메뉴 건너뛰기




Volumn 169, Issue 2, 2008, Pages 223-231

Monte Carlo simulations of site-specific radical attack to DNA bases

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DNA B; DNA BASE; GUANINE; HYDROGEN; HYDROXYL RADICAL; NUCLEIC ACID BASE; NUCLEOTIDE; PYRIMIDINE; THYMINE; WATER;

EID: 39749176152     PISSN: 00337587     EISSN: None     Source Type: Journal    
DOI: 10.1667/RR0293.1     Document Type: Article
Times cited : (43)

References (50)
  • 1
    • 0032557407 scopus 로고    scopus 로고
    • Hydroxyl radicals are involved in the oxidation of isolated and cellular DNA bases by 5-aminolevulinic acid
    • T. Douki, J. Onuki, M. H. G. Medeiros, E. J. Bechara, J. Cadet and P. Di Mascio, Hydroxyl radicals are involved in the oxidation of isolated and cellular DNA bases by 5-aminolevulinic acid. FEBS Lett. 428, 93-96 (1998).
    • (1998) FEBS Lett , vol.428 , pp. 93-96
    • Douki, T.1    Onuki, J.2    Medeiros, M.H.G.3    Bechara, E.J.4    Cadet, J.5    Di Mascio, P.6
  • 2
    • 11644276221 scopus 로고    scopus 로고
    • Resonant dissociation of DNA bases by sub-ionization electrons
    • M. A. Huels, I. Hahndorf, E. Illenberger and L. Sanche, Resonant dissociation of DNA bases by sub-ionization electrons. J. Chem. Phys. 108, 1309-1312 (1998).
    • (1998) J. Chem. Phys , vol.108 , pp. 1309-1312
    • Huels, M.A.1    Hahndorf, I.2    Illenberger, E.3    Sanche, L.4
  • 4
    • 0026295112 scopus 로고
    • The chemistry of free-radical-mediated DNA damage
    • W. A. Glass and M. N. Varma, Eds, pp, Plenum Press, New York
    • C. von Sonntag, The chemistry of free-radical-mediated DNA damage. In Physical and Chemical Mechanisms in Molecular Radiation Biology (W. A. Glass and M. N. Varma, Eds.), pp. 287-321. Plenum Press, New York, 1991.
    • (1991) Physical and Chemical Mechanisms in Molecular Radiation Biology , pp. 287-321
    • von Sonntag, C.1
  • 5
    • 0029947555 scopus 로고    scopus 로고
    • Radiation-induced DNA damage as a function of hydration. II. Base damage from electron-loss centers
    • S. G. Swarts, D. Becker, M. Sevilla and K. T. Wheeler, Radiation-induced DNA damage as a function of hydration. II. Base damage from electron-loss centers. Radiat. Res. 145, 304-314 (1996).
    • (1996) Radiat. Res , vol.145 , pp. 304-314
    • Swarts, S.G.1    Becker, D.2    Sevilla, M.3    Wheeler, K.T.4
  • 6
    • 0026456788 scopus 로고
    • Electron-transfer-induced acidity/basicity and reactivity changes of purine and pyrimidine bases. Consequences of redox processes for DNA base pairs
    • S. Steenken, Electron-transfer-induced acidity/basicity and reactivity changes of purine and pyrimidine bases. Consequences of redox processes for DNA base pairs. Free Radic. Res. Commun. 16, 349-379 (1992).
    • (1992) Free Radic. Res. Commun , vol.16 , pp. 349-379
    • Steenken, S.1
  • 7
    • 0025127407 scopus 로고
    • Pattern of hydroxy radical reaction with adenine and its nucleosides and nucleotides. Characterization of two types of isomeric hydroxy adduct and their unimolecular transformation reactions
    • A. J. Vieira and S. Steenken, Pattern of hydroxy radical reaction with adenine and its nucleosides and nucleotides. Characterization of two types of isomeric hydroxy adduct and their unimolecular transformation reactions. J. Am. Chem. Soc. 112, 6986-6994 (1990).
    • (1990) J. Am. Chem. Soc , vol.112 , pp. 6986-6994
    • Vieira, A.J.1    Steenken, S.2
  • 11
    • 0025061775 scopus 로고
    • Simulation of space and time evolution of radiolytic species induced by electrons in water
    • M. Terrisol and A. Beaudre, Simulation of space and time evolution of radiolytic species induced by electrons in water. Radiat. Prot. Dosimetry 31, 171-175 (1990).
