Extending single molecule fluorescence observation time by amplitude-modulated excitation

Methods and Applications in Fluorescence

Volumn 1, Issue 3, 2013, Pages

  Kisley, Lydia ^a   Chang, Wei Shun ^a   Cooper, David ^a   Mansur, Andrea P ^a   Landes, Christy F ^a,b  

^a RICE UNIVERSITY   (United States)

^b Rice University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84890102569     PISSN: None     EISSN: 20506120     Source Type: Journal    
DOI: 10.1088/2050-6120/1/3/037001     Document Type: Article

References (61)

1. Landes C F, Rambhadran A, Taylor J N, Salatan F and Jayaraman V 2011 Structural landscape of isolated agonist-binding domains from single AMPA receptors Nature Chem. Biol. 7 168-73
2. Michalet X, Weiss S and Jäger M 2006 Single-molecule fluorescence studies of protein folding and conformational dynamics Chem. Rev. 106 1785-8133
3. Merchant K A, Best R B, Louis J M, Gopich I V and Eaton W A 2007 Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations Proc. Natl Acad. Sci. USA 104 1528-33
4. Schuler B and Eaton W A 2008 Protein folding studied by single-molecule FRET Curr. Opin. Struct. Biol. 18 16-26
5. Rhoades E, Cohen M, Schuler B and Haran G 2004 Two-state folding observed in individual protein molecules J. Am. Chem. Soc. 126 14686-7
6. Darugar Q, Kim H, Gorelick R J and Landes C 2008 HTLV-1 nucleocapsid protein-induced structural changes in TAR-DNA hairpin measured by single-molecule FRET J. Virol. 82 12164-71
7. Nick Taylor J, Darugar Q, Kourentzi K, Willson R C and Landes C F 2008 Dynamics of an anti-VEGF DNA aptamer: a single-molecule study Biochem. Biophys. Res. Commun. 373 213-8
8. Zhuang X 2005 Single-molecule RNA science Annu. Rev. Biophys. Biomol. Struct. 34 399-414
9. Roy R, Hohng S and Ha T 2008 A practical guide to single-molecule FRET Nature Methods 5 507-16
10. Shuang B, Byers C P, Kisley L, Wang L-Y, Zhao J, Morimura H, Link S and Landes C F 2012 Improved analysis for determining diffusion coefficients from short, single-molecule trajectories with photoblinking Langmuir 29 228-34
11. Bonnet I et al 2008 Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA Nucl. Acids Res. 36 4118-27
12. Claytor K, Khatua S, Guerrero J M, Tcherniak A, Tour J M and Link S 2009 Accurately determining single molecule trajectories of molecular motion on surfaces J. Chem. Phys. 130 164710
13. Khatua S, Godoy J, Tour J M and Link S 2010 Influence of the substrate on the mobility of individual nanocars J. Phys. Chem. Lett. 1 3288-91
14. Khatua S, Guerrero J M, Claytor K, Vives G, Kolomeisky A B, Tour J M and Link S 2009 Micrometer-scale translation and monitoring of individual nanocars on glass ACS Nano 3 351-6
15. Chu P-L E, Wang L-Y, Khatua S, Kolomeisky A B, Link S and Tour J M 2013 Synthesis and single-molecule imaging of highly mobile adamantane-wheeled nanocars ACS Nano 7 35-41
16. Yildiz A, Forkey J N, McKinney S A, Ha T, Goldman Y E and Selvin P R 2003 Myosin V walks hand-over-hand: single fluorophore imaging with 1.5 nm localization Science 300 2061-5
17. Veigel C and Schmidt C F 2011 Moving into the cell: single-molecule studies of molecular motors in complex environments Nature Rev. Mol. Cell Biol. 12 163-76
18. Sako Y and Yanagida T 2003 Single-molecule visualization in cell biology Nature Rev. Mol. Cell Bio. 4 (Suppl) SS1-15
19. Lakowicz J R 2006 Principles of Fluorescence Spectroscopy (New York: Springer)
