Single-molecule kinetics of λ exonuclease reveal base dependence and dynamic disorder

Science

Volumn 301, Issue 5637, 2003, Pages 1235-1238

  Van Oijen, Antoine M ^a   Blainey, Paul C ^a   Crampton, Donald J ^b   Richardson, Charles C ^b   Ellenberger, Tom ^b   Xie, X Sunney ^a  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; ENZYMES; FREE ENERGY; HYDROGEN BONDS; STATISTICAL METHODS;

SINGLE-MOLECULE KINETICS;

DNA;

DNA; EXONUCLEASE; LAMBDA EXONUCLEASE; UNCLASSIFIED DRUG;

DNA; MOLECULAR ANALYSIS;

ARTICLE; BACTERIOPHAGE LAMBDA; CATALYSIS; HYDROGEN BOND; KINETICS; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

BACTERIOPHAGE LAMBDA; BASE COMPOSITION; BASE SEQUENCE; BINDING SITES; CATALYSIS; DNA, SINGLE-STRANDED; DNA, VIRAL; EXODEOXYRIBONUCLEASES; HYDROGEN BONDING; HYDROLYSIS; KINETICS; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; THERMODYNAMICS; VIRAL PROTEINS;

BACTERIOPHAGE LAMBDA;

EID: 0041821716     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1084387     Document Type: Article

References (31)

1. J. T. Finer, R. M. Simmons, J. A. Spudich, Nature 368, 113 (1994).
2. T. Funatsu, Y. Harada, M. Tokunaga, K. Saito, T. Yanagida, Nature 374, 555 (1995).
3. H. Yin et al., Science 270, 1653 (1995).
4. H. P. Lu, L. Xun, X. S. Xie, Science 282, 1877 (1998).
5. X. Zhuang et al., Science 288, 2048 (2000).
6. R. Yasuda, H. Noji, M. Yoshida, K. Kinosita Jr., H. Itoh, Nature 410, 898 (2001).
7. C. Bustamante, Z. Bryant, S. B. Smith, Nature 421, 423 (2003).
8. Materials and methods are available as supporting material on Science Online.
9. T. R. Strick, J. F. Allemand, D. Bensimon, V. Croquette, Biophys. J. 74, 2016 (1998).
10. S. B. Smith, L Finzi, C. Bustamante, Science 258, 1122 (1992).
11. C. Bustamante, J. F. Marko, E. D. Siggia, S. Smith, Science 265, 1599 (1994).
12. T. R. Stdck, J. F. Allemand, D. Bensimon, A. Bensimon, V. Croquette, Science 271, 1835 (1996).
13. G. J. L. Wuite, S. B. Smith, M. Young, D. Keller, C. Bustamante, Nature 404, 103 (2000).
14. R. Kovall, B. W. Matthews, Science 277, 1824 (1997).
15. J. Dapprich, Cytometry 36, 163 (1999).
16. S.-I. Matsuura et al., Nucleic Acids Res. 29, e79 (2001).
17. K. Subramanian, W. Rutvisuttinunt, W. Scott, R. S. Myers, Nucleic Acids Res. 31, 1585 (2003).
18. Pearson's correlation coefficient r is defined as Equation Presentation
19. P. G. Mitsis, J. G. Kwagh, Nucleic Acids Res. 27, 3057 (1999).
20. K. S. Dickson, C. M. Burns, J. P. Richardson, J. Biol. Chem. 275, 15828 (2000).
21. E.T. Kool, Annu. Rev. Biophys. Biomol. Struct. 30, 1 (2001).
22. S. Bommarito, N. Peyret, J. SantaLucia Jr., Nucleic Acids Res. 28, 1929 (2000).
23. A. Fersht, Structure and Mechanism in Protein Science (Freeman, New York, 1999).
24. R. A. Kovall, B. W. Matthews, Proc. Natl. Acad. Sci. U.S.A. 95, 7893 (1998).
25. C. Rauch et al., J. Mol. Biol. 324, 491 (2002).
26. W.-C. Lam et al., Biochemistry 41, 3943 (2002).
27. H. Frauenfelder, S. G. Sligar, P. G. Wolynes, Science 254, 1598 (1991).
28. X. S. Xie, J. Chem. Phys. 117, 11024 (2002).
29. Q. Xue, E. S. Yeung, Nature 373, 681 (1995).
30. R. Polakowski, D. B. Craig, A. Skelley, N. J. Dovichi, J. Am. Chem. Soc. 122, 4853 (2000).
31. We thank A. Goel and D. Herschbach for helpful discussions. This work is funded by NIH (grant 5RO1GM61577-03 to X.S.X. and #RO1GM55390-07 to T.E.). A.M.v.O. thanks the Human Frontier Science Program for financial support.