    • (1990) Radiat. Prot. Dosimetry , vol.31 , pp. 171-175
    • Terrisol, M.1    Beaudre, A.2
  • 12
    • 0028201715 scopus 로고
    • A stochastic model of ion track structure
    • W. E. Wilson and H. G. Paretzke, A stochastic model of ion track structure. Radiat. Prot. Dosimetry 52, 249-253 (1994).
    • (1994) Radiat. Prot. Dosimetry , vol.52 , pp. 249-253
    • Wilson, W.E.1    Paretzke, H.G.2
  • 13
    • 0030845071 scopus 로고    scopus 로고
    • Monte Carlo simulation of physicochemical processes of liquid water radiolysis. The effects of dissolved oxygen and OH scavenger
    • H. Tomita, M. Kai, T. Kusama and A. Ito, Monte Carlo simulation of physicochemical processes of liquid water radiolysis. The effects of dissolved oxygen and OH scavenger. Radiat. Environ. Biophys. 36, 105-116 (1997).
    • (1997) Radiat. Environ. Biophys , vol.36 , pp. 105-116
    • Tomita, H.1    Kai, M.2    Kusama, T.3    Ito, A.4
  • 15
    • 0002775963 scopus 로고
    • Calculation of range and distributions of damage to DNA by high- and low-LET radiations
    • A. F. Fuciarelli and J. D. Zimbrick, Eds, Battelle Press, Columbus, OH
    • H. Nikjoo and D. E. Charlton, Calculation of range and distributions of damage to DNA by high- and low-LET radiations. In Radiation Damage to DNA: Structure/Function Relationships at Early Times (A. F. Fuciarelli and J. D. Zimbrick, Eds.). Battelle Press, Columbus, OH, 1995.
    • (1995) Radiation Damage to DNA: Structure/Function Relationships at Early Times
    • Nikjoo, H.1    Charlton, D.E.2
  • 16
    • 0029583626 scopus 로고
    • Calculation of hydroxyl radical attack on different forms of DNA
    • V. Michalik, M. S. Maurizot and M. Charlier, Calculation of hydroxyl radical attack on different forms of DNA. J. Biomol. Struct. Dyn. 13, 565-575 (1995).
    • (1995) J. Biomol. Struct. Dyn , vol.13 , pp. 565-575
    • Michalik, V.1    Maurizot, M.S.2    Charlier, M.3
  • 17
    • 0031981518 scopus 로고    scopus 로고
    • Monte Carlo simulation of DNA strand-break induction in supercoiled plasmid pBR322 DNA from indirect effects
    • H. Tomita, M. Kai, T. Kusama and A. Ito, Monte Carlo simulation of DNA strand-break induction in supercoiled plasmid pBR322 DNA from indirect effects. Radiat. Environ. Biophys. 36, 235-241 (1998).
    • (1998) Radiat. Environ. Biophys , vol.36 , pp. 235-241
    • Tomita, H.1    Kai, M.2    Kusama, T.3    Ito, A.4
  • 18
    • 0036149302 scopus 로고    scopus 로고
    • Site-specific OH attack to the sugar moiety of DNA: A comparison of experimental data and computational simulation
    • B. Aydogan, D. T. Marshall, S. G. Swarts, J. E. Turner, A. J. Boone, N. G. Richards and W. E. Bolch, Site-specific OH attack to the sugar moiety of DNA: A comparison of experimental data and computational simulation. Radiat. Res. 157, 38-44 (2002).
    • (2002) Radiat. Res , vol.157 , pp. 38-44
    • Aydogan, B.1    Marshall, D.T.2    Swarts, S.G.3    Turner, J.E.4    Boone, A.J.5    Richards, N.G.6    Bolch, W.E.7
  • 19
    • 34347383811 scopus 로고    scopus 로고
    • Theoretical modeling of radiolytic damage of free DNA bases and within DNA macromolecule
    • V. Stepán and M. Davídková, Theoretical modeling of radiolytic damage of free DNA bases and within DNA macromolecule. Radiat. Prot. Dosimetry 122, 110-112 (2007).
    • (2007) Radiat. Prot. Dosimetry , vol.122 , pp. 110-112
    • Stepán, V.1    Davídková, M.2
  • 20
    • 0032544035 scopus 로고    scopus 로고
    • DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone
    • B. Balasubramanian, W. K. Pogozelski and T. D. Tullius, DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc. Natl. Acad. Sci. USA 95, 9738-9743 (1998).