20. Wang B, Anthony S M, Bae S C and Granick S 2009 Anomalous yet brownian Proc. Natl. Acad. Sci. USA 106 15160-4
21. Calamai M and Pavone F S 2011 Single molecule tracking analysis reveals that the surface mobility of amyloid oligomers is driven by their conformational structure J. Am. Chem. Soc. 133 12001-8
22. Gunnarsson A, Jonsson P, Marie R, Tegenfeldt J O and Hook F 2007 Single-molecule detection and mismatch discrimination of unlabeled DNA targets Nano Lett. 8 183-8
23. Guan J, Wang B and Granick S 2011 Automated singlemolecule imaging to track DNA shape Langmuir 27 6149-54
24. Thompson R E, Larson D R and Webb W W 2002 Precise nanometer localization analysis for individual fluorescent probes Biophys. J. 82 2775-83
25. Tcherniak A, Reznik C, Link S and Landes C F 2008 Fluorescence correlation spectroscopy: criteria for analysis in complex systems Anal. Chem. 81 746-54
26. Ha T and Tinnefeld P 2012 Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging Annu. Rev. Phys. Chem. 63 595-617
27. Vogelsang J, Kasper R, Steinhauer C, Person B, Heilemann M, Sauer M and Tinnefeld P 2008 A reducing and oxidizing system minimizes photobleaching and blinking of fluorescent dyes Angew. Chem. Int. Edn 47 5465-9
28. Aitken C E, Marshall R A and Puglisi J D 2008 An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments Biophys. J. 94 1826-35
29. Shi X, Lim J and Ha T 2010 Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe Anal. Chem. 82 6132-8
30. Dave R, Terry D S, Munro J B and Blanchard S C 2009 Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging Biophys. J. 96 2371-81
31. Campos L A, Liu J, Wang X, Ramanathan R, English D S and Munoz V 2011 A photoprotection strategy for microsecond-resolution single-molecule fluorescence spectroscopy Nature Methods 8 143-6
32. Rasnik I, McKinney S A and Ha T 2006 Nonblinking and long-lasting single-molecule fluorescence imaging Nature Methods 3 891-3
33. Altman R B et al 2012 Cyanine fluorophore derivatives with enhanced photostability Nature Methods 9 68-71
34. Altman R B, Zheng Q, Zhou Z, Terry D S, Warren J D and Blanchard S C 2012 Enhanced photostability of cyanine fluorophores across the visible spectrum Nature Methods 9 428-9
35. Schmidt T, Schuetz G J, Baumgartner W, Gruber H J and Schindler H 1995 Characterization of photophysics and mobility of single molecules in a fluid lipid membrane J. Phys. Chem. 99 17662-8
36. Willets K A, Ostroverkhova O, He M, Twieg R J and Moerner W E 2003 Novel fluorophores for single-molecule imaging J. Am. Chem. Soc. 125 1174-5
37. Bouffard J, Kim Y, Swager T M, Weissleder R and Hilderbrand S A 2007 A highly selective fluorescent probe for thiol bioimaging Org. Lett. 10 37-40
38. Butler R N, Fahy A M, Fox A, Stephens J C, McArdle P, Cunningham D and Ryder A G 2006 New reactive fluorophores in the 1, 2, 3-triazine series Tetrahedron Lett. 47 1721-4
39. Landes C F, Zeng Y, Liu H-W, Musier-Forsyth K and Barbara P F 2007 Single-molecule study of the inhibition of HIV-1 transactivation response region DNA/DNA annealing by argininamide J. Am. Chem. Soc. 129 10181-8
40. Zeng Y, Liu H-W, Landes C F, Kim Y J, Ma X, Zhu Y, Musier-Forsyth K and Barbara P F 2007 Probing nucleation, reverse annealing, and chaperone function along the reaction path of HIV-1 single-strand transfer Proc. Natl Acad. Sci. USA 104 12651-6
