Simple method to enhance the photostability of the fluorescence reporter R6G for prolonged single-molecule studies

Journal of Physical Chemistry A

Volumn 117, Issue 29, 2013, Pages 6164-6170

  Guo, Lin ^a   Gai, Feng ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL REAGENTS; CONFINED ENVIRONMENT; FLUORESCENT DYES; PHOTO-STABILITY; POLYDIMETHYLSILOXANE PDMS; SIMPLE METHOD; SINGLE-MOLECULE DETECTION; SINGLE-MOLECULE STUDIES;

FLUORESCENCE; MICROCHANNELS; PHOTOBLEACHING; SILICONES;

MOLECULES;

EID: 84880790154     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp4003643     Document Type: Article

References (48)

1. Sherman, E.; Itkin, A.; Kuttner, Y. Y.; Rhoades, E.; Amir, D.; Haas, H.; Haran, G. Using Fluorescence Correlation Spectroscopy to Study Conformational Changes in Denatured Proteins Biophys. J. 2008, 94, 4819-4827
2. Guo, L.; Chowdhury, P.; Glasscock, J. M.; Gai, F. Denaturant-Induced Expansion and Compaction of a Multi-Domain Protein: IgG J. Mol. Biol. 2008, 384, 1029-1036
3. Wennmalm, S.; Edman, L.; Rigler, R. Conformational Fluctuations in Single DNA Molecules Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 10641-10646
4. Ha, T.; Tinnefeld, P. Photophysics of Fluorescent Probes for Single-Molecule Biophysics and Super-Resolution Imaging Annu. Rev. Phys. Chem. 2012, 63, 595-617
5. Joo, C.; Balci, H.; Ishitsuka, Y.; Buranachai, C.; Ha, T. Advances in Single-Molecule Fluorescence Methods for Molecular Biology Annu. Rev. Biochem. 2008, 77, 51-76
6. Altman, R. B.; Zheng, Q.; Zhou, Z.; Terry, D. S.; Warren, J. D.; Blanchard, S. C. Enhanced Photostability of Cyanine Fluorophores Across the Visible Spectrum Nat. Methods 2012, 9, 428-429
7. Aitken, C. E.; Marshall, R. A.; Puglisi, J. D. An Oxygen Scavenging System for Improvement of Dye Stability in Single-Molecule Fluorescence Experiments Biophys. J. 2008, 94, 1826-1835
8. Donnert, G.; Eggeling, C.; Hell, S. W. Major Signal Increase in Fluorescence Microscopy through Dark-State Relaxation Nat. Methods 2007, 4, 81-86
9. Bernas, T.; Zarebski, M.; Dobrucki, J. W.; Cook, P. R. Minimizing Photobleaching During Confocal Microscopy of Fluorescent Probes Bound to Chromatin: Role of Anoxia and Photon Flux J. Microsc. 2004, 215, 281-296
10. Harada, Y.; Sakurada, K.; Aoki, T.; Thomas, D. D.; Yanagida, T. Mechanochemical Coupling in Actomyosin Energy Transduction Studied by in Vitro Movement Assay J. Mol. Biol. 1990, 216, 49-68
11. Mei, E.; Tang, J. Y.; Vanderkooi, J. M.; Hochstrasser, R. M. Motions of Single Molecules and Proteins in Trehalose Glass J. Am. Chem. Soc. 2003, 125, 2730-2735
12. Widengren, J.; Rigler, R. Mechanisms of Photobleaching Investigated by Fluorescence Correlation Spectroscopy Bioimaging 1996, 4, 149-157
13. Zondervan, R.; Kulzer, F.; Kol'chenko, M. A.; Orrit, M. Photobleaching of Rhodamine 6G in Poly(vinyl alcohol) at the Ensemble and Single-Molecule Levels J. Phys. Chem. A 2004, 108, 1657-1665
14. English, D. S.; Furube, A.; Barbara, P. F. Single-Molecule Spectroscopy in Oxygen-Depleted Polymer Films Chem. Phys. Lett. 2000, 324, 15-19
