메뉴 건너뛰기




Volumn 44, Issue 40, 2005, Pages 13342-13353

Structural and thermodynamic features of spiroiminodihydantoin damaged DNA duplexes

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; FREE ENERGY; ISOMERS; MOLECULAR DYNAMICS; MUTAGENS; OXIDATION;

EID: 26444571743     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050790v     Document Type: Article
Times cited : (48)

References (91)
  • 1
    • 0028814266 scopus 로고    scopus 로고
    • DNA damage profiles induced by oxidizing agents
    • Epe, B. (1996) DNA damage profiles induced by oxidizing agents, Rev. Physiol. Biochem. Pharmacol. 127, 223-249.
    • (1996) Rev. Physiol. Biochem. Pharmacol. , vol.127 , pp. 223-249
    • Epe, B.1
  • 2
    • 0025973703 scopus 로고
    • Chemical determination of free radical-induced damage to DNA
    • Dizdaroglu, M. (1991) Chemical determination of free radical-induced damage to DNA, Free Radical Biol. Med. 10, 225-242.
    • (1991) Free Radical Biol. Med. , vol.10 , pp. 225-242
    • Dizdaroglu, M.1
  • 3
    • 0028342951 scopus 로고
    • Repair of oxidative damage to DNA: Enzymology and biology
    • Demple, B., and Harrison, L. (1994) Repair of oxidative damage to DNA: enzymology and biology, Annu. Rev. Biochem. 63, 915-948.
    • (1994) Annu. Rev. Biochem. , vol.63 , pp. 915-948
    • Demple, B.1    Harrison, L.2
  • 4
    • 0030634292 scopus 로고    scopus 로고
    • Oxidative damage to DNA: Formation, measurement, and biological significance
    • Cadet, J., Berger, M., Douki, T., and Ravanat, J. L. (1997) Oxidative damage to DNA: formation, measurement, and biological significance, Rev. Physiol. Biochem. Pharmacol. 131, 1-87.
    • (1997) Rev. Physiol. Biochem. Pharmacol. , vol.131 , pp. 1-87
    • Cadet, J.1    Berger, M.2    Douki, T.3    Ravanat, J.L.4
  • 5
    • 3543019650 scopus 로고    scopus 로고
    • Oxidative DNA damage associated with combination of guanine and superoxide radicals and repair mechanisms via radical trapping
    • Misiaszek, R., Crean, C., Joffe, A., Geacintov, N. E., and Shafirovich, V. (2004) Oxidative DNA damage associated with combination of guanine and superoxide radicals and repair mechanisms via radical trapping, J. Biol. Chem. 279, 32106-32115.
    • (2004) J. Biol. Chem. , vol.279 , pp. 32106-32115
    • Misiaszek, R.1    Crean, C.2    Joffe, A.3    Geacintov, N.E.4    Shafirovich, V.5
  • 6
    • 0027278557 scopus 로고
    • Instability and decay of the primary structure of DNA
    • Lindahl, T. (1993) Instability and decay of the primary structure of DNA, Nature 362, 709-715.
    • (1993) Nature , vol.362 , pp. 709-715
    • Lindahl, T.1
  • 7
    • 0032716383 scopus 로고    scopus 로고
    • Base excision repair of 8-hydroxyguanine protects DNA from endogenous oxidative stress
    • Boiteux, S., and Radicella, J. P. (1999) Base excision repair of 8-hydroxyguanine protects DNA from endogenous oxidative stress, Biochimie 81, 59-67.
    • (1999) Biochimie , vol.81 , pp. 59-67
    • Boiteux, S.1    Radicella, J.P.2
  • 8
    • 0032531758 scopus 로고    scopus 로고
    • The mutations induced by oxidatively damaged nucleotides, 5-formyl-dUTP and 5-hydroxy-dCTP, in Escherichia coli
    • Fujikawa, K., Kamiya, H., and Kasai, H. (1998) The mutations induced by oxidatively damaged nucleotides, 5-formyl-dUTP and 5-hydroxy-dCTP, in Escherichia coli, Nucleic Acids Res. 26, 4582-4587.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4582-4587
    • Fujikawa, K.1    Kamiya, H.2    Kasai, H.3
  • 10
    • 0032806606 scopus 로고    scopus 로고
    • Peroxynitrite-induced reactions of synthetic oligonucleotides containing 8-oxoguanine
    • Tretyakova, N. Y., Niles, J. C., Burney, S., Wishnok, J. S., and Tannenbaum, S. R. (1999) Peroxynitrite-induced reactions of synthetic oligonucleotides containing 8-oxoguanine, Chem. Res. Toxicol. 12, 459-466.
