID: 16541077
  20. Macromolecular-scale resolution in biological fluorescence microscopy.
    Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11440-5 PMID: 16864773
  21. Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase.
    Nature. 2002 Oct 10;419(6907):638-41 PMID: 12374984
  22. Information bounds and optimal analysis of dynamic single molecule measurements.
    Biophys J. 2004 Jun;86(6):4015-29 PMID: 15189897
  23. Real-time observation of RecA filament dynamics with single monomer resolution.
    Cell. 2006 Aug 11;126(3):515-27 PMID: 16901785
  24. Single molecule fluorescence spectroscopy at ambient temperature.
    Chem Rev. 1999 Oct 13;99(10):2929-56 PMID: 11749506
  25. A photoactivatable GFP for selective photolabeling of proteins and cells.
    Science. 2002 Sep 13;297(5588):1873-7 PMID: 12228718
  26. Autofluorescent proteins in single-molecule research: applications to live cell imaging microscopy.
    Biophys J. 2001 May;80(5):2396-408 PMID: 11325739
  27. Suppressing Brownian motion of individual biomolecules in solution.
    Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4362-5 PMID: 16537418
  28. Nanoscale resolution in GFP-based microscopy.
    Nat Methods. 2006 Sep;3(9):721-3 PMID: 16896340
  29. Sequence information can be obtained from single DNA molecules.
    Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3960-4 PMID: 12651960
  30. Free energy surfaces from single-molecule force spectroscopy.
    Acc Chem Res. 2005 Jul;38(7):504-13 PMID: 16028884
  31. Protein conformational dynamics probed by single-molecule electron transfer.
    Science. 2003 Oct 10;302(5643):262-6 PMID: 14551431
  32. I5M: 3D widefield light microscopy with better than 100 nm axial resolution.
    J Microsc. 1999 Jul;195(Pt 1):10-6 PMID: 10444297
  33. Three-color alternating-laser excitation of single molecules: monitoring multiple interactions and distances.
    Biophys J. 2007 Jan 1;92(1):303-12 PMID: 17040983
  34. Optical trapping.
    Rev Sci Instrum. 2004 Sep;75(9):2787-809 PMID: 16878180
  35. Single-molecule fluorescence resonance energy transfer.
    Methods. 2001 Sep;25(1):78-86 PMID: 11558999
  36. Diffusion of lipid-like single-molecule fluorophores in the cell membrane.
    J Phys Chem B. 2006 Apr 20;110(15):8151-7 PMID: 16610918
  37. Biological and chemical applications of fluorescence correlation spectroscopy: a review.
    Biochemistry. 2002 Jan 22;41(3):697-705 PMID: 11790090
  38. Nanometer-localized multiple single-molecule fluorescence microscopy.
    Proc Natl Acad Sci U S A. 2004 Aug 3;101(31):11298-303 PMID: 15277661
  39. Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time.
    Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1419-23 PMID: 15668396
  40. Magnetic tweezers: micromanipulation and force measurement at the molecular level.
    Biophys J. 2002 Jun;82(6):3314-29 PMID: 12023254
  41. Examining nanoenvironments in solids on the scale of a single, isolated impurity molecule.
    Science. 1994 Jul 1;265(5168):46-53 PMID: 17774688
  42. Single-molecule optics.
    Annu Rev Phys Chem. 2004;55:585-611 PMID: 15117263
  43. Single molecules observed by near-field scanning optical microscopy.
    Science. 1993 Nov 26;262(5138):1422-5 PMID: 17736823
  44. Single-molecule imaging of EGFR signalling on the surface of living cells.
    Nat Cell Biol. 2000 Mar;2(3):168-72 PMID: 10707088
  45. Branching out of single-molecule fluorescence spectroscopy: challenges for chemistry and influence on biology.
    Angew Chem Int Ed Engl. 2005 Apr 29;44(18):2642-71 PMID: 15849689
  46. Using photon statistics to boost microscopy resolution.
    Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4797-8 PMID: 16549771
  47. Visualization of single RNA transcripts in situ.
    Science. 1998 Apr 24;280(5363):585-90 PMID: 9554849
  48. Precise nanometer localization analysis for individual fluorescent probes.
    Biophys J. 2002 May;82(5):2775-83 PMID: 11964263
  49. Fluctuating enzymes: lessons from single-molecule studies.
    Acc Chem Res. 2005 Dec;38(12):923-31 PMID: 16359164
  50. Localization accuracy in single-molecule microscopy.
    Biophys J. 2004 Feb;86(2):1185-200 PMID: 14747353
  51. Dynamic polymorphism of single actin molecules in the actin filament.
    Nat Chem Biol. 2006 Feb;2(2):83-6 PMID: 16415860
  52. On/off blinking and switching behaviour of single molecules of green fluorescent protein.
    Nature. 1997 Jul 24;388(6640):355-8 PMID: 9237752
  53. Sorting single molecules: application to diagnostics and evolutionary biotechnology.
    Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):5740-7 PMID: 7517036
  54. Observation of a single-beam gradient force optical trap for dielectric particles.
    Opt Lett. 1986 May 1;11(5):288 PMID: 19730608
  55. Visualization of the movement of single histidine kinase molecules in live Caulobacter cells.
    Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15921-6 PMID: 15522969
  56. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy.
    Nature. 2002 Oct 17;419(6908):743-7 PMID: 12384704
  57. Observation of individual microtubule motor steps in living cells with endocytosed quantum dots.
    J Phys Chem B. 2005 Dec 29;109(51):24220-4 PMID: 16375416
  58. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy.
    Biophys J. 2006 Dec 1;91(11):4258-72 PMID: 16980368
  59. Single pentacene molecules detected by fluorescence excitation in a p-terphenyl crystal.
    Phys Rev Lett. 1990 Nov 19;65(21):2716-2719 PMID: 10042674
  60. Fluorophore-quencher distance correlation functions from single-molecule photon arrival trajectories.
    J Phys Chem B. 2005 Apr 14;109(14):6845-8 PMID: 16851770
  61. Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting.
    Science. 2004 Nov 19;306(5700):1370-3 PMID: 15550670
  62. Single-molecule nanoprobes explore defects in spin-grown crystals.
    J Phys Chem B. 2006 Sep 28;110(38):18939-44 PMID: 16986887
  63. Beyond Rayleigh's criterion: a resolution measure with application to single-molecule microscopy.
    Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4457-62 PMID: 16537357
  64. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy.
    Opt Lett. 1994 Jun 1;19(11):780-2 PMID: 19844443
  65. Probing individual molecules with confocal fluorescence microscopy.
    Science. 1994 Nov 11;266(5187):1018-21 PMID: 7973650
  66. Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution.
    Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13081-6 PMID: 16141335
  67. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM).
    Nat Methods. 2006 Oct;3(10):793-5 PMID: 16896339
  68. Visualizing infection of individual influenza viruses.
    Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9280-5 PMID: 12883000
  69. Creating new fluorescent probes for cell biology.
    Nat Rev Mol Cell Biol. 2002 Dec;3(12):906-18 PMID: 12461557
  70. Probing gene expression in live cells, one protein molecule at a time.
    Science. 2006 Mar 17;311(5767):1600-3 PMID: 16543458
  71. Ten years of tension: single-molecule DNA mechanics.
    Nature. 2003 Jan 23;421(6921):423-7 PMID: 12540915
  72. Cholesterol depletion suppresses the translational diffusion of class II major histocompatibility complex proteins in the plasma membrane.
    Biophys J. 2005 Jan;88(1):334-47 PMID: 15516525
  73. The fluorescent toolbox for assessing protein location and function.
    Science. 2006 Apr 14;312(5771):217-24 PMID: 16614209
  74. A non-Gaussian distribution quantifies distances measured with fluorescence localization techniques.
    Biophys J. 2006 Jan 15;90(2):668-71 PMID: 16258038
  75. Surfaces and orientations: much to FRET about?
    Acc Chem Res. 2005 Jul;38(7):542-8 PMID: 16028888
  76. Single-molecule high-resolution imaging with photobleaching.
    Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6462-5 PMID: 15096603
  77. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism.
