title: On the chemical yield of base lesions, strand breaks, and clustered damage generated in plasmid DNA by the direct effect of X rays.
abstract: The purpose of this study was to determine the yield of DNA base damages, deoxyribose damage, and clustered lesions due to the direct effects of ionizing radiation and to compare these with the yield of DNA trapped radicals measured previously in the same pUC18 plasmid. The plasmids were prepared as films hydrated in the range 2.5 < Gamma < 22.5 mol water/mol nucleotide. Single-strand breaks (SSBs) and double-strand breaks (DSBs) were detected by agarose gel electrophoresis. Specific types of base lesions were converted into SSBs and DSBs using the base-excision repair enzymes endonuclease III (Nth) and formamidopyrimidine-DNA glycosylase (Fpg). The yield of base damage detected by this method displayed a strikingly different dependence on the level of hydration (Gamma) compared with that for the yield of DNA trapped radicals; the former decreased by 3.2 times as Gamma was varied from 2.5 to 22.5 and the later increased by 2.4 times over the same range. To explain this divergence, we propose that SSB yields produced in plasmid DNA by the direct effect cannot be analyzed properly with a Poisson process that assumes an average of one strand break per plasmid and neglects the possibility of a single track producing multiple SSBs within a plasmid. The yields of DSBs, on the other hand, are consistent with changes in free radical trapping as a function of hydration. Consequently, the composition of these clusters could be quantified. Deoxyribose damage on each of the two opposing strands occurs with a yield of 3.5 +/- 0.5 nmol/J for fully hydrated pUC18, comparable to the yield of 4.1 +/- 0.9 nmol/J for DSBs derived from opposed damages in which at least one of the sites is a damaged base.
authors: Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA.
authors: Shubhadeep
authors: S
authors: Purkayastha
authors: Jamie R
authors: JR
authors: Milligan
authors: William A
authors: WA
authors: Bernhard
mesh_terms: D020029:Base Pairing / Q000528:radiation effects*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000528:radiation effects*; D053903:DNA Breaks, Double-Stranded / Q000528:radiation effects; D004249:DNA Damage / Q000528:radiation effects*; D004307:Dose-Response Relationship, Radiation; D008956:Models, Chemical; D008957:Models, Genetic; D005810:Multigene Family / Q000528:radiation effects*; D011829:Radiation Dosage; D014965:X-Rays
chemical_list: D004247:DNA
references: Radiat Res. 1996 Jun;145(6):673-80
references: 8643826
references: Radiat Res. 1996 Mar;145(3):304-14
references: 8927698
references: Mutat Res. 1998 Jun 18;402(1-2):93-102
references: 9675252
references: Radiat Res. 1998 Nov;150(5 Suppl):S60-79
references: 9806610
references: Radiat Res. 1999 Jan;151(1):39-49
references: 9973082
references: Radiat Res. 1999 Mar;151(3):334-42
references: 10073672
references: Biochemistry. 1999 Mar 16;38(11):3335-44
references: 10079077
references: Radiat Res. 2005 Apr;163(4):447-54
references: 15799701
references: DNA Repair (Amst). 2005 Dec 8;4(12):1442-9
references: 16199212
references: Radiat Res. 2006 Jul;166(1 Pt 1):1-8
references: 16808596
references: J Phys Chem B. 2005 Sep 8;109(35):16967-73
references: 16853159
references: Nucleic Acids Res. 2006;34(13):3722-30
references: 16893955
references: J Phys Chem B. 2006 Dec 28;110(51):26286-91
references: 17181287
references: Radiat Res. 2007 May;167(5):501-7
references: 17474798
references: J Biol Chem. 2000 Apr 21;275(16):11865-73
references: 10766813
references: Biochemistry. 2000 May 9;39(18):5586-92
references: 10820032
references: Int J Radiat Biol. 2000 Nov;76(11):1475-83
references: 11098850
references: Radiat Res. 2001 Nov;156(5 Pt 2):584-9
references: 11604076
references: Radiat Res. 2002 Mar;157(3):235-42
references: 11839084
references: J Am Chem Soc. 2002 Jul 31;124(30):8859-66
references: 12137539
references: J Am Chem Soc. 2003 Feb 26;125(8):2030-1
references: 12590514
references: J Am Chem Soc. 2003 Apr 16;125(15):4467-77
references: 12683817
references: DNA Repair (Amst). 2004 Oct 5;3(10):1323-34
references: 15336627
references: Biochemistry. 1987 Dec 15;26(25):8200-6
references: 3327518
references: Biochem J. 1989 Sep 1;262(2):581-9
references: 2679549
references: Biochemistry. 1992 Jan 14;31(1):106-10
references: 1731864
references: Radiat Res. 1992 Jul;131(1):10-7
references: 1320766
references: Nucleic Acids Symp Ser. 1992;(27):181-2
references: 1289810
references: Radiat Res. 1993 Aug;135(2):146-54
references: 8396268
references: J Photochem Photobiol B. 1993 Jul;19(2):87-96
references: 8377077
references: Biochemistry. 1993 Nov 16;32(45):12105-11
references: 8218289
references: Radiat Res. 1994 Apr;138(1):9-17
references: 8146305
references: J Biol Chem. 1994 Jul 22;269(29):18814-20
references: 8034633
references: Radiat Res. 1994 Oct;140(1):123-9
references: 7938445
references: Radiat Res. 1994 Nov;140(2):199-214
references: 7938469
references: Int J Radiat Biol. 1994 Nov;66(5):453-7
references: 7983431
references: Radiat Res. 1995 Dec;144(3):251-7
references: 7494867
references: Int J Radiat Biol. 1998 Apr;73(4):355-64
references: 9587072