41. Peterson E M and Harris J M 2009 Quantitative detection of single molecules in fluorescence microscopy images Anal. Chem. 82 189-96
42. Michalet X et al 2013 Development of new photon-counting detectors for single-molecule fluorescence microscopy Phil. Trans. R. Soc. B 368 20120035
43. Andor iXon3 897 specifications sheet. www.andor.com/scientific-cameras/ixon-emccd-camera-series/ixon3-897 (accessed 2 April 2013)
44. Eggeling C, Widengren J, Brand L, Schaffer J, Felekyan S and Seidel C A M 2006 Analysis of photobleaching in single-molecule multicolor excitation and förster resonance energy transfer measurements J. Phys. Chem. A 110 2979-95
45. Kong X, Nir E, Hamadani K and Weiss S 2007 Photobleaching pathways in single-molecule FRET experiments J. Am. Chem. Soc. 129 4643-54
46. Hubner C G, Renn A, Renge I and Wild U P 2001 Direct observation of the triplet lifetime quenching of single dye molecules by molecular oxygen J. Chem. Phys. 115 9619-22
47. Rust M J, Bates M and Zhuang X 2006 Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) Nature Methods 3 793-6
48. Betzig E, Patterson G H, Sougrat R, Lindwasser O W, Olenych S, Bonifacino J S, Davidson M W, Lippincott-Schwartz J and Hess H F 2006 Imaging intracellular fluorescent proteins at nanometer resolution Science 313 1642-5
49. Hess S T, Girirajan T P K and Mason M D 2006 Ultra-high resolution imaging by fluorescence photoactivation localization microscopy Biophys. J. 91 4258-72
50. Sharonov A and Hochstrasser R M 2006 Wide-field subdiffraction imaging by accumulated binding of diffusing probes Proc. Natl Acad. Sci. USA 103 18911-6
51. Zhou X, Andoy N M, Liu G, Choudhary E, Han K-S, Shen H and Chen P 2012 Quantitative super-resolution imaging uncovers reactivity patterns on single nanocatalysts Nature Nanotechnol. 7 237-41
52. Weber M L and Willets K A 2012 Nanoscale studies of plasmonic hot spots using super-resolution optical imaging MRS Bull. 37 745-51
53. Patterson G, Davidson M, Manley S and Lippincott-Schwartz J 2010 Superresolution imaging using single-molecule localization Annu. Rev. Phys. Chem. 61 345-67
54. Kasper R, Harke B, Forthmann C, Tinnefeld P, Hell S W and Sauer M 2010 Single-molecule sted microscopy with photostable organic fluorophores Small 6 1379-84
55. Bates M, Huang B, Dempsey G T and Zhuang X 2007 Multicolor super-resolution imaging with photo-switchable fluorescent probes Science 317 1749-53
56. Kapanidis A N, Laurence T A, Lee N K, Margeat E, Kong X and Weiss S 2005 Alternating-laser excitation of single molecules Acc. Chem. Res. 38 523-33
57. Kapanidis A N, Lee N K, Laurence T A, Doose S, Margeat E and Weiss S 2004 Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules Proc. Natl Acad. Sci. USA 101 8936-41
58. Koopmans W, Brehm A, Logie C, Schmidt T and van Noort J 2007 Single-pair FRET microscopy reveals mononucleosome dynamics J. Fluorescence 17 785-95
59. Margeat E, Kapanidis A N, Tinnefeld P, Wang Y, Mukhopadhyay J, Ebright R H and Weiss S 2006 Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes Biophys. J. 90 1419-31
60. Traub M C, Lakhwani G, Bolinger J C, Vanden Bout D and Barbara P F 2011 Electronic energy transfer in highly aligned MEH-PPV single chains J. Phys. Chem. B 115 9941-7
61. Wei C-Y J and Vanden Bout D A 2009 Nonexponential relaxation of poly(cyclohexyl acrylate): comparison of single-molecule and ensemble fluorescence studies J. Phys. Chem. B 113 2253-61