    • (1999) Chem. Res. Toxicol. , vol.12 , pp. 459-466
    • Tretyakova, N.Y.1    Niles, J.C.2    Burney, S.3    Wishnok, J.S.4    Tannenbaum, S.R.5
  • 11
    • 0035852024 scopus 로고    scopus 로고
    • A novel nitroimidazole compound formed during the reaction of peroxynitrite with 2′,3′,5′-tri-O-acetyl-guanosine
    • Niles, J. C., Wishnok, J. S., and Tannenbaum, S. R. (2001) A novel nitroimidazole compound formed during the reaction of peroxynitrite with 2′,3′,5′-tri-O-acetyl-guanosine, J. Am. Chem. Soc. 123, 12147-12151.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 12147-12151
    • Niles, J.C.1    Wishnok, J.S.2    Tannenbaum, S.R.3
  • 12
    • 0037154121 scopus 로고    scopus 로고
    • Oxidation of 7,8-dihydro-8-oxoguanine affords lesions that are potent sources of replication errors in vivo
    • Henderson, P. T., Delaney, J. C., Gu, F., Tannenbaum, S. R., and Essigmann, J. M. (2002) Oxidation of 7,8-dihydro-8-oxoguanine affords lesions that are potent sources of replication errors in vivo, Biochemistry 41, 914-921.
    • (2002) Biochemistry , vol.41 , pp. 914-921
    • Henderson, P.T.1    Delaney, J.C.2    Gu, F.3    Tannenbaum, S.R.4    Essigmann, J.M.5
  • 13
    • 12144279499 scopus 로고    scopus 로고
    • Urea lesion formation in DNA as a consequence of 7,8-dihydro-8-oxoguanine oxidation and hydrolysis provides a potent source of point mutations
    • Henderson, P. T., Neeley, W. L., Delaney, J. C., Gu, F., Niles, J. C., Hah, S. S., Tannenbaum, S. R., and Essigmann, J. M. (2005) Urea Lesion Formation in DNA as a Consequence of 7,8-Dihydro-8-oxoguanine Oxidation and Hydrolysis Provides a Potent Source of Point Mutations, Chem. Res. Toxicol. 18, 12-18.
    • (2005) Chem. Res. Toxicol. , vol.18 , pp. 12-18
    • Henderson, P.T.1    Neeley, W.L.2    Delaney, J.C.3    Gu, F.4    Niles, J.C.5    Hah, S.S.6    Tannenbaum, S.R.7    Essigmann, J.M.8
  • 14
    • 6344233798 scopus 로고    scopus 로고
    • In vivo bypass efficiencies and mutational signatures of the guanine oxidation products 2-aminoimidazolone and 5-guanidino-4-nitroimidazole
    • Neeley, W. L., Delaney, J. C., Henderson, P. T., and Essigmann, J. M. (2004) In vivo bypass efficiencies and mutational signatures of the guanine oxidation products 2-aminoimidazolone and 5-guanidino-4-nitroimidazole, J. Biol. Chem. 279, 43568-43573.
    • (2004) J. Biol. Chem. , vol.279 , pp. 43568-43573
    • Neeley, W.L.1    Delaney, J.C.2    Henderson, P.T.3    Essigmann, J.M.4
  • 15
    • 0035810395 scopus 로고    scopus 로고
    • Spiroiminodihydantoin is the major product of the 8-oxo-7,8- dihydroguanosine reaction with peroxynitrite in the presence of thiols and guanosine photooxidation by methylene blue
    • Niles, J. C., Wishnok, J. S., and Tannenbaum, S. R. (2001) Spiroiminodihydantoin is the major product of the 8-oxo-7,8-dihydroguanosine reaction with peroxynitrite in the presence of thiols and guanosine photooxidation by methylene blue, Org. Lett. 3, 963-966.
    • (2001) Org. Lett. , vol.3 , pp. 963-966
    • Niles, J.C.1    Wishnok, J.S.2    Tannenbaum, S.R.3
  • 16
    • 0034624588 scopus 로고    scopus 로고
    • Characterization of Spiroiminodihydantoin as a product of one-electron oxidation of 8-Oxo-7,8-dihydroguanosine
    • Luo, W., Muller, J. G., Rachlin, E. M., and Burrows, C. J. (2000) Characterization of Spiroiminodihydantoin as a product of one-electron oxidation of 8-Oxo-7,8-dihydroguanosine, Org. Lett. 2, 613-616.
    • (2000) Org. Lett. , vol.2 , pp. 613-616
    • Luo, W.1    Muller, J.G.2    Rachlin, E.M.3    Burrows, C.J.4
  • 17
    • 0035817980 scopus 로고    scopus 로고
    • The pH-dependent role of superoxide in riboflavin-catalyzed photooxidation of 8-oxo-7,8-dihydroguanosine
    • Luo, W., Muller, J. G., and Burrows, C. J. (2001) The pH-dependent role of superoxide in riboflavin-catalyzed photooxidation of 8-oxo-7,8- dihydroguanosine, Org. Lett. 3, 2801-2804.
    • (2001) Org. Lett. , vol.3 , pp. 2801-2804
    • Luo, W.1    Muller, J.G.2    Burrows, C.J.3
  • 18
    • 0034932109 scopus 로고    scopus 로고
    • Characterization of hydantoin products from one-electron oxidation of 8-oxo-7,8-dihydroguanosine in a nucleoside model
    • Luo, W., Muller, J. G., Rachlin, E. M., and Burrows, C. J. (2001) Characterization of hydantoin products from one-electron oxidation of 8-oxo-7,8-dihydroguanosine in a nucleoside model, Chem. Res. Toxicol. 14, 927-938.