    Science. 2006 Nov 17;314(5802):1144-7 PMID: 17110578
  78. Principal-components analysis of shape fluctuations of single DNA molecules.
    Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12622-7 PMID: 17496147
  79. Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins.
    Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17565-9 PMID: 16314572
  80. 3-D particle tracking in a two-photon microscope: application to the study of molecular dynamics in cells.
    Biophys J. 2005 Apr;88(4):2919-28 PMID: 15653748
  81. Living cells as test tubes.
    Science. 2006 Apr 14;312(5771):228-30 PMID: 16614211
  82. Toward fluorescence nanoscopy.
    Nat Biotechnol. 2003 Nov;21(11):1347-55 PMID: 14595362
  83. Single molecules of the bacterial actin MreB undergo directed treadmilling motion in Caulobacter crescentus.
    Proc Natl Acad Sci U S A. 2006 Jul 18;103(29):10929-34 PMID: 16829583
  84. Repetitive shuttling of a motor protein on DNA.
    Nature. 2005 Oct 27;437(7063):1321-5 PMID: 16251956
  85. Optical detection and spectroscopy of single molecules in a solid.
    Phys Rev Lett. 1989 May 22;62(21):2535-2538 PMID: 10040013
  86. Three-dimensional imaging of single molecules solvated in pores of poly(acrylamide) gels.
    Science. 1996 Nov 8;274(5289):966-9 PMID: 8875935
  87. Holding forces of single-particle dielectrophoretic traps.
    Biophys J. 2001 Jan;80(1):531-41 PMID: 11159423
  88. Wide-field subdiffraction imaging by accumulated binding of diffusing probes.
    Proc Natl Acad Sci U S A. 2006 Dec 12;103(50):18911-6 PMID: 17142314
  89. Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models.
    J Phys Chem A. 2003 Sep 3;107(38):7454-7464 PMID: 19626138
  90. Proton-powered subunit rotation in single membrane-bound F0F1-ATP synthase.
    Nat Struct Mol Biol. 2004 Feb;11(2):135-41 PMID: 14730350
  91. Tracking individual kinesin motors in living cells using single quantum-dot imaging.
    Nano Lett. 2006 Jul;6(7):1491-5 PMID: 16834436
  92. Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization.
    Science. 2003 Jun 27;300(5628):2061-5 PMID: 12791999
  93. Imaging intracellular fluorescent proteins at nanometer resolution.
    Science. 2006 Sep 15;313(5793):1642-5 PMID: 16902090
  94. Fluorescence spectroscopy of single biomolecules.
    Science. 1999 Mar 12;283(5408):1676-83 PMID: 10073925
  95. Single-molecule imaging of l-type Ca(2+) channels in live cells.
    Biophys J. 2001 Nov;81(5):2639-46 PMID: 11606277
  96. Alternating-laser excitation of single molecules.
    Acc Chem Res. 2005 Jul;38(7):523-33 PMID: 16028886
  97. Detection of intensity change points in time-resolved single-molecule measurements.
    J Phys Chem B. 2005 Jan 13;109(1):617-28 PMID: 16851054
  98. Control of nanoparticles with arbitrary two-dimensional force fields.
    Phys Rev Lett. 2005 Mar 25;94(11):118102 PMID: 15903893
  99. Fluorescent proteins: maturation, photochemistry and photophysics.
    Curr Opin Struct Biol. 2006 Dec;16(6):714-21 PMID: 17064887
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
Published
2007-07-31
Epub
2007-00-30
Pages
12596-602
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC1937512
Subset
IM
Grants
NCRR NIH HHS · R21 RR023149-02 · United States
NIGMS NIH HHS · R21 GM075166-02 · United States
NIGMS NIH HHS · R21 GM075166 · United States
NHGRI NIH HHS · P20 HG003638 · United States
NHGRI NIH HHS · P20 HG003638-04 · United States
NCRR NIH HHS · 1R21 RR 023149 · United States
NHGRI NIH HHS · 1P20 HG 003638 · United States
NIGMS NIH HHS · 1R21 GM 075166 · United States
NCRR NIH HHS · R21 RR023149-01 · United States
NCRR NIH HHS · R21 RR023149 · United States
Corrections
ErratumIn
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