Calculation of the stabilization energies of oxidatively damaged guanine base pairs with guanine

Molecules

Volumn 17, Issue 6, 2012, Pages 6705-6715

  Suzuki, Masayo ^a   Kino, Katsuhito ^a   Morikawa, Masayuki ^a   Kobayashi, Takanobu ^a   Komori, Rie ^a   Miyazawa, Hiroshi ^a  

^a TOKUSHIMA BUNRI UNIVERSITY   (Japan)

Author keywords

Base pair; Hydrogen bond; Oxidative guanine damage; Stabilization energy

Indexed keywords

GUANINE;

ARTICLE; BASE PAIRING; CHEMISTRY; DNA DAMAGE; GENOMIC INSTABILITY; HYDROGEN BOND; METABOLISM; OXIDATION REDUCTION REACTION; OXIDATIVE STRESS;

BASE PAIRING; DNA DAMAGE; GENOMIC INSTABILITY; GUANINE; HYDROGEN BONDING; OXIDATION-REDUCTION; OXIDATIVE STRESS;

EID: 84862985327     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules17066716     Document Type: Article

References (22)

1. Maehira, F.; Miyagi, I.; Asato, T.; Eguchi, Y.; Takei, H.; Nakatsuki, K.; Fukuoka, M.; Zaha, F. Alterations of protein kinase C, 8-hydroxydeoxyguanosine, and K-ras oncogene in rat lungs exposed to passive smoking. Clin. Chim. Acta 1999, 289, 133-144. (Pubitemid 29505206)
2. Shibutani, S.; Takeshita, M.; Grollman, A. P. Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG. Nature 1991, 349, 431-434. (Pubitemid 21926107)
3. Cadet, J.; Berger, M.; Buchko, G. W.; Joshi, P. C.; Raoul, S.; Ravanat, J.-L. 2, 2-Diamino-4-[(3, 5-di-O-acetyl-2-deoxy-β-D-erythro-pentofuranosyl) amino]-5-(2H)-oxazolone: A novel and predominant radical oxidation product of 3', 5'-di-O-acetyl-2'-deoxyguanosine. J. Am. Chem. Soc. 1994, 116, 7403-7404.
4. Kino, K.; Saito, I.; Sugiyama, H. Product analysis of GG-specific photooxidation of DNA via electron transfer: 2-Aminoimidazolone as a major guanine oxidation product. J. Am. Chem. Soc. 1998, 120, 7373-7374. (Pubitemid 28389374)
5. Kino, K.; Sugiyama, H. Possible cause of G•C->C•G transversion mutation by guanine oxidation product, imidazolone. Chem. Biol. 2001, 8, 369-378. (Pubitemid 32449300)
6. Kino, K.; Sugasawa, K.; Mizuno, T.; Bando, T.; Sugiyama, H.; Akita, M.; Miyazawa, H.; Hanaoka, F. Eukaryotic DNA polymerases α, β and ε incorporate guanine opposite 2, 2, 4-triamino-5 (2H)-oxazolone. ChemBioChem 2009, 10, 2613-2616.
7. Duarte, V.; Gasparutto, D.; Jaquinod, M.; Cadet, J. In vitro DNA synthesis opposite oxazolone and repair of this DNA damage using modified oligonucleotides. Nucleic Acids Rec. 2000, 28, 1555-1563. (Pubitemid 30160568)
8. Luo, W.; Muller, J. G.; Rachlin, E. M.; Burrows, C. J. Characterization of spiroiminodihydantoin as a product of one-electron oxidation of 8-oxo-7, 8-dihydroguanosine. Org. Lett. 2000, 2, 613-616.
9. Kino, K.; Morikawa, M.; Kobayashi, T.; Komori, R.; Sei, Y.; Miyazawa, H. The oxidation of 8-oxo-7, 8-dihydroguanine by iodine. Bioorg. Med. Chem. Lett. 2010, 20, 3818-3820.
10. Munk, B. H.; Burrows, C. J.; Schlegel, H. B. An exploration of mechanisms for the transformation of 8-oxoguanine to guanidinohydantoin and spiroiminodihydantoin by density functional theory. J. Am. Chem. Soc. 2008, 130, 5245-5256. (Pubitemid 351537084)
11. Ye, Y.; Munk, B. H.; Muller, J. G.; Gogbill, A.; Burrows, C. J.; Schlegel, H. B. Mechanistic aspects of the formation of guanidinohydantoin from spiroiminodihydantoin under acidic conditions. Chem. Res. Toxicol. 2009, 22, 526-535.
12. Kornyushyna, O.; Berges, A. M.; Muller, J. G.; Burrows, C. J. 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 2002, 41, 15304-15314. (Pubitemid 36008140)
13. Luo, W.; Muller, J. G.; Rachlin, E. M.; Burrows, C. J. Characterization of hydantoin products from one-electron oxidation of 8-oxo-7, 8-dihydroguanosine in a nucleoside model. Chem. Res. Toxicol. 2001, 14, 927-938. (Pubitemid 32661350)
14. Kino, K.; Sugiyama, H. UVR-induced G-C to C-G transversions from oxidative DNA damage. Mutat. Res. 2005, 571, 33-42. (Pubitemid 40313430)
15. Ding, S.; Jia, L.; Durandin, A.; Crean, C.; Kolbanovskiy, A.; Shafirovich, V.; Broyde, S.; Geacintov, N. E. Absolute configurations of spiroiminodihydantoin and allantoin stereoisomers: comparison of computed and measured electronic circular dichroism spectra. Chem. Res. Toxicol. 2009, 22, 1189-1193.
16. Wong, M. W.; Frisch, M. J.; Wiberg, K. B. Solvent effects. 1. The mediation of electrostatic effects by solvents. J. Am. Chem. Soc. 1991, 113, 4776-4782.
17. Beckman, J.; Wang, M.; Blaha, G.; Wang, J.; Konigsberg, W. H. Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP and dGMP to be inserted opposite guanidinohydantoin. Biochemistry 2010, 49, 8554-8563.
18. Verdolino, V.; Cammi, R.; Munk, B. H.; Schlegel, H. B. Calculation of pKa values of nucleobases and the guanine oxidation products guanidinohydantoin and spiroiminodihydantoin using density functional theory and a polarizable continuum model. J. Phys. Chem. B 2008, 112, 16860-16873.
19. Aller, P.; Ye, Y.; Wallace, S. S.; Burrows, C. J.; Doublié, S. Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin. Biochemistry 2010, 49, 2502-2509.
20. Chinyengetere, F.; Jamieson, E. R. Impact of the oxidized guanine lesion spiroiminodihydantoin on the conformation and thermodynamic stability of a 15-mer DNA duplex. Biochemistry 2008, 47, 2584-2591. (Pubitemid 351304564)
21. Yanson, I. K.; Teplitsky, A. B.; Sukhodub, L. F. Experimental studies of molecular interactions between nitrogen bases of nucleic acids. Biopolymers 1979, 18, 1149-1170.
22. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A.; Vreven, T., Jr.; Kudin, K. N.; Burant, J. C.; et al. Gaussian 03, Revision C.02; Gaussian, Inc.: Wallingford, CT, USA, 2004.