Quantitative Analysis of DNA-Looping Kinetics from Tethered Particle Motion Experiments

Methods in Enzymology

Volumn 475, Issue C, 2010, Pages 199-220

  Manzo, Carlo ^a   Finzi, Laura ^a  

^a EMORY UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN; PROTEIN BINDING;

BOOK; IN VITRO STUDY; KINETICS; LYSOGENIZATION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; ALGORITHM; CHEMISTRY; METABOLISM; PARTICLE SIZE;

ALGORITHMS; DNA; KINETICS; PARTICLE SIZE; PROTEIN BINDING; PROTEINS;

EID: 77954571156     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(10)75009-6     Document Type: Chapter

References (38)

1. Anderson L.M., Yang H. DNA looping can enhance lysogenic CI transcription in phage lambda. Proc. Natl. Acad. Sci. USA 2008, 105:5827-5832.
2. Beausang J.F., Zurla C., Dunlap D., Finzi L., Nelson P.C. Hidden Markov analysis of tethered particle motion. Biophys. J. 2007, 417A.
3. Beausang J.F., Zurla C., Finzi L., Sullivan L., Nelson P.C. Elementary simulation of tethered Brownian motion. Am. J. Phys. 2007, 75:520-523.
4. Beausang J.F., Zurla C., Manzo C., Dunlap D., Finzi L., Nelson P.C. DNA looping kinetics analyzed using diffusive hidden Markov model. Biophys. J. 2007, 92:L64-L66.
5. Colquhoun D., Sakmann B. Fluctuations in the microsecond time range of the current through single acetylcholine-receptor ion channels. Nature 1981, 294:464-466.
6. Colquhoun D., Sigworth F.J. Fitting and Statistical Analysis of Single Channel Recording 1983, 191-263. Plenum Press, New York. B. Sakmann, E. Neher (Eds.).
7. Dempster A.P., Laird N.M., Rubin D.B. Maximum likelihood from incomplete data via EM algorithm. J.R. Sta. Soc. Series B Method 1977, 39:1-38.
8. Dodd I.B., Perkins A.J., Tsemitsidis D., Egan J.B. Octamerization of lambda CI repressor is needed for effective repression of P-RM and efficient switching from lysogeny. Genes Dev. 2001, 15:3013-3022.
9. Dodd I.B., Shearwin K.E., Perkins A.J., Burr T., Hochschild A., Egan J.B. Cooperativity in long-range gene regulation by the lambda CI repressor. Genes Dev. 2004, 18:344-354.
10. Finzi L., Dunlap D. Single-molecule studies of DNA architectural changes induced by regulatory proteins. Methods Enzymol. 2003, 370:369-378.
11. Finzi L., Gelles J. Measurement of lactose repressor-mediated loop formation and breakdown in single DNA-molecules. Science 1995, 267:378-380.
12. Fraley C., Raftery A.E. How many clusters? Which clustering method? Answer via model-based cluster analysis. Comp. J. 1998, 41:578-588.
13. Fraley C., Raftery A.E. Model-based clustering, discriminant analysis, and density estimation. J. Am. Stat. Assoc. 2002, 97:611-631.
14. Gelles J., Yin H., Finzi L., Wong O.K., Landick R. Single-molecule kinetic-studies on DNA-transcription and transcriptional regulation. Biophys. J. 1995, 68:S73.
15. Gombay E., Horvath L.J. On the rate of approximations for maximum likelihood tests in change-point models. J. Multivar. Anal. 1996, 56:120-152.
16. Liao J.C., Spudich J.A., Parker D., Delp S.L. Extending the absorbing boundary method to fit dwell-time distributions of molecular motors with complex kinetic pathways. Proc. Natl. Acad. Sci. USA 2007, 104:3171-3176.
17. Liebovitch L.S., Sullivan J.M. Fractal analysis of a voltage-dependent potassium channel from cultured mouse hippocampal-neurons. Biophys. J. 1987, 52:979-988.
