Analysis of single-molecule FRET trajectories using hidden Markov modeling

Biophysical Journal

Volumn 91, Issue 5, 2006, Pages 1941-1951

  McKinney, Sean A ^a   Joo, Chirlmin ^a   Ha, Taekjip ^a  

^a University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; FLUORESCENCE RESONANCE ENERGY TRANSFER; MATHEMATICAL COMPUTING; MEDICAL RESEARCH; NOISE;

EID: 33746747438     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.082487     Document Type: Article

References (24)

1. Lee, J. Y., B. Okumus, D. S. Kim, and T. Ha. 2005. Extreme conformational diversity in human telomeric DNA. Proc. Natl. Acad. Sci. USA. 102:18938-18943.
2. McKinney, S. A., A. D. Freeman, D. M. Lilley, and T. Ha. 2005. Observing spontaneous branch migration of Holliday junctions one step at a time. Proc. Natl. Acad. Sci. USA. 102:5715-5720.
3. Nahas, M., T. J. Wilson, S. C. Hohng, K. Jarvie, D. M. J. Lilley, and T. Ha. 2004. Observation of internal cleavage and ligation reactions of a ribozyme. Nat. Struct. Mol. Biol. 11:1107-1113.
4. Okumus, B., T. J. Wilson, D. M. J. Lilley, and T. Ha. 2004. Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic. Biophys. J. 87:2798-2806.
5. Rueda, D., G. Bokinsky, M. M. Rhodes, M. J. Rust, X. W. Zhuang, and N. G. Walter. 2004. Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance. Proc. Natl. Acad. Sci. USA. 101:10066-10071.
6. Tan, E., T. J. Wilson, M. K. Nahas, R. M. Clegg, D. M. Lilley, and T. Ha. 2003. A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc. Natl. Acad. Sci. USA. 100:9308-9313.
7. Zhuang, X., H. Kim, M. J. Pereira, H. P. Babcock, N. G. Walter, and S. Chu. 2002. Correlating structural dynamics and function in single ribozyme molecules. Science. 296:1473-1476.
8. McKinney, S. A., A. C. Declais, D. M. J. Lilley, and T. Ha. 2003. Structural dynamics of individual Holliday junctions. Nat. Struct. Biol. 10:93-97.
9. Eddy, S. R. 2004. What is a hidden Markov model? Nat. Biotechnol. 22:1315-1316.
10. Qin, F., A. Auerbach, and F. Sachs. 2000. A direct optimization approach to hidden Markov modeling for single channel kinetics. Biophys. J. 79:1915-1927.
11. Qin, F., A. Auerbach, and F. Sachs. 2000. Hidden Markov modeling for single channel kinetics with filtering and correlated noise. Biophys. J. 79:1928-1944.
12. Yang, H., and X. S. Xie. 2002. Statistical approaches for probing single-molecule dynamics photon-by-photon. Chem. Phys. 284:423-437.
13. Yang, H., G. B. Luo, P. Karnchanaphanurach, T. M. Louie, I. Rech, S. Cova, L. Y. Xun, and X. S. Xie. 2003. Protein conformational dynamics probed by single-molecule electron transfer. Science. 302:262-266.
14. Andrec, M., R. M. Levy, and D. S. Talaga. 2003. Direct determination of kinetic rates from single-molecule photon arrival trajectories using hidden Markov models. J. Phys. Chem. A. 107:7454-7464.
15. Schroder, G. F., and H. Grubmuller. 2003. Maximum likelihood trajectories from single molecule fluorescence resonance energy transfer experiments. J. Chem. Phys. 119:9920-9924.
16. Ha, T., I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman, and S. Chu. 2002. Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature. 419:638-641.
17. Zhuang, X., L. E. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu. 2000. A single-molecule study of RNA catalysis and folding. Science. 288:2048-2051.
18. Dahan, M., A. A. Deniz, T. J. Ha, D. S. Chemla, P. G. Schultz, and S. Weiss. 1999. Ratiometric measurement and identification of single diffusing molecules. Chem. Phys. 247:85-106.
19. Viterbi, A. J. 1967. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans. Inf. Theory. 13:260-267.
20. Press, W. H., S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery. 1992. Numerical recipes in C. Cambridge University Press, Cambridge.
21. Baum, L. E., T. Petrie, G. Soules, and N. Weiss. 1970. A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann. Math. Stat. 41:164-171.
22. Hastie, T., R. Tibshirani, and J. Friedman. 2001. The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Springer-Verlag, New York.
23. Joo, C., S. A. McKinney, M. Nakamura, I. Rasnik, S. Myong, and T. Ha. 2005. Real time observation of RecA filament dynamics with single monomer resolution. Cell. In press.
24. Eddy, S. R. 1998. Profile hidden Markov models. Bioinformatics. 14:755-763.