Measuring single-molecule nucleic acid dynamics in solution by two-color filtered ratiometric fluorescence correlation spectroscopy

Proceedings of the National Academy of Sciences of the United States of America

Volumn 101, Issue 40, 2004, Pages 14425-14430

  Li, Haitao ^a   Ren, Xiaojun ^a   Ying, Liming ^a   Balasubramanian, Shankar ^a   Klenerman, David ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENT DYE; GREEN FLUORESCENT PROTEIN; MAGNESIUM ION; PROTEIN; RNA; TELOMERASE;

ARTICLE; DNA STRUCTURE; FILTERED RATIOMETRIC AUTOFLUORESCENCE CORRELATION SPECTROSCOPY; FLUORESCENCE CORRELATION SPECTROSCOPY; INTERMETHOD COMPARISON; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

BASE SEQUENCE; COLOR; DIMERIZATION; DNA; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; HUMANS; LASERS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS; RADIOMETRY; RNA; SOLUTIONS; SPECTROMETRY, FLUORESCENCE; TELOMERASE; THERMODYNAMICS;

MUS;

EID: 5144220668     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0404295101     Document Type: Article

References (49)

1. Xie, X. S. & Trautman, J. K. (1998) Annu. Rev. Phys. Chem. 49, 441-480.
2. Weiss, S. (1999) Science 283, 1676-1683.
3. Schuler, B., Lipman, E. A. & Eaton, W. A. (2002) Nature 419, 743-747.
4. Plakhotnik, T., Donley, E. A. & Wild, U. P. (1997) Annu. Rev. Phys. Chem. 48, 181-212.
5. Nie, S. M. & Zare, R. N. (1997) Annu. Rev. Biophys. Biomol. Struct. 26, 567-596.
6. Ha, T. J. (2004) Biochemistry 43, 4055-4063.
7. Eggeling, C., Fries, J. R., Brand, L., Gunther, R. & Seidel, C. A. M. (1998) Proc. Natl. Acad. Sci. USA 95, 1556-1561.
8. Zhuang, X. W., Kim, H., Pereira, M. J. B., Babcock, H. P., Walter, N. G. & Chu, S. (2002) Science 296, 1473-1476.
9. Grunwell, J. R., Glass, J. L., Lacoste, T. D., Deniz, A. A., Chemla, D. S. & Schultz, P. G. (2001) J. Am. Chem. Soc. 123, 4295-4303.
10. Edman, L., Mets, U. & Rigler, R. (1996) Proc. Natl. Acad. Sci. USA 93, 6710-6715.
11. Neuweiler, H., Schulz, A., Bohmer, M., Enderlein, J. & Sauer, M. (2003) J. Am. Chem. Soc. 125, 5324-5330.
12. Magde, D., Elson, E. & Webb, W. W. (1972) Phys. Rev. Lett. 29, 705-708.
13. Ha, T. J., Ting, A. Y., Liang, J., Caldwell, W. B., Deniz, A. A., Chemla, D. S., Schultz, P. G. & Weiss, S. (1999) Proc. Natl. Acad. Sci. USA 96, 893-898.
14. Hess, S. T., Huang, S. H., Heikal, A. A. & Webb, W. W. (2002) Biochemistry 41, 697-705.
15. Haustein, E. & Schwille, P. (2003) Methods 29, 153-166.
16. Ying, L. M., Green, J. J., Li, H. T., Klenerman, D. & Balasubramanian, S. (2003) Proc. Natl. Acad. Sci. USA 100, 14629-14634.
17. Chen, Y., Muller, J. D., So, P. T. C. & Gratton, E. (1999) Biophys. J. 77, 553-567.
18. Muller, J. D., Chen, Y. & Gratton, E. (2000) Biophys. J. 78, 474-486.
19. Perroud, T. D., Bo, H. A., Wallace, M. I. & Zare, R. N. (2003) ChemPhysChem 4, 1121-1123.
20. Bonnet, G., Krichevsky, O. & Libchaber, A. (1998) Proc. Natl. Acad. Sci. USA 95, 8602-8606.
