A polymer, random walk model for the size-distribution of large DNA fragments after high linear energy transfer radiation

Radiation and Environmental Biophysics

Volumn 39, Issue 2, 2000, Pages 111-120

  Ponomarev, Artem L ^a   Brenner, David ^c   Hlatky, Lynn R ^d   Sachs, Rainer K ^b  

^a NASA HEADQUARTERS   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Och Spine at New York Presbyterian Hospitals   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA;

ARTICLE; CALCULATION; CELL STRAIN V 79; COMPUTER SIMULATION; DNA STRAND BREAKAGE; DOSE RESPONSE; IONIZING RADIATION; LINEAR ENERGY TRANSFER; PARTICLE SIZE; STOCHASTIC MODEL; SYSTEM ANALYSIS;

EID: 0033912212     PISSN: 0301634X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s004119900040     Document Type: Article

References (51)

1. Kellerer AM (1985) Fundamentals of microdosimetry. In: Kase K, Bjarngard B, Attix F (eds) The dosimetry of ionizing radiation, Vol I. Academic Press, Orlando, pp 77-162
2. Löbrich M, Cooper PK, Rydberg B (1996) Non-random distribution of DNA double-strand breaks induced by particle irradiation. Int J Radiat Biol 70: 493-503
3. Kraxenberger A (1996) Verbesserungen der Methoden zur Pulsfeld-Gelelektrophorese und Anwendung der Technik auf die Analyse von DNA-Schaeden durch dicht ionisierende Strahlung. Thesis, Technical University of Munich, Germany, pp 74-91
4. Newman HC, Prise KM, Folkard M, Michael BD (1997) DNA double-strand break distributions in X-ray and alpha-particle irradiated V79 cells: evidence for non-random breakage. Int J Radiat Biol 71: 347-363
5. Kraxenberger F, Weber KJ, Friedl AA, Eckardt-Schupp F, Flentje M, Quicken P, Kellerer AM (1998) DNA double-strand breaks in mammalian cells exposed to gamma-rays and very heavy ions. Fragment-size distributions determined by pulsed-field gel electrophoresis. Radiat Environ Biophys 37: 107-115
6. Höglund E, Blomquist E, Carlsson J, Stenerlöw B (2000) DNA damage induced by radiation of different linear energy transfer. Initial fragmentation. Radiat Res (in press)
7. Brenner DJ (1990) Track structure, lesion development, and cell survival. Radiat Res 124: S29-S37
8. Chatterjee A, Holley WR (1991) Energy deposition mechanisms and biochemical aspects of DNA strand breaks by ionizing radiation. Int J Quantum Chem 391: 709-727
9. Rydberg B, Löbrich M, Cooper PK (1994) DNA double strand breaks induced by high-energy neon and iron ions in human fibroblasts. I. Pulsed field gel electrophoresis method. Radiat Res 139: 133-141
10. Cedervall B, Wong R, Albright N, Dynlacht J, Lambin P, Dewey WC (1995) Methods for the quantification of DNA double-strand breaks determined from the distribution of DNA fragment sizes measured by pulsed-field gel electrophoresis. Radiat Res 143: 8-16
11. Friedl AA, Kraxenberger A, Eckardt-Schupp F (1995) An electrophoretic approach to the assessment of the spatial distribution of DNA double-strand breaks in mammalian cells. Electrophoresis 16: 1865-1874
12. Holley WR, Chatterjee A (1996) Clusters of DNA induced by ionizing radiation: formation of short DNA fragments. I. Theoretical modeling. Radiat Res 145: 188-199
13. Rydberg B (1996) Clusters of DNA damage induced by ionizing radiation: formation of short DNA fragments. II. Experimental detection. Radiat Res 145: 200-209
14. Sachs RK, Brenner DJ, Hahnfeldt PJ, Hlatky LR (1998) A formalism for analyzing large-scale clusters of radiation-induced breaks along chromosomes. Int J Radiat Biol 74: 185-206
15. Moiseenko VV, Edwards AA, Nikjoo H, Prestwich WV (1997) Modeling of chromosome exchanges in human lymphocytes exposed to radiations of different quality. In: Goodhead DT, O'Neill P, Menzel HG (eds) Microdosimetry: an interdisciplinary approach. Royal Society of Chemistry, Cambridge, UK, pp 152-155
16. Friedland W, Jacob P. Paretzke HG (1997) Biophysical simulation of DNA fragments from low-LET radiation. Radiat Res 148: 486-487
17. Friedland W, Jacob P, Paretzke HG, Stork T (1998) Monte Carlo simulation of the production of short DNA fragments by low-linear energy transfer radiation using higher-order DNA models. Radiat Res 150: 170-182
18. Friedland W, Jacob P, Paretzke HG, Merzagora M, Ottolenghi A (1999) Simulation of DNA fragment distributions after irradiation with photons. Radiat Environ Biophys 38: 39-47
19. Andreev SG, Khvostunov IK, Spitkovsky DM, Chepel V (1997) Clustering of DNA breaks in chromatin fiber: dependence on radiation quality. In: Goodhead DT, O'Neill P, Menzel HG (eds) Microdosimetry: an interdisciplinary approach. Royal Society of Chemistry, Cambridge, UK, pp 133-136
20. Brahme A, Rydberg B, Blomquist P (1997) Dual spatially correlated nucleosomal double strand breaks in cell inactivation. In: Goodhead DT, O'Neill P, Menzel HG (eds) Microdosimetry: an interdisciplinary approach. Royal Society of Chemistry, Cambridge, UK, pp 125-128