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 9738-9743
    • Balasubramanian, B.1    Pogozelski, W.K.2    Tullius, T.D.3
  • 21
    • 0004327380 scopus 로고
    • Monte Carlo Simulation of Indirect Damage to Biomolecules Irradiated in Aqueous Solution - The Radiolysis of Glycylglycine
    • Report ORNL/TM-10851, Oak Ridge National Laboratory, Oak Ridge, TN
    • J. E. Turner, W. E. Bolch, H. Yoshida, K. B. Jacobson, H. A. Wright, R. N. Hamm, R. H. Ritchie and C. E. Klots, Monte Carlo Simulation of Indirect Damage to Biomolecules Irradiated in Aqueous Solution - The Radiolysis of Glycylglycine. Report ORNL/TM-10851, Oak Ridge National Laboratory, Oak Ridge, TN, 1988.
    • (1988)
    • Turner, J.E.1    Bolch, W.E.2    Yoshida, H.3    Jacobson, K.B.4    Wright, H.A.5    Hamm, R.N.6    Ritchie, R.H.7    Klots, C.E.8
  • 22
    • 0031761637 scopus 로고    scopus 로고
    • Product yields from irradiated glycylglycine in oxygen-free solutions: Monte Carlo simulations and comparison with experiments
    • W. E. Bolch, J. E. Turner, H. Yoshida, K. B. Jacobson, R. N. Hamm and O. H. Crawford, Product yields from irradiated glycylglycine in oxygen-free solutions: Monte Carlo simulations and comparison with experiments. Radiat. Environ. Biophys. 37, 157-166 (1998).
    • (1998) Radiat. Environ. Biophys , vol.37 , pp. 157-166
    • Bolch, W.E.1    Turner, J.E.2    Yoshida, H.3    Jacobson, K.B.4    Hamm, R.N.5    Crawford, O.H.6
  • 23
    • 39749085434 scopus 로고    scopus 로고
    • HyperChem Professional, Release 6. Hypercube Inc, Gainesville, FL, 2000
    • HyperChem Professional, Release 6. Hypercube Inc., Gainesville, FL, 2000.
  • 26
    • 0001138912 scopus 로고
    • Three discourses on diffusion, Brownian movements, and coagulation of colloid particles
    • M. V. Smoluchowski, Three discourses on diffusion, Brownian movements, and coagulation of colloid particles. Phys. Zeits 17, 557-565 (1916).
    • (1916) Phys. Zeits , vol.17 , pp. 557-565
    • Smoluchowski, M.V.1
  • 28
    • 0000965687 scopus 로고    scopus 로고
    • Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations
    • P. Hobza and J. Šponer, Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations. Chem. Rev. 99, 3247-3276 (1999).
    • (1999) Chem. Rev , vol.99 , pp. 3247-3276
    • Hobza, P.1    Šponer, J.2
  • 29
    • 0037012390 scopus 로고    scopus 로고
    • D. Reha, M. Kabelác, F. Ryjácek, J. E. Šponer, M. Elstner, S. Suhai and P. Hobza, Intercalators. 1. Nature of stacking interactions between intercalcalators (ethidium, daunomycin, ellipticine, and 4′,6-diamide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study. J. Am. Chem. Soc. 124, 3366-3376 (2002).
    • D. Reha, M. Kabelác, F. Ryjácek, J. E. Šponer, M. Elstner, S. Suhai and P. Hobza, Intercalators. 1. Nature of stacking interactions between intercalcalators (ethidium, daunomycin, ellipticine, and 4′,6-diamide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study. J. Am. Chem. Soc. 124, 3366-3376 (2002).
  • 31
    • 33748366270 scopus 로고
    • - and OH adducts
    • - and OH adducts. Chem. Rev. 89, 503-520 (1989).
    • (1989) Chem. Rev , vol.89 , pp. 503-520
    • Steenken, S.1
  • 32
    • 0000419648 scopus 로고
    • Pattern of OH radical addition to uracil and methyl- and carboxyl-substituted uracils. Electron transfer of OH adducts with N′,N′,N′,N′-tetramethyl-p-phenylenediamine and tetranitromethane
    • Chem. Soc
    • S. Fujita and S. Steenken, Pattern of OH radical addition to uracil and methyl- and carboxyl-substituted uracils. Electron transfer of OH adducts with N′,N′,N′,N′-tetramethyl-p-phenylenediamine and tetranitromethane. J. Am. Chem. Soc. 103, 2540-2545 (1981).