21. Wallace, M. I., Ying, L. M., Balasubramanian, S. & Klenerman, D. (2001) Proc. Natl. Acad. Sci. USA 98, 5584-5589.
22. Ying, L. M., Wallace, M. I., Balasubramanian, S. & Klenerman, D. (2000) J. Phys. Chem. B 104, 5171-5178.
23. Dahan, M., Deniz, A. A., Ha, T. J., Chemla, D. S., Schultz, P. G. & Weiss, S. (1999) Chem. Phys. 247, 85-106.
24. Deniz, A. A., Dahan, M., Grunwell, J. R., Ha, T. J., Faulhaber, A. E., Chemla, D. S., Weiss, S. & Schultz, P. G. (1999) Proc. Natl. Acad. Sci. USA 96, 3670-3675.
25. Kapanidis, A., Lee, N. K., Laurence, T., Doose, S., Margeat, E. & Weiss, S. (2004) Proc. Natl. Acad. Sci. USA 101, 8936-8941.
26. Ren, X. J., Gavory, G., Li, H. T., Ying, L. M., Klenerman, D. & Balasubramanian, S. (2003) Nucleic Acids Res. 31, 6509-6515.
27. Li, H. T., Ying, L. M., Green, J. J., Balasubramanian, S. & Klenerman, D. (2003) Anal. Chem. 75, 1664-1670.
28. Wallace, M. I., Ying, L. M., Balasubramanian, S. & Klenerman, D. (2000) J. Phys. Chem. B 104, 11551-11555.
29. Kim, H. D., Nienhaus, G. U., Ha, T., Orr, J. W., Williamson, J. R. & Chu, S. (2002) Proc. Natl. Acad. Sci. USA 99, 4284-4289.
30. Xie, Z., Srividya, N., Sosnick, T. R., Pan, T. & Scherer, N. F. (2004) Proc. Natl. Acad. Sci. USA 101, 534-539.
31. Draper, D. E. (1996) Nat. Struct. Biol. 3, 397-400.
32. Al-Hashimi, H. M., Gosser, Y., Gorin, A., Hu, W. D., Majumdar, A. & Patel, D. J. (2002) J. Mol. Biol. 315, 95-102.
33. Al-Hashimi, H. M., Gorin, A., Majumdar, A., Gosser, Y. & Patel, D. J. (2002) J. Mol. Biol. 318, 637-649.
34. Furtig, B., Richter, C., Wohnert, J. & Schwalbe, H. (2003) Chembiochem 4, 936-962.
35. Al-Hashimi, H. M., Pitt, S. W., Majumdar, A., Xu, W. J. & Patel, D. J. (2003) J. Mol. Biol. 329, 867-873.
36. Li, Y., Bevilacqua, P. C., Mathews, D. & Turner, D. H. (1995) Biochemistry 34, 14394-14399.
37. Batey, R. T. & Doudna, J. A. (1998) Nat. Struct. Biol. 5, 337-340.
38. Cohen, S. B. & Cech, T. R. (1997) J. Am. Chem. Soc. 119, 6259-6268.
39. Szewczak, A. A. & Cech, T. R. (1997) RNA Publ. RNA Soc. 3, 838-849.
40. Zhuang, X. W. & Rief, M. (2003) Curr. Opin. Struct. Biol. 13, 88-97.
41. Liphardt, J., Onoa, B., Smith, S. B., Tinoco, I. & Bustamante, C. (2001) Science 292, 733-737.
42. Hoogstraten, C. G., Wank, J. R. & Pardi, A. (2000) Biochemistry 39, 9951-9958.
43. Menger, M., Eckstein, F. & Porschke, D. (2000) Biochemistry 39, 4500-4507.
44. Menger, M., Eckstein, F. & Porschke, D. (2000) Nucleic Acids Res. 28, 4428-4434.
45. Craig, M. E., Crothers, D. M. & Doty, P. (1971) J. Mol. Biol. 62, 383-401.
46. Crotheres, D. M., Cole, P., Hilberts, C. W. & Shulman, R. G. (1974) J. Mol. Biol. 87, 63-88.
47. Qin, P. Z., Hideg, K., Feigon, J. & Hubbell, W. L. (2003) Biochemistry 42, 6772-6783.
48. Dayie, K. T., Brodsky, A. S. & Williamson, J. R. (2002) J. Mol. Biol. 317, 263-278.
49. Cole, P. E. & Crothers, D. M. (1972) Biochemistry 11, 4368-4374.