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. 2002 Jan;82(1 Pt 1):19–28. doi: 10.1016/S0006-3495(02)75370-8

Fluid mechanics of DNA double-strand filter elution.

George Rudinger 1, Ed Robert Blazek 1
PMCID: PMC1302445  PMID: 11751292

Abstract

Measurement of infrequent DNA double-strand breaks (DSB) in mammalian cells is essential for the understanding of cell damage by ionizing radiation and many DNA-reactive drugs. One of the most important assays for measuring DSB in cellular DNA is filter elution. This study is an attempt to determine whether standard concepts of fluid mechanics can yield a self-consistent model of this process. Major assumptions of the analysis are reptation through a channel formed by surrounding strands, with only strand ends captured by filter pores. Both viscosity and entanglement with surrounding strands are considered to determine the resistance to this motion. One important result is that the average elution time of a strand depends not only on its length, but also on the size distribution of the surrounding strands. This model is consistent with experimental observations, such as the dependence of elution kinetics upon radiation dose, but independence from the size of the DNA sample up to a critical filter loading, and possible overlap of elution times for strands of different length. It indicates how the dependence of elution time on the flow rate could reveal the relative importance of viscous and entanglement resistance, and also predicts the consequences of using different filters.

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Selected References

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  1. Ahnström G., Erixon K. Radiation induced strand breakage in DNA from mammalian cells. Strand separation in alkaline solution. Int J Radiat Biol Relat Stud Phys Chem Med. 1973 Mar;23(3):285–289. doi: 10.1080/09553007314550311. [DOI] [PubMed] [Google Scholar]
  2. Balbi C., Pala M., Parodi S., Figari G., Cavazza B., Trefiletti V., Patrone E. A simple model for DNA elution from filters. J Theor Biol. 1986 Jan 21;118(2):183–198. doi: 10.1016/s0022-5193(86)80133-3. [DOI] [PubMed] [Google Scholar]
  3. Boulton S., Kyle S., Durkacz B. W. Mechanisms of enhancement of cytotoxicity in etoposide and ionising radiation-treated cells by the protein kinase inhibitor wortmannin. Eur J Cancer. 2000 Mar;36(4):535–541. doi: 10.1016/s0959-8049(99)00311-1. [DOI] [PubMed] [Google Scholar]
  4. Bradley M. O., Kohn K. W. X-ray induced DNA double strand break production and repair in mammalian cells as measured by neutral filter elution. Nucleic Acids Res. 1979 Oct 10;7(3):793–804. doi: 10.1093/nar/7.3.793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Burki H. J., Bunker S., Ritter M., Cleaver J. E. DNA damage from incorporated radioisotopes: influence of the 3H location in the cell. Radiat Res. 1975 May;62(2):299–312. [PubMed] [Google Scholar]
  6. Cedervall B., Källman P. Randomly distributed DNA double-strand breaks as measured by pulsed field gel electrophoresis: a series of explanatory calculations. Radiat Environ Biophys. 1994;33(1):9–21. doi: 10.1007/BF01255270. [DOI] [PubMed] [Google Scholar]
  7. Contopoulou C. R., Cook V. E., Mortimer R. K. Analysis of DNA double strand breakage and repair using orthogonal field alternation gel electrophoresis. Yeast. 1987 Jun;3(2):71–76. doi: 10.1002/yea.320030203. [DOI] [PubMed] [Google Scholar]
  8. Dasika G. K., Lin S. C., Zhao S., Sung P., Tomkinson A., Lee E. Y. DNA damage-induced cell cycle checkpoints and DNA strand break repair in development and tumorigenesis. Oncogene. 1999 Dec 20;18(55):7883–7899. doi: 10.1038/sj.onc.1203283. [DOI] [PubMed] [Google Scholar]
  9. Duke T. A., Austin R. H., Cox E. C., Chan S. S. Pulsed-field electrophoresis in microlithographic arrays. Electrophoresis. 1996 Jun;17(6):1075–1079. doi: 10.1002/elps.1150170616. [DOI] [PubMed] [Google Scholar]
  10. Kantor R. M., Guo X. H., Huff E. J., Schwartz D. C. Dynamics of DNA molecules in gel studied by fluorescence microscopy. Biochem Biophys Res Commun. 1999 Apr 29;258(1):102–108. doi: 10.1006/bbrc.1999.0592. [DOI] [PubMed] [Google Scholar]
  11. Kaur B. S., Blazek E. R. Subdenaturing (pH 11.1) filter elution: more sensitive quantification of DNA double-strand breaks. Radiat Res. 1997 May;147(5):569–578. [PubMed] [Google Scholar]