    • (1981) J. Am , vol.103 , pp. 2540-2545
    • Fujita, S.1    Steenken, S.2
  • 33
    • 0020764934 scopus 로고
    • Pattern of OH radical addition to cytosine and 1-, 3-, 5-, and 6-substituted cytosines. Electron transfer and dehydration reactions of the OH adducts
    • D. K. Hazra and S. Steenken, Pattern of OH radical addition to cytosine and 1-, 3-, 5-, and 6-substituted cytosines. Electron transfer and dehydration reactions of the OH adducts. J. Am. Chem. Soc. 105, 4380-4386 (1983).
    • (1983) J. Am. Chem. Soc , vol.105 , pp. 4380-4386
    • Hazra, D.K.1    Steenken, S.2
  • 34
    • 85173821468 scopus 로고    scopus 로고
    • The chemical pathways
    • DNA damage dictates the biological consequences of ionizing irradiation:, A. Mozumder and Y. Hatano, Eds, pp, Marcel Dekker, New York
    • W. A. Bernhard and D. M. Close, DNA damage dictates the biological consequences of ionizing irradiation: The chemical pathways. In Charged Particle and Photon Interactions with Matter (A. Mozumder and Y. Hatano, Eds.), pp. 431-470. Marcel Dekker, New York, 2003.
    • (2003) Charged Particle and Photon Interactions with Matter , pp. 431-470
    • Bernhard, W.A.1    Close, D.M.2
  • 35
    • 0000130135 scopus 로고    scopus 로고
    • Solvent mode participation in the nonradiative relaxation of the hydrated electron
    • O. V. Prezhdo and P. J. Rossky, Solvent mode participation in the nonradiative relaxation of the hydrated electron. J. Phys. Chem. 100, 17094-17102 (1996).
    • (1996) J. Phys. Chem , vol.100 , pp. 17094-17102
    • Prezhdo, O.V.1    Rossky, P.J.2
  • 36
    • 0041940866 scopus 로고
    • A natural bond orbital analysis of the bonding in solvated electrons within a localised electron model
    • A. E. Reed and T. Clark, A natural bond orbital analysis of the bonding in solvated electrons within a localised electron model. Faraday Discuss. Chem. Soc. 85, 365-372 (1988).
    • (1988) Faraday Discuss. Chem. Soc , vol.85 , pp. 365-372
    • Reed, A.E.1    Clark, T.2
  • 38
    • 33845556007 scopus 로고
    • Free radicals generated by radiolysis of aqueous solutions
    • H. A. Schwarz, Free radicals generated by radiolysis of aqueous solutions. J. Chem. Ed. 58, 101-105 (1981).
    • (1981) J. Chem. Ed , vol.58 , pp. 101-105
    • Schwarz, H.A.1
  • 39
    • 0016799032 scopus 로고
    • Electron transfer oxidation of DNA radicals by paranitroacetophenone
    • D. W. Whillans and G. E. Adams, Electron transfer oxidation of DNA radicals by paranitroacetophenone. Int. J. Radiat. Biol. 28, 501-510 (1975).
    • (1975) Int. J. Radiat. Biol , vol.28 , pp. 501-510
    • Whillans, D.W.1    Adams, G.E.2
  • 40
    • 0015116255 scopus 로고
    • Factors affecting the rate of hydrated electron attack on polynucleotides
    • P. C. Schragge, H. B. Michaels and J. W. Hunt, Factors affecting the rate of hydrated electron attack on polynucleotides. Radiat. Res. 47, 598-611 (1971).
    • (1971) Radiat. Res , vol.47 , pp. 598-611
    • Schragge, P.C.1    Michaels, H.B.2    Hunt, J.W.3
  • 41
    • 0023058919 scopus 로고
    • Production of dihydrothymidine stereoisomers in DNA by gamma-irradiation
    • E. A. Furlong, T. J. Jorgensen and W. D. Henner, Production of dihydrothymidine stereoisomers in DNA by gamma-irradiation. Biochemistry 25, 4344-4349 (1986).
    • (1986) Biochemistry , vol.25 , pp. 4344-4349
    • Furlong, E.A.1    Jorgensen, T.J.2    Henner, W.D.3
  • 42
    • 0021957619 scopus 로고
    • Radiation-induced decomposition of the purine bases within DNA and related model compounds
    • J. Cadet and M. Berger, Radiation-induced decomposition of the purine bases within DNA and related model compounds. Int. J. Radiat. Biol. 47, 127-143 (1985).
