Location of Repository

Two time constants for the binding of proteins to DNA from micromechanical data

By Matthew S. Turner

Abstract

Recent experimental advances allow the direct measurement of the force/extension behavior for DNA in the presence of strongly binding proteins. Such experiments reveal information about the cooperative mechanism of protein binding. We have studied the irreversible binding of such proteins to DNA using a simple simulation and present a method for estimating quantitative rate constants for the nucleation and growth of linear domains of proteins bound to DNA. Such rate constants also give information about the relative energetics of the two binding processes. We discuss our results in the context of recent data for the DNA-recA-ATPγs system, for which the nucleation time is 4.7 × 104 min per recA binding site and the total growth rate of each domain is 1400 recA/min

Topics: QH426, QC
Publisher: Biophysical Society
Year: 2000
OAI identifier: oai:wrap.warwick.ac.uk:916

Suggested articles

Preview

Citations

  1. (1998). Backscattering from a tethered bead as a probe of DNA flexibility. doi
  2. (1982). Characterization of complexes between recA protein and duplex DNA by electronmicroscopy. doi
  3. (1999). DNA–protein cooperative binding through variable-range elastic coupling. doi
  4. (1981). Elongation of duplex DNA by recA protein. doi
  5. (1989). Extent of duplex DNA underwinding induced by recA protein binding in the presence of ATP. doi
  6. (1997). Folding-unfolding transitions in single titin molecules characterized with laser tweezers. doi
  7. (1988). General mechanism for recA protein binding to duplex DNA. doi
  8. (1991). Laser manipulation of atoms and particles. doi
  9. McGhee .1972. DNA–protein interactions. doi
  10. (1999). Polymerization and mechanical properties of single recA-DNA filaments. doi
  11. (1997). RecA as a motor protein—testing models for the role of ATP hydrolysis in DNA strand exchange. doi
  12. (1998). RecA binding to a single double-stranded DNA molecule: a possible role of DNA conformational fluctuations. doi
  13. (1999). RecA polymerization on double-stranded DNA by using single molecule manipulation: the role of ATP hydrolysis. doi
  14. (1988). RecA protein selfassembly—multiple discrete aggregation states. doi
  15. (1997). RecA protein: structure, function and role in recombinational DNA repair. doi
  16. Reverse unfolding of individual titin immunoglobulin domains by AFM. doi
  17. (1997). Single DNA molecule grafting and manipulation using a combined atomic force microscope and an optical tweezer. doi
  18. (1998). Single molecule observation of duplex DNA extension by recA.
  19. (1987). Stable binding of recA protein to duplex DNA. doi
  20. (1998). Stretching individual recA-DNA filaments with optical tweezers.
  21. (1985). The direction of recA protein assembly onto single stranded SNA is the same as the direction of strand assimilation during strand exchange.
  22. (1987). The distribution of Escherichia coli recA protein bound to duplex DNA with single stranded ends.
  23. (1982). The Principles of Quantum Mechanics. doi
  24. (1990). The recA protein: structure and function. doi

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.