Hydrogen abstraction from deoxyribose by a neighbouring uracil-5-yl radical

Schyman, Patric; Zhang, Ru Bo; Eriksson, Leif A.; Laaksonen, Aatto

doi:10.1039/b711083a

Cited by 22 publications

(33 citation statements)

References 28 publications

(35 reference statements)

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“…[26][27][28] This process shows a resonance at very low electron energies (< 2.0 eV) indicating that it occurs by DEA. 35,36 Similar results are obtained for 5BrU in the condensed phase. 29,30 The loss of Br ions from T5BrUT may be explained by the initial formation of a transient molecular ion followed DEA in which the negative charge goes to Br.…”

Section: Resultssupporting

confidence: 76%

“…According to theoretical studies, C-Br cleavage is the lowest energy process (about 1.88 kcal/mol) 31 whereas the energy for C-O bond cleavage and C-N bond cleavage are higher by at least 3-fold and 10-fold, respectively. 34,35 Interestingly, the yield of damage by these three pathways is inversely proportional to the distance between the nucleobase moiety and the bond undergoing cleavage, i.e., the farther away from the nucleobase, the lower the yield of damage. Similarly, the lack of damage at sites next to abasic sites in short oligonucleotides may be attributed to initial capture of LEEs by the nucleobase and subsequent transfer to other positions of the molecule.…”

Section: Resultsmentioning

confidence: 99%

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Low-Energy Electron-Induced Damage in a Trinucleotide Containing 5-Bromouracil

Cloutier

Sanche

et al. 2011

J. Phys. Chem. B

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The reaction of low-energy electrons (LEEs; 10 eV) with 5'-TpXpT-3' (TXT), where X is uracil (U), thymine (T), and 5-bromouracil (5BrU), was examined by HPLC-UV analysis. The presence of 5BrU increased total damage by >50%. The radiation products of T5BrUT included TUT (40%), free U, T, 5BrU (23%), and fragments (13%). These products may be explained by initial capture of LEEs by the nucleobase to form a transient anion, followed by transfer of the electron within the molecule and cleavage of susceptible bonds by dissociative electron attachment (C-Br, C-N, or C-O bonds). In addition, these products may arise from the uracilyl-5-yl (U-5-yl) radicals that undergo H-atom abstraction from the sugar moiety. Interestingly, several products contained two sites of cleavage (U, pUT, and TUp). The formation of these products was linear with dose, and thus, they arise from the single-electron reactions. To explain these products, we propose that the reaction of LEEs (10 eV) involves the coupling of two dissociative processes in the same molecule (for example, dissociative excitation and dissociative electron attachment). The latter reactions may contribute to the formation of clustered damage, which is the most deleterious damage induced by ionizing radiation.

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Section: Resultssupporting

confidence: 76%

Section: Resultsmentioning

confidence: 99%

Low-Energy Electron-Induced Damage in a Trinucleotide Containing 5-Bromouracil

Cloutier

Sanche

et al. 2011

J. Phys. Chem. B

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“…34,35 The latter radical is formed via hydrogen atom transfer from the 2′ site of 5′-neighbouring sugar to the uracil/cytosine radical (this uracil/cytosine radical is a product of the primary dissociative electron attachment (DEA) process). 36 The formation of dTI in the current studies and no evidence for dTBr formation in the previous one 10 may be explained by the difference in masses between the iodide and bromide anions. Probably, the dT radical cation forms before the heavier iodide leaves the reaction centre while the lighter bromide anion moves too far, in the time needed for the formation of the dT cation radical, to interact with it effectively (forming dTBr).…”

Section: Resultscontrasting

confidence: 55%

Radiation damage to single stranded oligonucleotide trimers labelled with 5-iodopyrimidines

et al. 2016

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The radiolysis of deoxygenated aqueous solution containing trimeric oligonucleotides labelled with iodinated pyrimidines and Tris-HCl as the hydroxyl radical scavenger leads to electron attachment to the halogenated bases that mainly results in single strand breaks. The iodinated trimers are 2-fold more sensitive to solvated electrons than the brominated oligonucleotides, which is explained by the barrier-free dissociation of the iodinated base anions. The present study fills the literature gap concerning the chemistry triggered by ionizing radiation in the iodinated pyrimidines incorporated into DNA.

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“…8 A key process, that ultimately results in DNA strand-cleavage, involves uracil-5-yl radicals abstracting H atoms from nearby functional groups. 9,10 Alternatively, several studies have investigated the possibility that, under aerobic conditions, reaction of the uracil-5-yl radicals with molecular oxygen will form peroxyl radical intermediates (Scheme 1 (i)), and that these peroxyl radicals might be key intermediates in rationalising the activity of these halouracils. 11,12 Following this line of enquiry, Schyman et al reported in a computational study that the peroxyl radical would actually be a less efficient at H atom abstraction from deoxyribose than the uracil-5-yl parent.…”

Section: Introductionmentioning

confidence: 99%

Gas-Phase Oxidation of the Protonated Uracil-5-yl Radical Cation

et al. 2018

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This study targets the kinetics and product detection of the gas-phase oxidation reaction of the protonated 5-dehydrouracil (uracil-5-yl) distonic radical cation using ion-trap mass spectrometry. Protonated 5-dehydrouracil radical ions (5-dehydrouracilH radical ion, m/z 112) are produced within an ion trap by laser photolysis of protonated 5-iodouracil. Storage of the 5-dehydrouracilH radical ion in the presence of controlled concentration of O reveals two main products. The major reaction product pathway is assigned as the formation of protonated 2-hydroxypyrimidine-4,5-dione (m/z 127) + OH. A second product ion (m/z 99), putatively assigned as a five-member-ring ketone structure, is tentatively explained as arising from the decarbonylation (-CO) of protonated 2-hydroxypyrimidine-4,5-dione. Because protonation of the 5-dehydrouracil radical likely forms a dienol structure, the O reaction at the 5 position is ortho to an -OH group. Following this addition of O, the peroxyl-radical intermediate isomerizes by H atom transfer from the -OH group. The ensuing hydroperoxide then decomposes to eliminate OH radical. It is shown that this elimination ofOH radical (-17 Da) is evidence for the presence of an -OH group ortho to the initial phenyl radical site, in good accord with calculations. The subsequent CO loss mechanism, to form the aforementioned five-member-ring structure, is unclear, but some pathways are discussed. By following the kinetics of the reaction, the room temperature second-order rate coefficient of the 5-dehydrouracilH distonic radical cation with molecular oxygen is measured at 7.2 × 10 cm molecule s, Φ = 12% (with ±50% total accuracy). For aryl radical reactions with O, the presence of the OH elimination product pathway, following the peroxyl-radical formation, is an indicator of an -OH group ortho to the radical site.

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Hydrogen abstraction from deoxyribose by a neighbouring uracil-5-yl radical

Cited by 22 publications

References 28 publications

Low-Energy Electron-Induced Damage in a Trinucleotide Containing 5-Bromouracil

Low-Energy Electron-Induced Damage in a Trinucleotide Containing 5-Bromouracil

Radiation damage to single stranded oligonucleotide trimers labelled with 5-iodopyrimidines

Gas-Phase Oxidation of the Protonated Uracil-5-yl Radical Cation

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