    • (2001) Chem. Res. Toxicol. , vol.14 , pp. 927-938
    • Luo, W.1    Muller, J.G.2    Rachlin, E.M.3    Burrows, C.J.4
  • 19
    • 0037149068 scopus 로고    scopus 로고
    • Spiroiminodihydantoin is a major product in the photooxidation of 2′-deoxyguanosine by the triplet states and oxyl radicals generated from hydroxyacetophenone photolysis and dioxetane thermolysis
    • Adam, W., Arnold, M. A., Grune, M., Nau, W. M., Pischel, U., and Saha-Moller, C. R. (2002) Spiroiminodihydantoin is a major product in the photooxidation of 2′-deoxyguanosine by the triplet states and oxyl radicals generated from hydroxyacetophenone photolysis and dioxetane thermolysis, Org. Lett. 4, 537-540.
    • (2002) Org. Lett. , vol.4 , pp. 537-540
    • Adam, W.1    Arnold, M.A.2    Grune, M.3    Nau, W.M.4    Pischel, U.5    Saha-Moller, C.R.6
  • 20
    • 0034814369 scopus 로고    scopus 로고
    • Direct oxidation of guanine and 7,8-dihydro-8-oxoguanine in DNA by a high-valent chromium complex: A possible mechanism for cnromate genotoxicity
    • Sugden, K. D., Campo, C. K., and Martin, B. D. (2001) Direct oxidation of guanine and 7,8-dihydro-8-oxoguanine in DNA by a high-valent chromium complex: a possible mechanism for cnromate genotoxicity, Chem. Res. Toxicol. 14, 1315 -1322.
    • (2001) Chem. Res. Toxicol. , vol.14 , pp. 1315-1322
    • Sugden, K.D.1    Campo, C.K.2    Martin, B.D.3
  • 21
    • 0034803009 scopus 로고    scopus 로고
    • Formation of spiroiminodihydantoin nucleoside by reaction of 8-oxo-7,8-dihydro-2′-deoxyguanosine with hypochlorous acid or a myeloperoxidase-H(2)O(2)-Cl(-) system
    • Suzuki, T., Masuda, M., Friesen, M. D., and Ohshima, H. (2001) Formation of spiroiminodihydantoin nucleoside by reaction of 8-oxo-7,8-dihydro-2′- deoxyguanosine with hypochlorous acid or a myeloperoxidase-H(2)O(2)-Cl(-) system, Chem. Res. Toxicol. 14, 1163-1169.
    • (2001) Chem. Res. Toxicol. , vol.14 , pp. 1163-1169
    • Suzuki, T.1    Masuda, M.2    Friesen, M.D.3    Ohshima, H.4
  • 22
    • 0037051890 scopus 로고    scopus 로고
    • Nicotine-modulated formation of spiroiminodihydantoin nucleoside via 8-oxo-7,8-dihydro-2′-deoxyguanosine in 2′-deoxyguanosine- hypochlorous acid reaction
    • Suzuki, T., and Ohshima, H. (2002) Nicotine-modulated formation of spiroiminodihydantoin nucleoside via 8-oxo-7,8-dihydro-2′-deoxyguanosine in 2′-deoxyguanosine-hypochlorous acid reaction, FEBS Lett. 516, 67-70.
    • (2002) FEBS Lett. , vol.516 , pp. 67-70
    • Suzuki, T.1    Ohshima, H.2
  • 23
    • 0347629021 scopus 로고    scopus 로고
    • DNA Lesions derived from the site selective oxidation of guanine by carbonate radical anions
    • Joffe, A., Geacintov, N. E., and Shafirovich, V. (2003) DNA Lesions Derived from the Site Selective Oxidation of Guanine by Carbonate Radical Anions, Chem. Res. Toxicol. 16, 1528-1538.
    • (2003) Chem. Res. Toxicol. , vol.16 , pp. 1528-1538
    • Joffe, A.1    Geacintov, N.E.2    Shafirovich, V.3
  • 24
    • 3543069474 scopus 로고    scopus 로고
    • Spermine participates in oxidative damage of guanosine and 8-oxoguanosine leading to deoxyribosylurea formation
    • Hosford, M. E., Muller, J. G., and Burrows, C. J. (2004) Spermine participates in oxidative damage of guanosine and 8-oxoguanosine leading to deoxyribosylurea formation, J. Am. Chem. Soc. 126, 9540-9541.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 9540-9541
    • Hosford, M.E.1    Muller, J.G.2    Burrows, C.J.3
  • 25
    • 0036012746 scopus 로고    scopus 로고
    • [18O]-labeled singlet oxygen as a tool for mechanistic studies of 8-oxo-7,8-dihydroguanine oxidative dam-age: Detection of Spiroiminodihydantoin, imidazolone and ox-azolone derivatives
    • Martinez, G. R., Medeiros, M. H., Ravanat, J. L., Cadet, J., and Di Mascio, P. (2002) [18O]-labeled singlet oxygen as a tool for mechanistic studies of 8-oxo-7,8-dihydroguanine oxidative dam-age: detection of Spiroiminodihydantoin, imidazolone and ox-azolone derivatives, Biol. Chem. 383, 607-617.
