Thermally stable sites for electron capture in directly ionized DNA : free radicals produced by the net gain of hydrogen at C5/C6 of cytosine and thymine in crystalline oligodeoxynucleotides

M.G. Debije, W.A. Bernhard

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Abstract

Electron paramagnetic resonance (EPR) spectroscopy is used to study radical trapping in crystalline oligodeoxynucleotides exposed to 70 keV x-irradiation at 4 K and annealed to 240 K. The four oligomers studied were the Z form d(CGCACG:GCGTGC), two A forms, d(CCCTAGGG)2 and d(GTGCGCAC)2, and the B form d(CGCGAATTCGCG)2. In each of these oligomers, evidence was found for trapping of a cytosine radical formed by the net gain of a hydrogen at C6 and a proton at N3 (the Cyt(C6+H, N3+H+)+• radical). The data are consistent with the trapping of another cytosine radical formed by the net gain of hydrogen at C5 (the Cyt(C5+H, N3+H)+• or Cyt(C5+H)• radical). The well-known thymine radical formed by the net gain of hydrogen at C5 (Thy(C6+H)• radical) was observed in the Z- and B-form duplexes but not in the A-form duplexes. The relative yields of these three reduction species indicate that cytosine is comparable to, or better than, thymine as a stable trapping site for reductive damage. These three radicals, Cyt(C6+H, N3+H+)+•, Cyt(C5+H, N3+H)+•, and Thy(C6+H)•, account for 85% of the total irreversibly trapped electrons in samples irradiated at 4 K and annealed to 240 K. Extrapolation of these results to B-form DNA hydrated to 9 waters per nucleotide, x-irradiated at 4 K, and warmed to room temperature predicts end product yields of 0.04-0.06 µmol/J for 5,6-dihydrouracil and 0.03-0.05 µmol/J for 5,6-dihydrothymine.
LanguageEnglish
Pages4608-4615
JournalJournal of Physical Chemistry A
Volume106
Issue number18
DOIs
StatePublished - 2002

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Thymine
thymine
Oligodeoxyribonucleotides
Cytosine
electron capture
free radicals
Free Radicals
Hydrogen
deoxyribonucleic acid
Crystalline materials
Oligomers
Electrons
DNA
hydrogen
B-Form DNA
trapping
Extrapolation
Paramagnetic resonance
Protons
Nucleotides

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@article{a9a266c603eb42379219fe3467195620,
title = "Thermally stable sites for electron capture in directly ionized DNA : free radicals produced by the net gain of hydrogen at C5/C6 of cytosine and thymine in crystalline oligodeoxynucleotides",
abstract = "Electron paramagnetic resonance (EPR) spectroscopy is used to study radical trapping in crystalline oligodeoxynucleotides exposed to 70 keV x-irradiation at 4 K and annealed to 240 K. The four oligomers studied were the Z form d(CGCACG:GCGTGC), two A forms, d(CCCTAGGG)2 and d(GTGCGCAC)2, and the B form d(CGCGAATTCGCG)2. In each of these oligomers, evidence was found for trapping of a cytosine radical formed by the net gain of a hydrogen at C6 and a proton at N3 (the Cyt(C6+H, N3+H+)+• radical). The data are consistent with the trapping of another cytosine radical formed by the net gain of hydrogen at C5 (the Cyt(C5+H, N3+H)+• or Cyt(C5+H)• radical). The well-known thymine radical formed by the net gain of hydrogen at C5 (Thy(C6+H)• radical) was observed in the Z- and B-form duplexes but not in the A-form duplexes. The relative yields of these three reduction species indicate that cytosine is comparable to, or better than, thymine as a stable trapping site for reductive damage. These three radicals, Cyt(C6+H, N3+H+)+•, Cyt(C5+H, N3+H)+•, and Thy(C6+H)•, account for 85{\%} of the total irreversibly trapped electrons in samples irradiated at 4 K and annealed to 240 K. Extrapolation of these results to B-form DNA hydrated to 9 waters per nucleotide, x-irradiated at 4 K, and warmed to room temperature predicts end product yields of 0.04-0.06 µmol/J for 5,6-dihydrouracil and 0.03-0.05 µmol/J for 5,6-dihydrothymine.",
author = "M.G. Debije and W.A. Bernhard",
year = "2002",
doi = "10.1021/jp014615+",
language = "English",
volume = "106",
pages = "4608--4615",
journal = "Journal of Physical Chemistry A",
issn = "1089-5639",
publisher = "American Chemical Society",
number = "18",

}

TY - JOUR

T1 - Thermally stable sites for electron capture in directly ionized DNA : free radicals produced by the net gain of hydrogen at C5/C6 of cytosine and thymine in crystalline oligodeoxynucleotides

AU - Debije,M.G.