15. van Dijk, M. A.; Kapitein, L. C.; van Mameren, J.; Schmidt, C. F.; Peterman, E. J. G. Combining Optical Trapping and Single-Molecule Fluorescence Spectroscopy: Enhanced Photobleaching of Fluorophores J. Phys. Chem. B 2004, 108, 6479-6484
16. Zheng, Q.; Jockusch, S.; Zhou, Z.; Altman, R. B.; Warren, J. D.; Turro, N. J.; Blanchard, S. C. On the Mechanisms of Cyanine Fluorophore Photostabilization J. Phys. Chem. Lett. 2012, 3, 2200-2203
17. Vogelsang, J. A Reducing and Oxidizing System Minimizes Photobleaching and Blinking of Fluorescent Dyes Angew. Chem., Int. Ed. 2008, 47, 5465-5469
18. Lemke, E. Microfluidic Device for Single-Molecule Experiments with Enhanced Photostability J. Am. Chem. Soc. 2009, 131, 13610-13612
19. Rondelez, Y.; Tresset, G.; Tabata, K. V.; Arata, H.; Fujita, H.; Takeuchi, S.; Noji, H. Microfabricated Arrays of Femtoliter Chambers Allow Single Molecule Enzymology Nat. Biotechnol. 2005, 23, 361-365
20. Iino, R. Single-Molecule Assay of Biological Reaction in Femtoliter Chamber Array Jpn. J. Appl. Phys. 2009, 48, 08JA04
21. Yeh, H. C.; Puleo, C. M.; Lim, T. C.; Ho, Y. P.; Giza, P. E.; Huang, R. C.; Wang, T. H. A Microfluidic-FCS Platform for Investigation on the Dissociation of Sp1-DNA Complex by Doxorubicin Nucleic Acids Res. 2006, 34, e144
22. Jung, S.-Y.; Liu, Y.; Collier, C. P. Fast Mixing and Reaction Initiation Control of Single-Enzyme Kinetics in Confined Volumes Langmuir 2008, 24, 4439-4442
23. MacDonald, J. C.; Whitesides, G. M. Poly(dimethylsiloxane) as a Material for Fabricating Microfluidic Devices Acc. Chem. Res. 2002, 35, 491-499
24. 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
25. Piwonski, H. M.; Goomanovsky, M.; Bensimon, D.; Horovitz, A.; Haran, G. Allosteric Inhibition of Individual Enzyme Molecules Trapped in Lipid Vesicles Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 1437-1443
26. Yeow, E. K.; Melnikov, S. M.; Bell, T. D.; De Schryver, F. C.; Hofkens, J. Characterizing the Fluorescence Intermittency and Photobleaching Kinetics of Dye Molecules Immobilized on a Glass Surface J. Phys. Chem. A 2006, 9, 1726-1734
27. Lee, S.; Lee, J.; Hohng, J. Single-Molecule Three-Color FRET with Both Negligible Spectral Overlap and Long Observation Time PLoS One 2010, 5, e12270
28. Yao, G.; Fang, X.; Yokota, H.; Yanagida, T.; Tan, W. Monitoring Molecular Beacon DNA Probe Hybridization at the Single-Molecule Level Chemistry 2003, 9, 5686-5692
29. Song, L.; Varma, C. A.; Verhoeven, J. W.; Tanke, H. J. Influence of the Triplet Excited State on the Photobleaching Kinetics of Fluorescein in Microscopy Biophys. J. 1996, 70, 2959-2968
30. Rasnik, I.; McKinney, S. A.; Ha, T. Nonblinking and Long-Lasting Single-Molecule Fluorescence Imaging Nat. Methods 2006, 3, 891-893
31. Dave, R.; Terry, D. S.; Munro, J. B.; Blanchard, S. C. Mitigating Unwanted Photophysical Processes for Improved Single-Molecule Fluorescence Imaging Biophys. J. 2009, 96, 2371-2381
32. Mondal, P. P. Minimizing Photobleaching in Fluorescence Microscopy by Depleting Triplet States Appl. Phys. Lett. 2007, 92, 013902