18. Liebovitch L.S., Scheurle D., Rusek M., Zochowski M. Fractal methods to analyze ion channel kinetics. Methods 2001, 24:359-375.
19. Millhauser G.L., Salpeter E.E., Oswald R.E. Diffusion-models of ion-channel gating and the origin of power law distributions from single-channel recording. Proc. Natl. Acad. Sci. USA 1988, 85:1503-1507.
20. Montiel D., Cang H., Yang H. Quantitative characterization of changes in dynamical behavior for single-particle tracking studies. J. Phys. Chem. B 2006, 110:19763-19770.
21. Nelson P.C., Zurla C., Brogioli D., Beausang J.F., Finzi L., Dunlap D. Tethered particle motion as a diagnostic of DNA tether length. J. Phys. Chem. B 2006, 110:17260-17267.
22. Oswald R.E., Millhauser G.L., Carter A.A. Diffusion model in ion channel gating. Biophys. J. 1991, 59:1136-1142.
23. Pouget N., Dennis C., Turlan C., Grigoriev M., Chandler M., Salome L. Single-particle tracking for DNA tether length monitoring. Nucleic Acids Res. 2004, 32:e73.
24. Qian H. A mathematical analysis for the Brownian dynamics of a DNA tether. J. Math. Biol. 2000, 41:331-340.
25. Qian H., Elson E.L. Quantitative study of polymer conformation and dynamics by single-particle tracking. Biophys. J. 1999, 76:1598-1605.
26. Qin F., Auerbach A., Sachs F. A direct optimization approach to hidden Markov modeling for single channel kinetics. Biophys. J. 2000, 79:1915-1927.
27. Sansom M.S.P., Ball F.G., Kerry C.J., McGee R., Ramsey R.L., Usherwood P.N.R. Markov, fractal, diffusion, and related models of ion channel gating. Biophys. J. 1989, 56:1229-1243.
28. Scott A.J., Symons M.J. Clustering methods based on likelihood ratio criteria. Biometrics 1971, 27:387-397.
29. Segall D.E., Nelson P.C., Phillips R. Volume-exclusion effects in tethered-particle experiments: Bead size matters. Phys. Rev. Lett. 2006, 96. 088306.
30. Serge A., Bertaux N., Rigneault H., Marguet D. Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes. Nat. Methods 2008, 5:687-694.
31. van den Broek B., Vanzi F., Normanno D., Pavone F.S., Wuite G.J.L. Real-time observation of DNA looping dynamics of type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res. 2006, 34:167-174.
32. Vanzi F., Broggio C., Sacconi L., Pavone F.S. Lac repressor hinge flexibility and DNA looping: Single molecule kinetics by tethered particle motion. Nucleic Acids Res. 2006, 34:3409-3420.
33. Vostrikova L.Y. Detection of a "disorder" in a Wiener process. Theory Probab. Appl. 1981, 26:356-362.
34. Watkins L.P., Yang H. Detection of intensity change points in time-resolved single-molecule measurements. J. Phys. Chem. B 2005, 109:617-628.
35. Yin H., Landick R., Gelles J. Tethered particle motion method for studying transcript elongation by a single RNA-polymerase molecule. Biophys. J. 1994, 67:2468-2478.
36. Zurla C., Franzini A., Galli G., Dunlap D.D., Lewis D.E.A., Adhya S., Finzi L. Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage lambda. J. Phys. Condens. Matter 2006, 18:S225-S234.
37. Zurla C., Samuely T., Bertoni G., Valle F., Dietler G., Finzi L., Dunlap D.D. Integration host factor alters LacI-induced DNA looping. Biophys. Chem. 2007, 128:245-252.
38. Zurla C., Manzo C., Dunlap D., Lewis D.E., Adhya S., Finzi L. Direct demonstration and quantification of long-range DNA looping by the {lambda} bacteriophage repressor. Nucleic Acids Res. 2009, 37:2789-2795.