Probing DNA surface attachment and local environment using single molecule spectroscopy

Journal of Physical Chemistry B

Volumn 105, Issue 15, 2001, Pages 3120-3126

  Osborne, M A ^a,b   Barnes, C L ^a,b   Balasubramanian, S ^a   Klenerman, D ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b Solexa Ltd   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

FLUOROPHORE; PHOTOBLEACHING; SINGLE MOLECULE SPECTROSCOPY;

FLUORESCENCE; MOLECULAR STRUCTURE; SILICA; SPECTROSCOPIC ANALYSIS;

DNA;

EID: 0037134590     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0038660     Document Type: Article

References (47)

1. Shera, E. B.; Seitzinger, N. K.; Davis, L. M.; Keller, R. A.; Soper, S. A. Chem. Phys. Lett. 1990, 174, 553-557.
2. Eigen, M.; Rigler, R. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 5740-5747.
3. Nie, S. M.; Chiu, D. T.; Zare, R. N. Science 1994, 266, 1018-1021.
4. Betzig, E.; Chichester, R. J. Science 1993, 262, 1422-1425.
5. Xie, X. S.; Dunn, R. C. Science 1994, 265, 361-364.
6. Trautman, J. K.; Macklin, J. J.; Brus, L. E.; Betzig, E. Nature 1994, 369, 40-42.
7. Funatsu, T.; Harada, Y.; Tokunaga, M.; Saito, K.; Yanagida, T. Nature 1995, 374, 555-559.
8. Schmidt, T.; Schutz, G. J.; Baumgartner, W.; Gruber, H. J.; Schindler, H. J. Phys. Chem. 1995, 99, 17662-17668.
9. Schmidt, T.; Schutz, G. J.; Baumgartner, W.; Gruber, H. J.; Schindler, H. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 2926-2929.
10. Dickson, R. M.; Norris, D. J.; Tzeng, Y. L.; Moerner, W. E. Science 1996, 274, 966-969.
11. Moerner, W. E.; Dickson, R. M.; Kummer, S. Biophys. J. 1998, 74, A10.
12. Moerner, W. E.; Peterman, E. J. G.; Brasselet, S.; Kummer, S.; Dickson, R. M. Cytometry 1999, 36, 232-238.
13. Bian, R. X.; Dunn, R. C.; Xie, X. S. Phys. Rev. Lett. 1995, 75, 4772-4775.
14. Ha, T.; Enderle, T.; Ogletree, D. F.; Chemla, D. S.; Selvin, P. R.; Weiss, S. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 6264-6268.
15. Yokota, H.; Ishii, Y.; Wazawa, T.; Funatsu, T.; Yanagida, T. Biophys. J. 1998, 74, A46.
16. Weiss, S. Science 1999, 283, 1676-1683.
17. Ishii, Y.; Yoshida, T.; Funatsu, T.; Wazawa, T.; Yanagida, T. Chem. Phys. 1999, 247, 163-173.
18. Moerner, W. E.; Peterman, E. J.; Sosa, H.; Brasselet, S.; Dickson, R. M.; Kummer, S.; Sakowicz, R.; Goldstein, L. S. B. Biophys. J. 1999, 76, 20.
19. Schutz, G. J.; Trabesinger, W.; Schmidt, T. Biophys. J. 1998, 74, 2223-2226.
20. Ha, T.; Zhuang, X. W.; Kim, H. D.; Orr, J. W.; Williamson, J. R.; Chu, S. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9077-9082.
21. Trabesinger, W.; Schutz, G. J.; Gruber, H. J.; Schindler, H.; Schmidt, T. Anal. Chem. 1999, 71, 279-283.
22. Lu, H. P.; Xun, L. Y.; Xie, X. S. Science 1998, 282, 1877-1882.
23. Ha, T. J.; Ting, A. Y.; Liang, J.; Caldwell, W. B.; Deniz, A. A.; Chemla, D. S.; Schultz, P. G.; Weiss, S. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 893-898.
24. Vale, R. D.; Funatsu, T.; Pierce, D. W.; Romberg, L.; Harada, Y.; Yanagida, T. Nature 1996, 380, 451-453.
25. Ambrose, W. P.; Goodwin, P. M.; Nolan, J. P. Cytometry 1999, 50, 224-231.
26. Tokunaga, M.; Kitamura, K.; Saito, K.; Iwane, A. H.; Yanagida, T. Biochem. Biophys. Res. Commun. 1997, 235, 47-53.
27. Harada, Y.; Funatsu, T.; Nonoyama, Y.; Yanagida, T. Biophys. J. 1998, 74, A69.
28. Wazawa, T.; Ishii, Y.; Funatsu, T.; Yanagida, T. Biophys. J. 1999, 76, A445.
29. Fang, X.; Tan, W. Anal. Chem. 1999, 71, 3101-3105.
30. Wennmalm, S.; Edman, L.; Rigler, R. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 10641-10646.
31. Wennmalm, S.; Edman, L.; Rigler, R. Chem. Phys. 1999, 247, 61-67.
32. Wennmalm, S.; Rigler, R. J. Phys. Chem. B 1999, 103, 2516-2519.
33. Lockhart, J. L.; Winzeler, E. A. Nature 2000, 405, 827-836.
34. Mir, K. U.; Southern, E. M. Nature Biotech. 1999, 17, 788-792.
35. Southern, E.; Mir, K.; Schepinov, M. Nature Genet. 1999, 21, 5-9.
36. Bernard, A. L.; Guedeau-Boudeville, M. A.; Jullien, L.; Di Meglio, J. M. Europhys. Lett. 1999, 46, 101-106.
37. Xie, X. S. Acc. Chem. Res. 1996, 29, 598-606.
38. Ha, T.; Enderle, T.; Chemla, D. S.; Selvin, P. R.; Weiss, S. Phys. Rev. Lett. 1996, 77, 3979-3982.
39. Dickson, R. M.; Cubitt, A. B.; Tsien, R. Y.; Moerner, W. E. Nature 1997, 388, 355-358.
40. 2 radius of 150 μm means that the laser intensity will vary at most by 15% between the center and edge of a 120 μm × 120 μm image.
41. The fluorescence lifetime of a near monolayer of TAMRA labeled oligonucleotide disperesed on a coverslip under aqueous conditions was measured using TCSPC (time correlated single photon counting). The fluorescence exhibited a biexponential decay composed of an 88% population with a long lifetime of 3.48 ± 0.11 ns and a 12% population with a short lifetime of 0.93 ± 0.09 ns.
42. Eggeling, C.; Fries, J. R.; Brand, L.; Gunther, R.; Seidel, C. A. M. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1556-1561.
43. Edman, L.; Mets, U.; Rigler, R. Proc. Natl. Acad. Sci. U.S.A. 1996, 95, 6710-6715.
44. Ha, T.; Glass, J.; Enderle, T.; Chemla, D. S.; Weiss, S. Phys. Rev. Lett. 1998, 80, 2093-2096.
45. Ha, T.; Laurence, T. A.; Chemla, D. S.; Weiss, S. J. Phys. Chem. B 1999, 103, 6839-6850.
46. 2.
47. Chandrasekar, S. Rev. Mod. Phys. 1943, 15, 1-89.