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. 2005 Dec;31(3-4):303–321. doi: 10.1007/s10867-005-4635-1

Model of DNA Dynamics and Replication

Leif Matsson 1,✉
PMCID: PMC3456345  PMID: 23345900

Abstract

Before DNA replication can be initiated a definite number of adenosine triphosphate (ATP) containing pre-replication protein complexes (pre-RCs) must be assembled and bound to DNA like in a super-critical mass. A chemically driven dynamics of the Ginzburg-Landau (GL) type is derived, using the non-equilibrium equation for binding of pre-RCs to DNA and a probabilistic conformational distribution of these protein complexes. This dynamics, in which the DNA-protein system behaves like a nonlinear elastically braced string (NEBS), can control the cell cycle via conformational transitions such that G2 cells contain exactly twice as much DNA as G1 cells. After adjustment of previously-made derivations, the model is compared with cell growth data from the T lymphocyte MLA-144.

Key words: DNA replication, cell cycle regulation, DNA dynamics, commitment, initiation, termination, DNA condensation, DNA conformation, DNA folding, DNA compaction, DNA packing, pre-replication complex, initiator protein assembly, origin recognition, non-equilibrium dynamics, Ginzburg-Landau model, elastically braced string, reaction coordinate

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References

  1. Kelly T.J., Brown G.W. Regulation of Chromosome Replication. Annu. Rev. Biochem. 2000;69:829–880. doi: 10.1146/annurev.biochem.69.1.829. [DOI] [PubMed] [Google Scholar]
  2. Sherr, C.J.: The Pezcoller Lecture: Cancer Cell Cycles Revisited, Cancer Res. 60 (2000), 3689–3695. [PubMed]
  3. Matsson L. DNA Replication and Cell Cycle Progression Regulated by Long Range Interaction between Protein Complexes Bound to DNA. J. Biol. Phys. 2001;27:329–359. doi: 10.1023/A:1014288212898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Smith K.A. The Interleukin-2 Receptor. Annu. Rev. Cell Biol. 1989;5:157–173. doi: 10.1146/annurev.cb.05.110189.002145. [DOI] [PubMed] [Google Scholar]
  5. Cantrell C.A., Smith K.A.The Interleukin-2 T-Cell System: A New Cell Growth Model Science 19842241312–1316.1984Sci...224.1312C [DOI] [PubMed] [Google Scholar]
  6. Dyson N. The Regulation of E2F by pRB-Family Proteins. Genes & Dev. 1998;12:2245–2262. doi: 10.1101/gad.12.15.2245. [DOI] [PubMed] [Google Scholar]
  7. Harbour J.W., Dean D.C. The Rb/E2F Pathway: Expanding Roles and Emerging Paradigms. Genes & Dev. 2000;14:2393–2409. doi: 10.1101/gad.813200. [DOI] [PubMed] [Google Scholar]
  8. Helin K. Regulation of Cell Proliferation by the E2F Transcription Factors. Curr. Opin. Gen. & Dev. 1998;8:28–35. doi: 10.1016/s0959-437x(98)80058-0. [DOI] [PubMed] [Google Scholar]
  9. Dutta A., Bell S.P. Initiation of DNA Replication in Eukaryotic Cells. Annu. Rev. Cell Dev. Biol. 1997;13:293–332. doi: 10.1146/annurev.cellbio.13.1.293. [DOI] [PubMed] [Google Scholar]
  10. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P.: Molecular Biology of the Cell, Garland Sci., New York 2002, p. 1006.
  11. Bell S.P., Stillman B.ATP-Dependent Recognition of Eukaryotic Origins of DNA Replication by a Multiprotein Complex Nature 1992357128–134.1992Natur.357..128B [DOI] [PubMed] [Google Scholar]
  12. Doi M., Edwards S.F. The Theory of Polymer Dynamics. Oxford: Clarendon Press; 1986. [Google Scholar]