AU - Bernhard,W.A.

PY - 2002

Y1 - 2002

N2 - Electron paramagnetic resonance (EPR) spectroscopy is used to study radical trapping in crystalline oligodeoxynucleotides exposed to 70 keV x-irradiation at 4 K and annealed to 240 K. The four oligomers studied were the Z form d(CGCACG:GCGTGC), two A forms, d(CCCTAGGG)2 and d(GTGCGCAC)2, and the B form d(CGCGAATTCGCG)2. In each of these oligomers, evidence was found for trapping of a cytosine radical formed by the net gain of a hydrogen at C6 and a proton at N3 (the Cyt(C6+H, N3+H+)+• radical). The data are consistent with the trapping of another cytosine radical formed by the net gain of hydrogen at C5 (the Cyt(C5+H, N3+H)+• or Cyt(C5+H)• radical). The well-known thymine radical formed by the net gain of hydrogen at C5 (Thy(C6+H)• radical) was observed in the Z- and B-form duplexes but not in the A-form duplexes. The relative yields of these three reduction species indicate that cytosine is comparable to, or better than, thymine as a stable trapping site for reductive damage. These three radicals, Cyt(C6+H, N3+H+)+•, Cyt(C5+H, N3+H)+•, and Thy(C6+H)•, account for 85% of the total irreversibly trapped electrons in samples irradiated at 4 K and annealed to 240 K. Extrapolation of these results to B-form DNA hydrated to 9 waters per nucleotide, x-irradiated at 4 K, and warmed to room temperature predicts end product yields of 0.04-0.06 µmol/J for 5,6-dihydrouracil and 0.03-0.05 µmol/J for 5,6-dihydrothymine.

AB - Electron paramagnetic resonance (EPR) spectroscopy is used to study radical trapping in crystalline oligodeoxynucleotides exposed to 70 keV x-irradiation at 4 K and annealed to 240 K. The four oligomers studied were the Z form d(CGCACG:GCGTGC), two A forms, d(CCCTAGGG)2 and d(GTGCGCAC)2, and the B form d(CGCGAATTCGCG)2. In each of these oligomers, evidence was found for trapping of a cytosine radical formed by the net gain of a hydrogen at C6 and a proton at N3 (the Cyt(C6+H, N3+H+)+• radical). The data are consistent with the trapping of another cytosine radical formed by the net gain of hydrogen at C5 (the Cyt(C5+H, N3+H)+• or Cyt(C5+H)• radical). The well-known thymine radical formed by the net gain of hydrogen at C5 (Thy(C6+H)• radical) was observed in the Z- and B-form duplexes but not in the A-form duplexes. The relative yields of these three reduction species indicate that cytosine is comparable to, or better than, thymine as a stable trapping site for reductive damage. These three radicals, Cyt(C6+H, N3+H+)+•, Cyt(C5+H, N3+H)+•, and Thy(C6+H)•, account for 85% of the total irreversibly trapped electrons in samples irradiated at 4 K and annealed to 240 K. Extrapolation of these results to B-form DNA hydrated to 9 waters per nucleotide, x-irradiated at 4 K, and warmed to room temperature predicts end product yields of 0.04-0.06 µmol/J for 5,6-dihydrouracil and 0.03-0.05 µmol/J for 5,6-dihydrothymine.

U2 - 10.1021/jp014615+

DO - 10.1021/jp014615+

M3 - Article

VL - 106

SP - 4608

EP - 4615

JO - Journal of Physical Chemistry A

T2 - Journal of Physical Chemistry A

JF - Journal of Physical Chemistry A

SN - 1089-5639

IS - 18

ER -