    • (2002) Biol. Chem. , vol.383 , pp. 607-617
    • Martinez, G.R.1    Medeiros, M.H.2    Ravanat, J.L.3    Cadet, J.4    Di Mascio, P.5
  • 26
    • 11344258928 scopus 로고    scopus 로고
    • Characterization of 5-hydroxy-8-oxo-7,8-dihydroguanosine in the photosensitized oxidation of 8-oxo-7,8-dihydroguanosine and its rearrangement to Spiroiminodihydantoin
    • McCallum, J. E., Kuniyoshi, C. Y., and Foote, C. S. (2004) Characterization of 5-hydroxy-8-oxo-7,8-dihydroguanosine in the photosensitized oxidation of 8-oxo-7,8-dihydroguanosine and its rearrangement to Spiroiminodihydantoin, J. Am. Chem. Soc. 126, 16777-16782.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 16777-16782
    • McCallum, J.E.1    Kuniyoshi, C.Y.2    Foote, C.S.3
  • 28
    • 1842634540 scopus 로고    scopus 로고
    • Epigallocatechin gallate markedly enhances formation of 8-oxo-7,8-dihydro-2′-deoxyguanosine in the reaction of 2′-deoxyguanosine with hypochlorous acid
    • Suzuki, T., Nakano, T., Masuda, M., and Ohshima, H. (2004) Epigallocatechin gallate markedly enhances formation of 8-oxo-7,8-dihydro- 2′-deoxyguanosine in the reaction of 2′-deoxyguanosine with hypochlorous acid, Free Radical Biol. Med. 36, 1087-1093.
    • (2004) Free Radical Biol. Med. , vol.36 , pp. 1087-1093
    • Suzuki, T.1    Nakano, T.2    Masuda, M.3    Ohshima, H.4
  • 30
    • 14844286411 scopus 로고    scopus 로고
    • Combination reactions of superoxide with 8-Oxo-7,8-dihydroguanine radicals in DNA: Kinetics and end products
    • Misiaszek, R., Uvaydov, Y., Crean, C., Geacintov, N. E., and Shafirovich, V. (2005) Combination reactions of superoxide with 8-Oxo-7,8-dihydroguanine radicals in DNA: kinetics and end products, J. Biol. Chem. 280, 6293-6300.
    • (2005) J. Biol. Chem. , vol.280 , pp. 6293-6300
    • Misiaszek, R.1    Uvaydov, Y.2    Crean, C.3    Geacintov, N.E.4    Shafirovich, V.5
  • 31
    • 13944273322 scopus 로고    scopus 로고
    • Combination of nitrogen dioxide radicals with 8-oxo-7,8-dihydroguanine and guanine radicals in DNA: Oxidation and nitration end-products
    • Misiaszek, R., Crean, C., Geacintov, N. E., and Shafirovich, V. (2005) Combination of nitrogen dioxide radicals with 8-oxo-7,8-dihydroguanine and guanine radicals in DNA: oxidation and nitration end-products, J. Am. Chem. Soc. 127, 2191-2200.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 2191-2200
    • Misiaszek, R.1    Crean, C.2    Geacintov, N.E.3    Shafirovich, V.4
  • 32
    • 22544434922 scopus 로고    scopus 로고
    • Guanine-Specific Oxidation of Double-Stranded DNA by Cr(VI) and Ascorbic Acid Forms Spiroiminodihydantoin and 8-Oxo-2′-deoxyguanosine
    • Slade, P. G., Hailer, M. K., Martin, B. D., and Sugden, K. D. (2005) Guanine-Specific Oxidation of Double-Stranded DNA by Cr(VI) and Ascorbic Acid Forms Spiroiminodihydantoin and 8-Oxo-2′-deoxyguanosine., Chem. Res. Toxicol. 18, 1140-1149.
    • (2005) Chem. Res. Toxicol. , vol.18 , pp. 1140-1149
    • Slade, P.G.1    Hailer, M.K.2    Martin, B.D.3    Sugden, K.D.4
  • 33
    • 25444521980 scopus 로고    scopus 로고
    • Nei deficient Escherichia coli are sensitive to chromate and accumulate the oxidized guanine lesion spiroiminodihydantoin
    • Web release date Aug
    • Hailer, M. K., Slade, P. G., Martin, B. D., and Sugden, K. D. (2005) Nei deficient Escherichia coli are sensitive to chromate and accumulate the oxidized guanine lesion spiroiminodihydantoin, Chem. Res. Toxicol. Web release date Aug 12, 2005.
    • (2005) Chem. Res. Toxicol. , vol.12 , pp. 2005
    • Hailer, M.K.1    Slade, P.G.2    Martin, B.D.3    Sugden, K.D.4
  • 34
    • 17644395664 scopus 로고    scopus 로고
    • Spiroiminodihydantoin lesions derived from guanine oxidation: Structures, energetics, and functional implications
    • Jia, L., Shafirovich, V., Shapiro, R., Geacintov, N. E., and Broyde, S. (2005) Spiroiminodihydantoin Lesions Derived from Guanine Oxidation: Structures, Energetics, and Functional Implications, Biochemistry 44, 6043-6051.
    • (2005) Biochemistry , vol.44 , pp. 6043-6051
    • Jia, L.1    Shafirovich, V.2    Shapiro, R.3    Geacintov, N.E.4    Broyde, S.5
  • 35
    • 0037168491 scopus 로고    scopus 로고
    • In vitro nucleotide misinsertion opposite the oxidized guanosine lesions spiroiminodihydantoin and guanidinohydantoin and DNA synthesis past the lesions using Escherichia coli DNA polymerase I (Klenow fragment)
    • Kornyushyna, O., Berges, A. M., Muller, J. G., and Burrows, C. J. (2002) In vitro nucleotide misinsertion opposite the oxidized guanosine lesions spiroiminodihydantoin and guanidinohydantoin and DNA synthesis past the lesions using Escherichia coli DNA polymerase I (Klenow fragment), Biochemistry 41, 15304-15314.
