Studying RecBCD helicase translocation along χ-DNA using tethered particle motion with a stretching force

Biophysical Journal

Volumn 96, Issue 5, 2009, Pages 1875-1883

  Fan, Hsiu Fang ^a   Li, Hung Wen ^a,b  

^a MCGILL UNIVERSITY   (Canada)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; DOUBLE STRANDED DNA; HELICASE; RECBCD HELICASE; UNCLASSIFIED DRUG; BACTERIAL DNA; EXODEOXYRIBONUCLEASE V; STREPTAVIDIN;

ARTICLE; BACTERIAL GENE; CHROMOSOME SIZE; CONTROLLED STUDY; DNA SEQUENCE; ENZYME ASSAY; IMAGE ANALYSIS; MOLECULAR RECOGNITION; MOTION ANALYSIS SYSTEM; OPTICAL RESOLUTION; PROTEIN TRANSPORT; TRANSPORT KINETICS; BIOPHYSICS; CHEMISTRY; ENZYMOLOGY; ESCHERICHIA COLI; METABOLISM; METHODOLOGY; STATISTICAL MODEL;

ESCHERICHIA COLI;

ADENOSINE TRIPHOSPHATE; BIOPHYSICS; DNA HELICASES; DNA, BACTERIAL; ESCHERICHIA COLI; EXODEOXYRIBONUCLEASE V; LINEAR MODELS; STREPTAVIDIN;

EID: 65549152342     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2008.11.048     Document Type: Article

References (28)

1. Kowalczykowski, S. C. 2000. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem. Sci. 25: 156-165.
2. Dillingham, M. S., M. Spies, and S. C. Kowalczykowski. 2003. RecBCD enzyme is a bipolar DNA helicase. Nature. 423:893-897.
3. Taylor, A. F., and G. R. Smith. 2003. RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity. Nature. 423: 889-893.
4. Spies, M., P. R. Bianco, M. S. Dillingham, N. Handa, R. J. Baskin, et al. 2003. A molecular throttle: the recombination hotspot χ controls DNA translocation by the RecBCD helicase. Cell. 114:647-654.
5. Handa, N., P. R. Bianco, R. J. Baskin, and S. C. Kowalczykowski. 2005. Direct visualization of RecBCD movement reveals cotranslocation of the RecD motor after χ recognition. Mol. Cell. 17:745-750.
6. Dohoney, K. M., and J. Gelles. 2001. χ-Sequence recognition and DNA translocation by single RecBCD helicase/nuclease molecules. Nature. 409:370-374.
7. Guerra, R. F., L. Imperadori, R. Mantovani, D. D. Dunlap, and L. Finzi. 2007. DNA compaction by the nuclear factor-Y. Biophys. J. 93: 176-182.
8. Mumm, J. P., A. Landy, and J. Gelles. 2006. Viewing single λ site-specific recombination events from start to finish. EMBO J. 25:4586-4595.
9. Pouget, N., C. Turlan, N. Destainville, L. Salome, and M. Chandler. 2006. IS911 transpososome assembly as analysed by tethered particle motion. Nucleic Acids Res. 34:4313-4323.
10. Qian, H. 2000. A mathematical analysis for the Brownian dynamics of a DNA tether. J. Math. Biol. 41:331-340.
11. Schafer, D. A., J. Gelles, M. P. Sheetz, and R. Landick. 1991. Transcription by single molecules of RNA-polymerase observed by light-microscopy. Nature. 352:444-448.
12. Tolic-Norrelykke, S. F., A. M. Engh, R. Landick, and J. Gelles. 2004. Diversity in the rates of transcript elongation by single RNA polymerase molecules. J. Biol. Chem. 279:3292-3299.
13. Vanzi, F., C. Broggio, L. Sacconi, and F. S. Pavone. 2006. Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion. Nucleic Acids Res. 34:3409-3420.
14. Yin, H., R. Landick, and J. Gelles. 1994. Tethered particel motion method for studying transcript elongation by a single RNA-polymerase molecule. Biophys. J. 67:2468-2478.
15. Pouget, N., C. Dennis, C. Turlan, M. Grigoriev, M. Chandler, et al. 2004. Single-particle tracking for DNA tether length monitoring. Nucleic Acids Res. 32:e73.
16. Nelson, P. C., C. Zurla, D. Brogioli, J. F. Beausang, L. Finzi, et al. 2006. Tethered particle motion as a diagnostic of DNA tether length. J. Phys. Chem. B. 110:17260-17267.
17. Strick, T. R., J. F. Allemand, D. Bensimon, and V. Croquette. 1998. Behavior of supercoiled DNA. Biophys. J. 74:2016-2028.
18. van Oijen, A. M., P. C. Blainey, D. J. Crampton, C. C. Richardson, T. Ellenberger, et al. 2003. Single-molecule kinetics of λ exonuclease reveal base dependence and dynamic disorder. Science. 301:1235-1238.
19. Young, E. C., E. Berliner, H. K. Mahtani, B. Perezramirez, and J. Gelles. 1995. Subunit interactions in dimeric kinesin heavy-chain derivatives that lack the kinesin rod. J. Biol. Chem. 270:3926-3931.
20. Smith, S. B., L. Finzi, and C. Bustamante. 1992. Direct mechanical measurements of the elasticity of single DNA-molecules by using magnetic beads. Science. 258:1122-1126.
21. Kim, S. J., P. C. Blainey, C. M. Schroeder, and X. S. Xie. 2007. Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA. Nat. Methods. 4:397-399.
22. Bustamante, C., J. F. Marko, E. D. Siggia, and S. Smith. 1994. Entropic elasticity of λ-phage DNA. Science. 265:1599-1600.
23. Prasad, T. K., C. C. Yeykal, and E. C. Greene. 2006. Visualizing the assembly of human Rad51 filaments on double-stranded DNA. J. Mol Biol. 363:713-728.
24. Bianco, P. R., L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, et al. 2001. Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature. 409:374-378.
25. Anderson, D. G., J. J. Churchill, and S. C. Kowalczykowski. 1997. χ-Activated RecBCD enzyme possesses 5′->3′ nucleolytic activity, but RecBC enzyme does not: evidence suggesting that the alteration induced by χ is not simply ejection of the RecD subunit. Genes Cells. 2:117-128.
26. Taylor, A. F., and G. R. Smith. 1995. Strand specificity of nicking of DNA at χ-sites by RecBCD enzyme - modulation by ATP and magnesium levels. J. Biol. Chem. 270:24459-24467.
27. Perkins, T. T., H. W. Li, R. V. Dalal, J. Gelles, and S. M. Block. 2004. Forward and reverse motion of single RecBCD molecules on DNA. Biophys. J. 86:1640-1648.
28. Singleton, M. R., M. S. Dillingham, M. Gaudier, S. C. Kowalczykowski, and D. B. Wigley. 2004. Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature. 432:187-193.