  13. Wartell R.M., Benight A.S.Thermal Denaturation of DNA Molecules: A Comparison of Theory with Experiment Phys. Rep 198512667–107. 10.1016/0370-1573(85)90060-21985PhR...126...67W [DOI] [Google Scholar]
  14. Jackiw R.Quantum Meaning of Classical Field Theory Rev. Mod. Pys. 197749681–706.1977RvMP...49..681J58 #19967 [Google Scholar]
  15. Matsson, L., Sa-yakanit, V. and Boribarn, S.: Lyotropic Ion Channel Current Model Compared with Ising Model, J. Biol. Phys. 31 (2005) 525–532. [DOI] [PMC free article] [PubMed]
  16. Morse P., Feshbach H. Methods of Mathematical Physics Part I. New-York: McGraw-Hill; 1953. [Google Scholar]
  17. Matsson L. Response Theory for Non-Stationary Ligand-Receptor Interaction and a Solution to the Growth Signal Firing Problem. J. Theor. Biol. 1996;180:93–104. doi: 10.1006/jtbi.1996.0084. [DOI] [PubMed] [Google Scholar]
  18. Grosberg A.Y., Khokhlov A.R. Statistical Physics of Macromolecules. New York: AIP; 1994. [Google Scholar]
  19. Case R.B., Chang Y.-P., Smith S.B., Gore J., Cozzarelli N.R., Bustamante C.The Bacterial Condensin MukBEF Compacts DNA into a Repetitive, Stable Structure Science 2004305222–227. 10.1126/science.10982252004Sci...305..222C [DOI] [PubMed] [Google Scholar]
  20. Matsson L. Long Range Interaction between Protein Complexes in DNA Controls Replication and Cell Cycle Progression. J. Biol. Syst. 2001;9:41–65. doi: 10.1023/A:1014288212898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Bustamante C., Marko J.F., Siggia E.D., Smith S.B.Entropic Elasticity of λ -Phage DNA Science 19942651599–1600.1994Sci...265.1599B [DOI] [PubMed] [Google Scholar]
  22. Wiegel F.W. Introduction to Path-Integral Methods in Physics and Polymer Science. Singapore: World Scientific; 1986. [Google Scholar]
  23. Poland D., Scheraga H.A. Occurrence of a Phase Transition in Nucleic Acid Model. J. Chem. Phys. 1966;45:1456–1463. doi: 10.1063/1.1727786. [DOI] [PubMed] [Google Scholar]
  24. Poland D., Scheraga H.A. Phase Transitions in One Dimension and the Helix-Coil Transition in Polyamino Acids. J. Chem. Phys. 1966;45:1464–1469. doi: 10.1063/1.1727785. [DOI] [PubMed] [Google Scholar]
  25. Fischer M.E. Effect of Excluded Volume on Phase Transitions in Biopolymers. J. Chem. Phys. 1966;45:1469–1473. [Google Scholar]
  26. Peyrard M., Bishop A.R.Statistical Mechanics of a Nonlinear Model for DNA Denaturation Phys. Rev. Lett 1989622755–2758. 10.1103/PhysRevLett.62.27551989PhRvL..62.2755P [DOI] [PubMed] [Google Scholar]
  27. Frauenfelder H., Wolynes P.G., Austin R.H. Biological Physics. Rev. Mod. Phys. 1999;71:S419–S430. doi: 10.1103/RevModPhys.71.S419. [DOI] [Google Scholar]
  28. Smith, K.A.: Determining to Divide: How do Cells Decide? J. Biol. Phys. 31 (2005), 261–272. [DOI] [PMC free article] [PubMed]
  29. Ekholm-Reed S., Mendez J., Tedesco D., Zetterberg A., Stillman B., Reed S.I. Deregulation of Cyclin E in Human Cells Interferes with Prereplication Complex Assembly. J. Cell. Biol. 2004;165:789–800. doi: 10.1083/jcb.200404092. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Matsson, L.: Soliton Growth-Signal Transduction in Topologically Quantized T Cells, Phys. Rev. E 48 (1993), 2217–2231. [DOI] [PubMed]
  31. Kramers H.A.Statistics of the Two-Dimensional Ferromagnet. Part I Phys. Rev. 194160252–262.1941PhRv...60..252K0027.285053,63i [Google Scholar]
  32. Jarzynski C.Nonequilibrium Equality for Free Energy Differences Phys. Rev. Lett. 1997782690–2693. 10.1103/PhysRevLett.78.26901997PhRvL..78.2690J [DOI] [Google Scholar]

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