    • (2002) Biochemistry , vol.41 , pp. 15304-15314
    • Kornyushyna, O.1    Berges, A.M.2    Muller, J.G.3    Burrows, C.J.4
  • 36
    • 0041571565 scopus 로고    scopus 로고
    • The hydantoin lesions formed from oxidation of 7,8-dihydro-8-oxoguanine are potent sources of replication errors in vivo
    • Henderson, P. T., Delaney, J. C., Muller, J. G., Neeley, W. L., Tannenbaum, S. R., Burrows, C. J., and Essigmann, J. M. (2003) The hydantoin lesions formed from oxidation of 7,8-dihydro-8-oxoguanine are potent sources of replication errors in vivo, Biochemistry 42, 9257-9262.
    • (2003) Biochemistry , vol.42 , pp. 9257-9262
    • Henderson, P.T.1    Delaney, J.C.2    Muller, J.G.3    Neeley, W.L.4    Tannenbaum, S.R.5    Burrows, C.J.6    Essigmann, J.M.7
  • 37
    • 7944222565 scopus 로고    scopus 로고
    • Recognition of the oxidized lesions spiroiminodihydantoin and guanidinohydantoin in DNA by the mammalian base excision repair glycosylases NEIL1 and NEIL2
    • Hailer, M. K., Slade, P. G., Martin, B. D., Rosenquist, T. A., and Sugden, K. D. (2005) Recognition of the oxidized lesions spiroiminodihydantoin and guanidinohydantoin in DNA by the mammalian base excision repair glycosylases NEIL1 and NEIL2, DNA Repair 4, 41-50.
    • (2005) DNA Repair , vol.4 , pp. 41-50
    • Hailer, M.K.1    Slade, P.G.2    Martin, B.D.3    Rosenquist, T.A.4    Sugden, K.D.5
  • 38
    • 0026684849 scopus 로고
    • Evidence that MutY and MutM combine to prevent mutations by an oxidatively damaged form of guanine in DNA
    • Michaels, M. L., Cruz, C., Grollman, A. P., and Miller, J. H. (1992) Evidence that MutY and MutM combine to prevent mutations by an oxidatively damaged form of guanine in DNA, Proc. Natl. Acad. Sci. U.S.A. 89, 7022-7025.
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 7022-7025
    • Michaels, M.L.1    Cruz, C.2    Grollman, A.P.3    Miller, J.H.4
  • 39
    • 0026447255 scopus 로고
    • A repair system for 8-oxo-7,8-dihydrodeoxyguanine
    • Michaels, M. L., Tchou, J., Grollman, A. P., and Miller, J. H. (1992) A repair system for 8-oxo-7,8-dihydrodeoxyguanine, Biochemistry 31, 10964-10968.
    • (1992) Biochemistry , vol.31 , pp. 10964-10968
    • Michaels, M.L.1    Tchou, J.2    Grollman, A.P.3    Miller, J.H.4
  • 40
    • 0001473891 scopus 로고    scopus 로고
    • Chemistry of glycosylases and endonucleases involved in base-excision repair
    • David, S. S., and Williams, S. D. (1998) Chemistry of Glycosylases and Endonucleases Involved in Base-Excision Repair, Chem. Rev. 98, 1221-1262.
    • (1998) Chem. Rev. , vol.98 , pp. 1221-1262
    • David, S.S.1    Williams, S.D.2
  • 41
    • 0034610403 scopus 로고    scopus 로고
    • Removal of hydantoin products of 8-oxoguanine oxidation by the Escherichia coli DNA repair enzyme, FPG
    • Leipold, M. D., Muller, J. G., Burrows, C. J., and David, S. S. (2000) Removal of hydantoin products of 8-oxoguanine oxidation by the Escherichia coli DNA repair enzyme, FPG, Biochemistry 39, 14984-14992.
    • (2000) Biochemistry , vol.39 , pp. 14984-14992
    • Leipold, M.D.1    Muller, J.G.2    Burrows, C.J.3    David, S.S.4
  • 42
    • 0035339684 scopus 로고    scopus 로고
    • Repair of hydantoins, one electron oxidation product of 8-oxoguanine, by DNA glycosylases of Escherichia coli
    • Hazra, T. K., Muller, J. G., Manuel, R. C., Burrows, C. J., Lloyd, R. S., and Mitra, S. (2001) Repair of hydantoins, one electron oxidation product of 8-oxoguanine, by DNA glycosylases of Escherichia coli, Nucleic Acids Res. 29, 1967-1974.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1967-1974
    • Hazra, T.K.1    Muller, J.G.2    Manuel, R.C.3    Burrows, C.J.4    Lloyd, R.S.5    Mitra, S.6
  • 43
    • 0141790433 scopus 로고    scopus 로고
    • Recognition and removal of oxidized guanines in duplex DNA by the base excision repair enzymes hOGG1, yOGG1, and yOGG2
    • Leipold, M. D., Workman, H., Muller, J. G., Burrows, C. J., and David, S. S. (2003) Recognition and removal of oxidized guanines in duplex DNA by the base excision repair enzymes hOGG1, yOGG1, and yOGG2, Biochemistry 42, 11373-11381.