    • (1985) Int. J. Radiat. Biol , vol.47 , pp. 127-143
    • Cadet, J.1    Berger, M.2
  • 43
    • 0029868695 scopus 로고    scopus 로고
    • Radiation-induced formation of a crosslink between base moieties of deoxyguanosine and thymidine in deoxygenated solutions of d(CpGpTpA)
    • H. C. Box, E. E. Budzinski, J. D. Dawidzik, J. C. Wallace, M. S. Evans and J. S. Gobey, Radiation-induced formation of a crosslink between base moieties of deoxyguanosine and thymidine in deoxygenated solutions of d(CpGpTpA). Radiat. Res. 145, 641-643 (1996).
    • (1996) Radiat. Res , vol.145 , pp. 641-643
    • Box, H.C.1    Budzinski, E.E.2    Dawidzik, J.D.3    Wallace, J.C.4    Evans, M.S.5    Gobey, J.S.6
  • 44
    • 0037337251 scopus 로고    scopus 로고
    • Electron and hole transfer from DNA base radicals to oxidized products of guanine in DNA
    • Z. Cai and M. D. Sevilla, Electron and hole transfer from DNA base radicals to oxidized products of guanine in DNA. Radiat. Res. 159, 411-419 (2003).
    • (2003) Radiat. Res , vol.159 , pp. 411-419
    • Cai, Z.1    Sevilla, M.D.2
  • 45
    • 0033000559 scopus 로고    scopus 로고
    • Stereoisomeric C5-C5′-linked dihydrothymine dimers produced by radiolytic one-electron reduction of thymine derivatives in anoxic aqueous solution: Structural characteristics in reference to cyclobutane photodimers
    • T. Ito, H. Shinohara, H. Hatta and S. Nishimoto, Stereoisomeric C5-C5′-linked dihydrothymine dimers produced by radiolytic one-electron reduction of thymine derivatives in anoxic aqueous solution: Structural characteristics in reference to cyclobutane photodimers. J. Org. Chem. 64, 5100-5108 (1999).
    • (1999) J. Org. Chem , vol.64 , pp. 5100-5108
    • Ito, T.1    Shinohara, H.2    Hatta, H.3    Nishimoto, S.4
  • 46
    • 0031075351 scopus 로고    scopus 로고
    • Relative efficiencies and relevance to intrastrand electron migration distances
    • Competitive electron scavenging by chemically modified pyrimidine bases in bromine-doped DNA
    • Y. Razskazovskii, S. G. Swarts, J. M. Falcone, C. Taylor and M. D. Sevilla, Competitive electron scavenging by chemically modified pyrimidine bases in bromine-doped DNA: Relative efficiencies and relevance to intrastrand electron migration distances. J. Phys. Chem. B 101, 460-1467 (1997).
    • (1997) J. Phys. Chem. B , vol.101 , pp. 460-1467
    • Razskazovskii, Y.1    Swarts, S.G.2    Falcone, J.M.3    Taylor, C.4    Sevilla, M.D.5
  • 47
    • 0026600950 scopus 로고
    • Radiation-induced DNA damage as a function of hydration. I. Release of unaltered bases
    • S. G. Swarts, M. D. Sevilla, D. Becker, C. J. Tokar and K. T. Wheeler, Radiation-induced DNA damage as a function of hydration. I. Release of unaltered bases. Radiat. Res. 129, 333-334 (1992).
    • (1992) Radiat. Res , vol.129 , pp. 333-334
    • Swarts, S.G.1    Sevilla, M.D.2    Becker, D.3    Tokar, C.J.4    Wheeler, K.T.5
  • 49
    • 0344401079 scopus 로고
    • Relative abundance and reactivity of primary ion radicals in gamma irradiated DNA at low temperatures. 2. single- vs. double-stranded DNA
    • M. Yan, D. Becker, S. Summerfield and M. D. Sevilla, Relative abundance and reactivity of primary ion radicals in gamma irradiated DNA at low temperatures. 2. single- vs. double-stranded DNA. J. Phys. Chem. B 96, 1983-1989 (1992).
    • (1992) J. Phys. Chem. B , vol.96 , pp. 1983-1989
    • Yan, M.1    Becker, D.2    Summerfield, S.3    Sevilla, M.D.4
  • 50
    • 0034245511 scopus 로고    scopus 로고
    • Electron and hole transfer induced by thermal annealing of crystalline DNA x-irradiated at 4 K
    • M. G. Debije and W. A. Bernhard, Electron and hole transfer induced by thermal annealing of crystalline DNA x-irradiated at 4 K. J. Phys. Chem. B 104, 7845-7851 (2000).
    • (2000) J. Phys. Chem. B , vol.104 , pp. 7845-7851
    • Debije, M.G.1    Bernhard, W.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.