The Effect of Packing and Conformation on Free Radical Yields in Films of Variably Hydrated DNA

Milano, Michael T.; Bernhard, William A.

doi:10.2307/3579745

Cited by 37 publications

(75 citation statements)

References 58 publications

(113 reference statements)

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“…3 and Table 2). DNA damage at high hydration levels is believed to be mediated by the hydroxyl radicals formed from outer loosely bound water molecules (20,22,26,45,46). Because no increase in DNA damage was observed in the DNA-PL films at high hydration levels, we argue that the hydroxyl radicals are efficiently scavenged by PL.…”

Section: Pcp Inhibits Hole Transfer From the Solvent Shell To Dnamentioning

confidence: 87%

“…As expected, hydration levels for the DNA-PL films far exceeded those observed for the DNA films (22,26) since water partitions between DNA and PL, with PL attaching more water than DNA due to its 3.5-fold or 10-fold molar excess. Table 2 and Fig.…”

Section: Effect Of the Dna-pl Film Hydrationmentioning

confidence: 92%

“…It has been demonstrated (20,26,(44)(45)(46) that at low hydration levels (when water molecules forming the first hydration layer are very tightly bound to DNA) all holes on water are rapidly transferred to DNA. However, the experiments with the hydrated DNA and DNA-PL films do not support mechanism (1) playing a major role.…”

Section: Pcp Inhibits Hole Transfer From the Solvent Shell To Dnamentioning

confidence: 99%

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Protection of DNA against Direct Radiation Damage by Complex Formation with Positively Charged Polypeptides

2006

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Radioprotection of DNA from direct-type radiation damage by histones has been studied in model systems using complexes of positively charged polypeptides (PCPs) with DNA. PCPs bind to DNA via ionic interactions mimicking the mode of DNA-histone binding. Direct radiation damage to DNA in films of DNA-PCP complexes was quantified as unaltered base release, which correlates closely with DNA strand breaks. All types of PCPs tested protected DNA from radiation, with the maximum radioprotection being approximately 2.5-fold compared with non-complexed DNA. Conformational changes of the DNA induced by PCPs or repair of free radical damage on the DNA sugar moiety by PCPs are considered the most feasible mechanisms of radioprotection of DNA. The degree of radioprotection of DNA by polylysine (PL) increased dramatically on going from pure DNA to a molar ratio of PL monomer:DNA nucleotide ~1:2, while a further increase in the PL:DNA ratio did not offer more radioprotection. This concentration dependence is in agreement with the model of PCP binding to DNA that assumes preferential binding of positively charged side groups to DNA phosphates in the minor groove, so that the maximum occupancy of all minor-groove PCP binding sites is at a molar ratio of PCP:DNA = 1:2.

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Section: Pcp Inhibits Hole Transfer From the Solvent Shell To Dnamentioning

confidence: 87%

Section: Effect Of the Dna-pl Film Hydrationmentioning

confidence: 92%

Section: Pcp Inhibits Hole Transfer From the Solvent Shell To Dnamentioning

confidence: 99%

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Protection of DNA against Direct Radiation Damage by Complex Formation with Positively Charged Polypeptides

2006

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“…This difference can be attributed to the different packing in the films compared to the lattice packing in the crystals, as observed in hydrated DNA films (23,24) and crystalline oligodeoxynucleotides (19).…”

Section: Shortfall Between Free Base Release and Deoxyribosetrapped Rmentioning

confidence: 99%

Unaltered Free Base Release from d(CGCGCG)₂Produced by the Direct Effect of Ionizing Radiation at 4 K and Room Temperature

Sharma¹,

Purkayastha²,

Bernhard³

2007

Radiation Research

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Unaltered free base release in d(CGCGCG) 2 exposed to X rays at 4 K or room temperature was measured by HPLC. Samples were prepared either as films hydrated to a level of Γ= 2.5 mol water/ mol nucleotide or as polycrystalline with Γ ∼ 7.5 mol water/mol nucleotide. X irradiation of films at 4 K, followed by annealing to room temperature, resulted in yields for cytosine and guanine of G (Cyt) = 0.036 ± 0.001 μmol/J and G(Gua) = 0.090 ± 0.002 μmol/J. Irradiation of films at room temperature gave similar yields. The yields for polycrystalline d(CGCGCG) 2 X-irradiated at room temperature were G(Cyt) = 0.035 ± 0.005 μmol/J and G(Gua) = 0.077 ± 0.023 μmol/J. The total free base release yield, G(fbr), was 0.124 ± 0.008 μmol/J for films and 0.112 ± 0.028 μmol/J for polycrystalline samples. G(fbr) is believed to be a good estimate of total strand break yield. The yields of total free radicals trapped [G(Σfr)] by the d(CGCGCG) 2 films at 4 K were measured by EPR. The measured value, G(Σfr) = 0.450 ± 0.005 μmol/J, was used to calculate the yield of trappable sugar radicals, giving G sugar (fr) = 0.04-0.07 μmol/J. We found that (1) guanine release exceeded cytosine release by more than twofold, (2) G sugar (fr) cannot account for more than half of the free base release, and (3) G(fbr), G(Cyt) and G(Gua) were independent of the sample temperature during irradiation. Finding (1) suggests that base and or sequence influences sugar damage, and finding (2) is consistent with our working hypothesis that an important pathway to strand break formation entails two one-electron oxidations at the same sugar site.

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“…In the outer shell, consisting of ~12 mol water per mol nucleotide (10 < Γ ≤ ~22), deprotonation of H 2 O •+ is faster than hole transfer so as to favor HO • formation (13,14). In contrast, the electrons generated from the entire solvation shell, 2.5 < Γ ≤ ~22, are trapped by DNA with yields comparable to ionization of DNA itself (15). Previous results (16) indicate that the distribution of all trapped radicals will be ~90% on the bases and ~10% on the sugar-phosphate backbone.…”

Section: Introductionmentioning

confidence: 99%

On the Chemical Yield of Base Lesions, Strand Breaks, and Clustered Damage Generated in Plasmid DNA by the Direct Effect of X Rays

2007

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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 < Γ < 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 (Γ) compared with that for the yield of DNA trapped radicals; the former decreased by 3.2 times as Γ 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.

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The Effect of Packing and Conformation on Free Radical Yields in Films of Variably Hydrated DNA

Cited by 37 publications

References 58 publications

Protection of DNA against Direct Radiation Damage by Complex Formation with Positively Charged Polypeptides

Protection of DNA against Direct Radiation Damage by Complex Formation with Positively Charged Polypeptides

Unaltered Free Base Release from d(CGCGCG)₂Produced by the Direct Effect of Ionizing Radiation at 4 K and Room Temperature

On the Chemical Yield of Base Lesions, Strand Breaks, and Clustered Damage Generated in Plasmid DNA by the Direct Effect of X Rays

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The Effect of Packing and Conformation on Free Radical Yields in Films of Variably Hydrated DNA

Cited by 37 publications

References 58 publications

Protection of DNA against Direct Radiation Damage by Complex Formation with Positively Charged Polypeptides

Protection of DNA against Direct Radiation Damage by Complex Formation with Positively Charged Polypeptides

Unaltered Free Base Release from d(CGCGCG)2Produced by the Direct Effect of Ionizing Radiation at 4 K and Room Temperature

On the Chemical Yield of Base Lesions, Strand Breaks, and Clustered Damage Generated in Plasmid DNA by the Direct Effect of X Rays

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Unaltered Free Base Release from d(CGCGCG)₂Produced by the Direct Effect of Ionizing Radiation at 4 K and Room Temperature