    • (2003) Biochemistry , vol.42 , pp. 11373-11381
    • Leipold, M.D.1    Workman, H.2    Muller, J.G.3    Burrows, C.J.4    David, S.S.5
  • 44
    • 0030240944 scopus 로고    scopus 로고
    • How cancer arises
    • Weinberg, R. A. (1996) How cancer arises, Sci. Am. 275, 62-70.
    • (1996) Sci. Am. , vol.275 , pp. 62-70
    • Weinberg, R.A.1
  • 45
    • 33645709633 scopus 로고    scopus 로고
    • Human cancer, carcinogenic exposures and mutation spectra
    • Vineis, P., Malats, N., Porta, M., and Real, F. X. (1999) Human cancer, carcinogenic exposures and mutation spectra, Mutat. Res. 436, 185-194.
    • (1999) Mutat. Res. , vol.436 , pp. 185-194
    • Vineis, P.1    Malats, N.2    Porta, M.3    Real, F.X.4
  • 46
    • 0035082454 scopus 로고    scopus 로고
    • The p53 tumor suppressor: Critical regulator of life & death in cancer
    • Fisher, D. E. (2001) The p53 tumor suppressor: critical regulator of life & death in cancer, Apoptosis 6, 7-15.
    • (2001) Apoptosis , vol.6 , pp. 7-15
    • Fisher, D.E.1
  • 47
    • 1442285090 scopus 로고    scopus 로고
    • In vitro and in vivo effects of oxidative damage to deoxyguanosine
    • Greenberg, M. M. (2004) In vitro and in vivo effects of oxidative damage to deoxyguanosine, Biochem. Soc. Trans. 32, 46-50.
    • (2004) Biochem. Soc. Trans. , vol.32 , pp. 46-50
    • Greenberg, M.M.1
  • 48
    • 0024394912 scopus 로고
    • Prediction of DNA-structure from sequence - A buildup technique
    • Hingerty, B. E., Figueroa, S., Hayden, T. L., and Broyde, S. (1989) Prediction of DNA-Structure from Sequence-a Buildup Technique, Biopolymers 28, 1195-1222.
    • (1989) Biopolymers , vol.28 , pp. 1195-1222
    • Hingerty, B.E.1    Figueroa, S.2    Hayden, T.L.3    Broyde, S.4
  • 49
    • 0011178497 scopus 로고
    • Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations
    • Brown, T., Hunter, W. N., Kneale, G., and Kennard, O. (1986) Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations, Proc. Natl. Acad. Sci. U.S.A. 83, 2402-2406.
    • (1986) Proc. Natl. Acad. Sci. U.S.A. , vol.83 , pp. 2402-2406
    • Brown, T.1    Hunter, W.N.2    Kneale, G.3    Kennard, O.4
  • 50
    • 0029071401 scopus 로고
    • Conformational flexibility in DNA duplexes containing single G.G mismatches
    • Lane, A. N., and Peck, B. (1995) Conformational flexibility in DNA duplexes containing single G.G mismatches, Eur. J. Biochem. 230, 1073-1087.
    • (1995) Eur. J. Biochem. , vol.230 , pp. 1073-1087
    • Lane, A.N.1    Peck, B.2
  • 54
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang, J. M., Cieplak, P., and Kollman, P. A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?, J. Comput. Chem. 21, 1049-1074.
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.M.1    Cieplak, P.2    Kollman, P.A.3
  • 55
    • 84986516411 scopus 로고
    • Application of the multimolecule and multiconformational resp methodology to biopolymers-charge derivation for DNA, RNA, and proteins
    • Cieplak, P., Cornell, W. D., Bayly, C., and Kollman, P. A. (1995) Application of the Multimolecule and Multiconformational Resp Methodology to Biopolymers-Charge Derivation for DNA, RNA, and Proteins, J. Comput. Chem. 16, 1357-1377.
    • (1995) J. Comput. Chem. , vol.16 , pp. 1357-1377
    • Cieplak, P.1    Cornell, W.D.2    Bayly, C.3    Kollman, P.A.4
  • 56
    • 0347170005 scopus 로고
    • Self-consistent molecular-orbital methods. 12. Further extensions of gaussian-type basis sets for use in molecular-orbital studies of organic-molecules
    • Hehre, W. J., Ditchfie, R., and Pople, J. A. (1972) Self-Consistent Molecular-Orbital Methods. 12. Further Extensions of Gaussian-Type Basis Sets for Use in Molecular-Orbital Studies of Organic-Molecules, J. Chem. Phys. 56, 2257-2261.
    • (1972) J. Chem. Phys. , vol.56 , pp. 2257-2261
    • Hehre, W.J.1    Ditchfie, R.2    Pople, J.A.3
  • 58
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
    • Bayly, C. I., Cieplak, P., Cornell, W., and Kollman, P. A. (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model, J. Phys. Chem. 97, 10269-10280.
