Theoretical study on the deoxyribose radicals formed by hydrogen abstraction

Mia̧skiewicz, Karol; Osman, Roman

doi:10.1021/ja00080a027

Cited by 133 publications

(158 citation statements)

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“…While the energies of the C-H bonds in the aliphatic chain of the Lys or Arg side chains in PL or PR, respectively, are supposed to be rather high, the theoretically calculated energy of the α-C-H bond in a peptide with a Lys or Arg side chain is as low as ~340 kJ/mol (50). This is lower than the weakest of C-H deoxyribose bonds, C1′-H, which is ~376 kJ/mol according to the theoretical calculations of Miaskiewicz and Osman (51). Therefore, the process of transfer of a neutral free radical from deoxyribose to PL or PR, with the formation of a tertiary α-C-centered free radical, is expected to be thermodynamically favorable.…”

Section: Pcp Repairs Free Radical Damage On the Dna Sugar Moiety By Dmentioning

confidence: 92%

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 Repairs Free Radical Damage On the Dna Sugar Moiety By Dmentioning

confidence: 92%

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

2006

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“…From theoretical calculations, hydrogen abstraction from C1′ , with formation of the 1′ -deoxyribosyl radical, is considered the most thermodynamically favorable among the five deoxyribose carbons (25,26). This finding suggests that two factors may play a role in governing the relative contributions of each pathway initiated by hydrogen abstraction from the different deoxyribose carbons.…”

Section: Introductionmentioning

confidence: 99%

The Release of 5-Methylene-2-Furanone from Irradiated DNA Catalyzed by Cationic Polyamines and Divalent Metal Cations

et al. 2005

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Release of 5-methylene-2-furanone (5-MF), a characteristic marker of DNA deoxyribose oxidative damage at the C1′ position, was observed in significant quantities from X-irradiated DNA. This observation, which held for DNA irradiated either in aqueous solution or as a film, requires postirradiation treatment at 90° C in the presence of polyamines and divalent metal cations at biological pH. The 5-MF product was quantified by using reverse-phase HPLC. The radiation chemical yield of 5-MF comprised more than 30% of the yield of total unaltered base release. Polylysine, spermine and Be(II) showed the strongest catalytic effect on 5-MF release, while Zn(II), Cu(II), Ni(II), putrescine and Mg(II) were substantially less efficient. We have hypothesized that the 5-MF release from irradiated DNA occurs through catalytic decomposition of the 2′ -deoxyribonolactone (dL) precursor through two consecutive β -and δ -phosphate elimination reactions. A stepwise character of the process was indicated by the S-shaped time course of 5-MF accumulation. If dL proves to be the precursor to 5-MF formation, it would then follow that dL is a very important lesion generated in DNA by ionizing radiation.

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“…In particular, studying the role of the sugar unit is critical, as it is now well established that one of the main sources of possible damage to DNA/RNA stems from changes in the D-ribose (DR) unit. 18 Recently, we have pursued in our laboratory a series of detailed studies on negative ion formation in collisions of potassium atoms with several bio-related molecular targets. [19][20][21][22][23][24][25] Further to the studies of atomic collisions with nucleobases, 23 herein we present the negative ion fragmentation pattern from collisions of potassium atoms with the D-ribose molecule (C 5 H 10 O 5 ), the monosaccharide pentose ring in the DNA/RNA structure.…”

Section: Introductionmentioning

confidence: 99%

Dynamic of negative ions in potassium-D-ribose collisions

Almeida

Silva

Garcı́a

et al. 2013

The Journal of Chemical Physics

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We present negative ion formation from collisions of neutral potassium atoms with D-ribose (C5H10O5), the sugar unit in the DNA/RNA molecule. From the negative ion time-of-flight (TOF) mass spectra, OH− is the main fragment detected in the collision range 50-100 eV accounting on average for 50% of the total anion yield. Prominence is also given to the rich fragmentation pattern observed with special attention to O− (16 m/z) formation. These results are in sharp contrast to dissociative electron attachment experiments. The TOF mass spectra assignments show that these channels are also observed, albeit with a much lower relative intensity. Branching ratios of the most abundant fragment anions as a function of the collision energy are obtained, allowing to establish a rationale on the collision dynamics. We present negative ion formation from collisions of neutral potassium atoms with D-ribose (C 5 H 10 O 5 ), the sugar unit in the DNA/RNA molecule. From the negative ion time-of-flight (TOF) mass spectra, OH − is the main fragment detected in the collision range 50-100 eV accounting on average for 50% of the total anion yield. Prominence is also given to the rich fragmentation pattern observed with special attention to O − (16 m/z) formation. These results are in sharp contrast to dissociative electron attachment experiments. The TOF mass spectra assignments show that these channels are also observed, albeit with a much lower relative intensity. Branching ratios of the most abundant fragment anions as a function of the collision energy are obtained, allowing to establish a rationale on the collision dynamics. © 2013 AIP Publishing LLC. [http://dx

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Theoretical study on the deoxyribose radicals formed by hydrogen abstraction

Cited by 133 publications

References 0 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

The Release of 5-Methylene-2-Furanone from Irradiated DNA Catalyzed by Cationic Polyamines and Divalent Metal Cations

Dynamic of negative ions in potassium-D-ribose collisions

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