21. Prise KM (1997) Ionizing radiation induced clustered damage to DNA - a review of the experimental evidence. In: Goodhead DT, O'Neill P, Menzel HG (eds) Microdosimetry: an interdisciplinary approach. Royal Society of Chemistry, Cambridge, UK, pp 111-116
22. Ottolenghi A, Merzagora M, Paretzke HG (1997) DNA complex lesions induced by protons and alpha-particles: track structure characteristics determining linear energy transfer and particle type dependence. Radiat Environ Biophys 36: 97-103
23. Brenner DJ, Ward JF (1992) Constraints on energy deposition and target size of multiply damaged sites associated with DNA double-strand breaks. Int J Radiat Biol 61: 737-748
24. Michalik V (1993) Energy deposition clusters in nanometer regions of charged-particle tracks. Radiat Res 134: 265-270
25. Moiseenko VV, Edwards AA, Nikjoo N (1996) Modeling the kinetics of chromosome exchange formation in human cells exposed to ionizing radiation. Radiat Environ Biophys 35: 31-35
26. Sachs RK, Yokota H, Engh G van den, Trask B, Hearst JE (1995) A random-walk/giant loop model for interphase chromosomes. Proc Natl Acad Sci USA 92: 2710-2714
27. Sachs RK, Hahnfeldt PJ, Ponomarev AL, Hlatky LR (1999) Genomic locations of radiation-produced DNA double strand breaks: a stochastic cluster process formalism. Math Biosci 159: 165-187
28. Kraxenberger A, Friedl AA, Kellerer AM (1994) Computer simulation of pulsed field gel runs allows the quantitation of radiation-induced double-strand breaks in yeast. Electrophoresis 15: 128-136
29. Radivoyevitch T, Cedervall B (1996) Mathematical analysis of DNA fragment distribution models used with pulsed-field gel electrophoresis. Electrophoresis 17: 1087-1093
30. Binder K (1995) Introduction: general aspects of computer simulation techniques and their applications in polymer physics. In: Binder K (ed) Monte Carlo and molecular dynamics simulations in polymer science. Oxford University Press, New York, p 8
31. Wu H, Sachs RK, Yang TC (1998) Radiation-induced total-deletion mutations in the human hprt gene: a biophysical model based on random walk interphase chromatin geometry. Int J Radiat Biol 73: 149-156
32. Hahnfeldt P, Hearst JE, Brenner DJ, Sachs RK, Hlatky LR (1993) Polymer models for interphase chromosomes. Proc Natl Acad Sci USA 90: 7854-7858
33. Ostashevsky JY, Lange CS (1994) The 30 nm chromatin fiber as a flexible polymer. J Biomol Struct Dynam 11: 813-820
34. Dernburg AF, Broman KW, Fung JC, Marshall WF, Philips J, Agard DA, Sedat JW (1996) Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85: 745-759
35. Chatterjee A, Schaefer HJ (1976) Microdosimetric structure of heavy ion tracks in tissue. Radiat Environ Biophys 13: 215-227
36. Cremer T, Kurz A, Zirbel R, Dietzel S, Rinke B, Schrock E, Speicher MR, Mathieu U, Jauch A, Emmerich P, Schertan H, Ried T, Cremer C, Lichter P (1993) Role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harbour Symp Q Biol 58: 777-792
37. Strouboulis J, Wolffe AP (1996) Functional compartmentalization of the nucleus. J Cell Sci 109: 1991-2000
38. Marshall WF, Fung JC, Sedat JW (1997) Deconstructing the nucleus: global architecture from local interactions. Curr Opin Genet Dev 7: 259-263
39. Ostashevsky J (1998) A polymer model for the structural organization of chromatin loops and minibands in interphase chromosomes. Mol Biol Cell 9: 3031-3040
40. Nikjoo H, Uehara S, Wilson WE, Hoshi M, Goodhead DT (1998) Track structure in radiation biology: theory and applications. Int J Radiat Biol 73: 355-364
41. Chandrasekhar S (1943) Stochastic problems in physics and astronomy. Rev Mod Phys 15: 1-20
42. Ponomarev AL, Sachs RK (1999) Polymer chromosome models and Monte Carlo simulations of radiation breaking DNA. Bioinformatics (in press). (Code also available at URL \\ http://math.berkeley.edu/ ∼sachs/ponomarev/artem.index.html)
43. Weiss GH (1994) Aspects and applications of the random walk. North Holland, Amsterdam
44. Gennes P-G de (1979) Scaling concepts in polymer physics. Cornell University Press, Ithaca, p 31
45. Shi Y, He S, Hearst JE (1996) Statistical mechanics of the extensible and shearable elastic rod and of DNA. J Chem Phys 105: 714-731
46. Bhattacharya RN, Waymire EC (1990) Stochastic processes with applications. Wiley, New York
47. Doi M (1996) Introduction to polymer physics. Clarendon Press, Oxford, p 10
48. Munkel C, Eils R, Dietzel S, Zink D, Mehring C, Wedemann G, Cremer T, Langowski J (1999) Compartmentalization of interphase chromosomes observed in simulation and experiment. J Mol Biol 285: 1053-1065
49. Tries V, Paul W, Baschnagel J, Binder K (1997) Modeling polyethylene with the bond fluctuation model. J Chem Phys 106: 738-748
50. Daley DJ, Vere-Jones D (1988) An introduction to the theory of point processes. Springer, New York Berlin Heidelberg
51. Koenig D, Schmidt V (1992) Zufaellige Punktprozesse. Teubner BG, Stuttgart