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.3    Kollman, P.A.4
  • 59
    • 33646940952 scopus 로고
    • Numerical-integration of cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes
    • Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical-Integration of Cartesian Equations of Motion of a System with Constraints-Molecular-Dynamics of N-Alkanes, J. Comput. Phys. 23, 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 60
    • 0001430231 scopus 로고    scopus 로고
    • The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
    • Harvey, S. C., Tan, R. K. Z., and Cheatham, T. E. (1998) The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition, J. Comput. Chem. 19, 726-740.
    • (1998) J. Comput. Chem. , vol.19 , pp. 726-740
    • Harvey, S.C.1    Tan, R.K.Z.2    Cheatham, T.E.3
  • 61
    • 33846823909 scopus 로고
    • Particle mesh ewald - An N.Log(N) method for ewald sums in large systems
    • Darden, T., York, D., and Pedersen, L. (1993) Particle Mesh Ewald-an N.Log(N) Method for Ewald Sums in Large Systems, J. Chem. Phys. 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 65
    • 0034822656 scopus 로고    scopus 로고
    • Stereochemical, structural, and thermodynamic origins of stability differences between stereoisomeric benzo[a]pyrene diol epoxide deoxyadenosine adducts in a DNA mutational hot spot sequence
    • Yan, S. X., Shapiro, R., Geacintov, N. E., and Broyde, S. (2001) Stereochemical, structural, and thermodynamic origins of stability differences between stereoisomeric benzo[a]pyrene diol epoxide deoxyadenosine adducts in a DNA mutational hot spot sequence, J. Am. Chem. Soc. 123, 7054-7066.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 7054-7066
    • Yan, S.X.1    Shapiro, R.2    Geacintov, N.E.3    Broyde, S.4
  • 66
    • 0015511563 scopus 로고
    • Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation
    • Altona, C., and Sundaralingam, M. (1972) Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation, J. Am. Chem. Soc. 94, 8205-8212.
    • (1972) J. Am. Chem. Soc. , vol.94 , pp. 8205-8212
    • Altona, C.1    Sundaralingam, M.2
  • 69
    • 0024556774 scopus 로고
    • Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "Curves", dials and windows
    • Ravishanker, G., Swaminathan, S., Beveridge, D. L., Lavery, R., and Sklenar, H. (1989) Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows, J. Biomol. Struct. Dyn. 6, 669-699.
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 669-699
    • Ravishanker, G.1    Swaminathan, S.2    Beveridge, D.L.3    Lavery, R.4    Sklenar, H.5
  • 71
    • 0024058085 scopus 로고
    • The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic-acids
    • Lavery, R., and Sklenar, H. (1988) The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic-Acids, J. Biomol. Struct. Dyn. 6, 63-91.
    • (1988) J. Biomol. Struct. Dyn. , vol.6 , pp. 63-91
    • Lavery, R.1    Sklenar, H.2
  • 73
    • 0034602373 scopus 로고    scopus 로고
    • Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model
    • Wang, W., and Kollman, P. A. (2000) Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model, J. Mol. Biol. 303, 567-582.
    • (2000) J. Mol. Biol. , vol.303 , pp. 567-582
    • Wang, W.1    Kollman, P.A.2
  • 74
    • 0034614387 scopus 로고    scopus 로고
    • Investigating the binding specificity of U1A-RNA by computational mutagenesis
    • Reyes, C. M., and Kollman, P. A. (2000) Investigating the binding specificity of U1A-RNA by computational mutagenesis, J. Mol. Biol. 295, 1-6.
    • (2000) J. Mol. Biol. , vol.295 , pp. 1-6
    • Reyes, C.M.1    Kollman, P.A.2
  • 75
    • 0034212858 scopus 로고    scopus 로고
    • Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece
    • Lee, M. R., Duan, Y., and Kollman, P. A. (2000) Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece, Proteins 39, 309-316.
    • (2000) Proteins , vol.39 , pp. 309-316
    • Lee, M.R.1    Duan, Y.2    Kollman, P.A.3
  • 76
    • 0034811498 scopus 로고    scopus 로고
    • Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
    • Wang, J., Morin, P., Wang, W., and Kollman, P. A. (2001) Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA, J. Am. Chem. Soc. 123, 5221-5230.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 5221-5230
    • Wang, J.1    Morin, P.2    Wang, W.3    Kollman, P.A.4
  • 77
    • 0037079570 scopus 로고    scopus 로고
    • Computational alanine scanning of the 1:1 human growth hormone-receptor complex
    • Huo, S., Massova, I., and Kollman, P. A. (2002) Computational alanine scanning of the 1:1 human growth hormone-receptor complex, J. Comput. Chem. 23, 15-27.
    • (2002) J. Comput. Chem. , vol.23 , pp. 15-27
    • Huo, S.1    Massova, I.2    Kollman, P.A.3
  • 78
    • 0001101548 scopus 로고    scopus 로고
    • Free energy analysis of protein-DNA binding: The EcoRI endonuclease-DNA complex
    • Jayaram, B., McConnell, K. J., Dixit, S. B., and Beveridge, D. L. (1999) Free energy analysis of protein-DNA binding: The EcoRI endonuclease-DNA complex, J. Comput. Phys. 151, 333-357.