33. Eggeling, C.; Volkmer, A.; Seidel, C. A. Molecular Photobleaching Kinetics of Rhodamine 6G by One- and Two-Photon Induced Confocal Fluorescence Microscopy ChemPhysChem 2005, 6, 791-804
34. Zondervan, R.; Kulzer, F.; Orlinskii, S. B.; Orrit, M. Photoblinking of Rhodamine 6G in Poly(vinyl alcohol): Radical Dark State Formed through the Triplet J. Phys. Chem. A 2003, 107, 6770-6776
35. Vogelsang, J.; Cordes, T.; Forthmann, C.; Steinhauer, C.; Tinnefeld, P. Controlling the Fluorescence of Ordinary Oxazine Dyes for Single-Molecule Switching and Superresolution Microscopy Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 8107-8112
36. Widengren, J.; Chmyrov, A.; Eggeling, C.; Löfdahl, P. A.; Seidel, C. A. Strategies to Improve Photostabilities in Ultrasensitive Fluorescence Spectroscopy J. Phys. Chem. A 2007, 111, 429-440
37. Cordes, T.; Vogelsang, J.; Tinnefeld, P. On the Mechanism of Trolox as Antiblinking and Antibleaching Reagent J. Am. Chem. Soc. 2009, 131, 5018-5019
38. Vogelsang, J.; Kasper, R.; Steinhauer, C.; Person, B.; Heilemann, M.; Sauer, M.; Tinnefeld, P. A Reducing and Oxidizing System Minimizes Photobleaching and Blinking of Fluorescent Dyes Angew. Chem., Int. Ed. 2008, 47, 5465-5469
39. Davies, K. J.; Lin, S. W.; Pacifici, R. E. Protein Damage and Degradation by Oxygen Radicals J. Biol. Chem. 1987, 262, 9914-9920
40. Roche, M.; Rondeau, P.; Singh, N. R.; Tarnus, E.; Bourdon, E. The Antioxidant Properties of Serum Albumin FEBS Lett. 2008, 582, 1783-1787
41. Bodas, D.; Khan-Malek, C. Hydrophilization and Hydrophobic Recovery of PDMS by Oxygen Plasma and Chemical Treatment: an SEM Investigation Sens. Actuators, B 2007, 123, 368-373
42. Wong, I.; Ho, C.-M. Surface Molecular Property Modifications for Poly(dimethylsiloxane) (PDMS) Based Microfluidic Devices Microfluid. Nanofluid. 2009, 7, 291-306
43. Tan, S. H.; Nguyen, N.-T.; Chua, Y. C.; Kang, T. G. Oxygen Plasma Treatment for Reducing Hydrophobicity of a Sealed Polydimethylsiloxane Microchannel Biomicrofluidics 2010, 4, 032204
44. de Menezes Atayde, C.; Doi, I. Highly Stable Hydrophilic Surfaces of PDMS Thin Layer Obtained by UV Radiation and Oxygen Plasma Treatments Phys. Status Solidi C 2010, 7, 189-192
45. Ly, C. T.; Altuntop, M. E.; Wang, Y. Single-Molecule Study of Viomycin's Inhibition Mechanism on Ribosome Translocation Biochemistry 2010, 49, 9732-9738
46. Campos, L. A.; Liu, J.; Wang, X.; Ramanathan, R.; English, D. S.; Munoz, V. A Photoprotection Strategy for Microsecond-Resolution Single-Molecule Fluorescence Spectroscopy Nat. Methods 2011, 8, 143-146
47. Elbaum-Garfinkle, S.; Rhoades, E. Identification of an Aggregation-Prone Structure of Tau J. Am. Chem. Soc. 2012, 134, 16607-16613
48. Soranno, A.; Buchli, B.; Nettels, D.; Cheng, R. R.; Müller- Späth, S.; Pfeil, S. H.; Hoffmann, A.; Lipman, E. A.; Makarov, D. E.; Schuler, B. Quantifying Internal Friction in Unfolded and Intrinsically Disordered Proteins with Single-Molecule Spectroscopy Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 17800-17806