  12. Kiltie A. E., Orton C. J., Ryan A. J., Roberts S. A., Marples B., Davidson S. E., Hunter R. D., Margison G. P., West C. M., Hendry J. H. A correlation between residual DNA double-strand breaks and clonogenic measurements of radiosensitivity in fibroblasts from preradiotherapy cervix cancer patients. Int J Radiat Oncol Biol Phys. 1997 Dec 1;39(5):1137–1144. doi: 10.1016/s0360-3016(97)00545-2. [DOI] [PubMed] [Google Scholar]
  13. Kohn K. W. DNA filter elution: a window on DNA damage in mammalian cells. Bioessays. 1996 Jun;18(6):505–513. doi: 10.1002/bies.950180613. [DOI] [PubMed] [Google Scholar]
  14. Kohn K. W., Erickson L. C., Ewig R. A., Friedman C. A. Fractionation of DNA from mammalian cells by alkaline elution. Biochemistry. 1976 Oct 19;15(21):4629–4637. doi: 10.1021/bi00666a013. [DOI] [PubMed] [Google Scholar]
  15. Kohn K. W., Grimek-Ewig R. A. Alkaline elution analysis, a new approach to the study of DNA single-strand interruptions in cells. Cancer Res. 1973 Aug;33(8):1849–1853. [PubMed] [Google Scholar]
  16. Kohn K. W. Principles and practice of DNA filter elution. Pharmacol Ther. 1991;49(1-2):55–77. doi: 10.1016/0163-7258(91)90022-e. [DOI] [PubMed] [Google Scholar]
  17. Lett J. T., Caldwell I., Dean C. J., Alexander P. Rejoining of x-ray induced breaks in the DNA of leukaemia cells. Nature. 1967 May 20;214(5090):790–792. doi: 10.1038/214790a0. [DOI] [PubMed] [Google Scholar]
  18. Löbrich M., Ikpeme S., Kiefer J. Measurement of DNA double-strand breaks in mammalian cells by pulsed-field gel electrophoresis: a new approach using rarely cutting restriction enzymes. Radiat Res. 1994 May;138(2):186–192. [PubMed] [Google Scholar]
  19. Mayer P. J., Lange C. S., Bradley M. O., Nichols W. W. Investigation of the neutral filter elution technique I. Effects of pore density and pore diameter on elution rate at pH 9.6. Radiat Res. 1991 Feb;125(2):197–205. [PubMed] [Google Scholar]
  20. McDonell M. W., Simon M. N., Studier F. W. Analysis of restriction fragments of T7 DNA and determination of molecular weights by electrophoresis in neutral and alkaline gels. J Mol Biol. 1977 Feb 15;110(1):119–146. doi: 10.1016/s0022-2836(77)80102-2. [DOI] [PubMed] [Google Scholar]
  21. Nevaldine B., Longo J. A., Hahn P. J. The scid defect results in much slower repair of DNA double-strand breaks but not high levels of residual breaks. Radiat Res. 1997 May;147(5):535–540. [PubMed] [Google Scholar]
  22. Nicolini C., Belmont A., Zietz S., Maura A., Pino A., Robbiano L., Brambilla G. Physico-chemical model for DNA alkaline elution: new experimental evidence and differential role of DNA length, chain flexibility and superpacking. J Theor Biol. 1983 Jan 21;100(2):341–357. doi: 10.1016/0022-5193(83)90357-0. [DOI] [PubMed] [Google Scholar]
  23. Perkins T. T., Smith D. E., Chu S. Direct observation of tube-like motion of a single polymer chain. Science. 1994 May 6;264(5160):819–822. doi: 10.1126/science.8171335. [DOI] [PubMed] [Google Scholar]
  24. Schwartz D. C., Cantor C. R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell. 1984 May;37(1):67–75. doi: 10.1016/0092-8674(84)90301-5. [DOI] [PubMed] [Google Scholar]
  25. Simon J. A., Szankasi P., Nguyen D. K., Ludlow C., Dunstan H. M., Roberts C. J., Jensen E. L., Hartwell L. H., Friend S. H. Differential toxicities of anticancer agents among DNA repair and checkpoint mutants of Saccharomyces cerevisiae. Cancer Res. 2000 Jan 15;60(2):328–333. [PubMed] [Google Scholar]
  26. West C. M. Invited review: intrinsic radiosensitivity as a predictor of patient response to radiotherapy. Br J Radiol. 1995 Aug;68(812):827–837. doi: 10.1259/0007-1285-68-812-827. [DOI] [PubMed] [Google Scholar]
  27. Zimm B. H. Anomalies in sedimentation. IV. Decrease in sedimentation coefficients of chains at high fields. Biophys Chem. 1974 Apr;1(4):279–291. doi: 10.1016/0301-4622(74)80014-1. [DOI] [PubMed] [Google Scholar]
  28. Zimm B. H., Schumaker V. N., Zimm C. B. Anomalies in sedimentation. V. Chains at high fields, practical consequences. Biophys Chem. 1976 Jul;5(1-2):265–270. doi: 10.1016/0301-4622(76)80039-7. [DOI] [PubMed] [Google Scholar]

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