    • (1999) J. Comput. Phys. , vol.151 , pp. 333-357
    • Jayaram, B.1    McConnell, K.J.2    Dixit, S.B.3    Beveridge, D.L.4
  • 79
    • 0037418535 scopus 로고    scopus 로고
    • Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[a]pyrene diol epoxide-adenine adducts
    • Yan, S., Wu, M., Buterin, T., Naegeli, H., Geacintov, N. E., and Broyde, S. (2003) Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[a]pyrene diol epoxide-adenine adducts, Biochemistry 42, 2339-2354.
    • (2003) Biochemistry , vol.42 , pp. 2339-2354
    • Yan, S.1    Wu, M.2    Buterin, T.3    Naegeli, H.4    Geacintov, N.E.5    Broyde, S.6
  • 80
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig, B., and Nicholls, A. (1995) Classical Electrostatics in Biology and Chemistry, Science 268, 1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 81
    • 0000538815 scopus 로고
    • Analytical molecular-surface calculation
    • Connolly, M. L. (1983) Analytical Molecular-Surface Calculation, J. Appl. Crystallogr. 16, 548-558.
    • (1983) J. Appl. Crystallogr. , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 82
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free-energies using macroscopic solvent models
    • Sitkoff, D., Sharp, K. A., and Honig, B. (1994) Accurate Calculation of Hydration Free-Energies Using Macroscopic Solvent Models, J. Phys. Chem. 98, 1978-1988.
    • (1994) J. Phys. Chem. , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 83
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • Sanner, M. F., Olson, A. J., and Spehner, J. C. (1996) Reduced surface: an efficient way to compute molecular surfaces, Biopolymers 38, 305-320.
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 84
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
    • Srinivasan, J., Cheatham, T. E., Cieplak, P., Kollman, P. A., and Case, D. A. (1998) Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices, J. Am. Chem. Soc. 120, 9401-9409.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham, T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 85
    • 0037380917 scopus 로고    scopus 로고
    • Simulating structural and thermodynamic properties of carcinogen-damaged DNA
    • Yan, S., Wu, M., Patel, D. J., Geacintov, N. E., and Broyde, S. (2003) Simulating structural and thermodynamic properties of carcinogen-damaged DNA, Biophys. J. 84, 2137-2148.
    • (2003) Biophys. J. , vol.84 , pp. 2137-2148
    • Yan, S.1    Wu, M.2    Patel, D.J.3    Geacintov, N.E.4    Broyde, S.5
  • 86
    • 0034979126 scopus 로고    scopus 로고
    • Hydrogen bonding, base stacking, and steric effects in DNA replication
    • Kool, E. T. (2001) Hydrogen bonding, base stacking, and steric effects in DNA replication, Annu. Rev. Biophys. Biomol. Struct. 30, 1-22.
    • (2001) Annu. Rev. Biophys. Biomol. Struct. , vol.30 , pp. 1-22
    • Kool, E.T.1
  • 87
    • 0032836651 scopus 로고    scopus 로고
    • Initiation of base excision repair: Glycosylase mechanisms and structures
    • McCullough, A. K., Dodson, M. L., and Lloyd, R. S. (1999) Initiation of base excision repair: glycosylase mechanisms and structures, Annu. Rev. Biochem. 68, 255-285.
    • (1999) Annu. Rev. Biochem. , vol.68 , pp. 255-285
    • McCullough, A.K.1    Dodson, M.L.2    Lloyd, R.S.3
  • 88
    • 0346435086 scopus 로고    scopus 로고
    • DNA lesion recognition by the bacterial repair enzyme MutM
    • Fromme, J. C., and Verdine, G. L. (2003) DNA lesion recognition by the bacterial repair enzyme MutM, J. Biol. Chem. 278, 51543-51548.
    • (2003) J. Biol. Chem. , vol.278 , pp. 51543-51548
    • Fromme, J.C.1    Verdine, G.L.2
  • 89
    • 11144256241 scopus 로고    scopus 로고
    • Substrate discrimination by formamidopyrimidine-DNA glycosylase: Distinguishing interactions within the active site
    • Perlow-Poehnelt, R. A., Zharkov, D. O., Grollman, A. P., and Broyde, S. (2004) Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site, Biochemistry 43, 16092-16105.
    • (2004) Biochemistry , vol.43 , pp. 16092-16105
    • Perlow-Poehnelt, R.A.1    Zharkov, D.O.2    Grollman, A.P.3    Broyde, S.4
  • 90
    • 3342891076 scopus 로고    scopus 로고
    • Insights into the DNA repair process by the formamidopyrimidine-DNA glycosylase investigated by molecular dynamics
    • Amara, P., Serre, L., Castaing, B., and Thomas, A. (2004) Insights into the DNA repair process by the formamidopyrimidine-DNA glycosylase investigated by molecular dynamics, Protein Sci. 13, 2009-2021.
    • (2004) Protein Sci. , vol.13 , pp. 2009-2021
    • Amara, P.1    Serre, L.2    Castaing, B.3    Thomas, A.4
  • 91
    • 2942547665 scopus 로고    scopus 로고
    • Simulation and modeling of nucleic acid structure, dynamics and interactions
    • Cheatham, T. E., 3rd (2004) Simulation and modeling of nucleic acid structure, dynamics and interactions, Curr. Opin. Struct. Biol. 14, 360-367.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 360-367
    • Cheatham III, T.E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.