Stability of N-glycosidic bond of (5′ S)-8,5′-Cyclo-2′- deoxyguanosine

Chemical Research in Toxicology

Volumn 25, Issue 11, 2012, Pages 2451-2461

  Das, Rajat S ^a   Samaraweera, Milinda ^a   Morton, Martha ^a,b   Gascón, José A ^a   Basu, Ashis K ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

^b UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5',8 CYCLODEOXYGUANOSINE; 7,8 DIHYDRO 8 OXO 2' DEOXYGUANOSINE; 8 METHYL 2' DEOXYGUANOSINE; 8,5' CYCLO 2',5' DIDEOXYGUANOSINE; CARBOHYDRATE DERIVATIVE; DEOXYRIBOFURANOSE; DEOXYRIBOPYRANOSE; DEOXYRIBOSE; FORMIC ACID; GUANINE; GUANOSINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; ATOM; CHEMICAL BOND; CHEMICAL STRUCTURE; HALF LIFE TIME; HYDROLYSIS; KINETICS; NUCLEAR MAGNETIC RESONANCE; PROTON TRANSPORT;

DEOXYGUANOSINE; GLYCOSIDES; MAGNETIC RESONANCE SPECTROSCOPY; QUANTUM THEORY; REFERENCE STANDARDS;

EID: 84869474533     PISSN: 0893228X     EISSN: 15205010     Source Type: Journal    
DOI: 10.1021/tx300302a     Document Type: Article

References (48)

1. Chatgilialoglu, C., Ferreri, C., and Terzidis, M. A. (2011) Purine 5′,8-cyclonucleoside lesions: chemistry and biology Chem. Soc. Rev. 40, 1368-1382
2. Jaruga, P. and Dizdaroglu, M. (2008) 8,5′-Cyclopurine-2′- deoxynucleosides in DNA: mechanisms of formation, measurement, repair and biological effects DNA Repair 7, 1413-1425
3. Jaruga, P., Xiao, Y., Nelson, B. C., and Dizdaroglu, M. (2009) Measurement of (5′R)- and (5′S)-8,5′-cyclo-2′- deoxyadenosines in DNA in vivo by liquid chromatography/isotope-dilution tandem mass spectrometry Biochem. Biophys. Res. Commun. 386, 656-660
4. Dizdaroglu, M., Jaruga, P., and Rodriguez, H. (2001) Identification and quantification of 8,5′-cyclo-2′-deoxy-adenosine in DNA by liquid chromatography/ mass spectrometry Free Radical Biol. Med. 30, 774-784
5. Keck, K. (1968) [Formation of cyclonucleotides during irradiation of aqueous solutions of purine nucleotides] Z. Naturforsch., B: Chem. Sci. 23, 1034-1043
6. Kuraoka, I., Bender, C., Romieu, A., Cadet, J., Wood, R. D., and Lindahl, T. (2000) Removal of oxygen free-radical-induced 5′,8-purine cyclodeoxynucleosides from DNA by the nucleotide excision-repair pathway in human cells Proc. Natl. Acad. Sci. U.S.A. 97, 3832-3837
7. Brooks, P. J., Wise, D. S., Berry, D. A., Kosmoski, J. V., Smerdon, M. J., Somers, R. L., Mackie, H., Spoonde, A. Y., Ackerman, E. J., Coleman, K., Tarone, R. E., and Robbins, J. H. (2000) The oxidative DNA lesion 8,5′-(S)-cyclo-2′-deoxyadenosine is repaired by the nucleotide excision repair pathway and blocks gene expression in mammalian cells J. Biol. Chem. 275, 22355-22362
8. Jaruga, P., Xiao, Y., Vartanian, V., Lloyd, R. S., and Dizdaroglu, M. (2010) Evidence for the involvement of DNA repair enzyme NEIL1 in nucleotide excision repair of (5′R)- and (5′S)-8,5′-cyclo-2′- deoxyadenosines Biochemistry 49, 1053-1055
9. Brooks, P. J. (2008) The 8,5′-cyclopurine-2′- deoxynucleosides: candidate neurodegenerative DNA lesions in xeroderma pigmentosum, and unique probes of transcription and nucleotide excision repair DNA Repair 7, 1168-1179
10. Kirkali, G., de Souza-Pinto, N. C., Jaruga, P., Bohr, V. A., and Dizdaroglu, M. (2009) Accumulation of (5′S)-8,5′-cyclo-2′- deoxyadenosine in organs of Cockayne syndrome complementation group B gene knockout mice DNA Repair 8, 274-278
11. Marietta, C., Gulam, H., and Brooks, P. J. (2002) A single 8,5′-cyclo-2′-deoxyadenosine lesion in a TATA box prevents binding of the TATA binding protein and strongly reduces transcription in vivo DNA Repair 1, 967-975
12. Kuraoka, I., Robins, P., Masutani, C., Hanaoka, F., Gasparutto, D., Cadet, J., Wood, R. D., and Lindahl, T. (2001) Oxygen free radical damage to DNA. Translesion synthesis by human DNA polymerase eta and resistance to exonuclease action at cyclopurine deoxynucleoside residues J. Biol. Chem. 276, 49283-49288
13. Jasti, V. P., Das, R. S., Hilton, B. A., Weerasooriya, S., Zou, Y., and Basu, A. K. (2011) 5′S)-8,5′-cyclo-2′-deoxyguanosine is a strong block to replication, a potent pol V-dependent mutagenic lesion, and is inefficiently repaired in Escherichia coli Biochemistry 50, 3862-3865
14. Yuan, B., Wang, J., Cao, H., Sun, R., and Wang, Y. (2011) High-throughput analysis of the mutagenic and cytotoxic properties of DNA lesions by next-generation sequencing Nucleic Acids Res. 39, 5945-5954
15. Huang, H., Das, R. S., Basu, A. K., and Stone, M. P. (2011) Structure of (5′S)-8,5′-cyclo-2′-deoxyguanosine in DNA J. Am. Chem. Soc. 133, 20357-20368
16. Huang, H., Das, R. S., Basu, A. K., and Stone, M. P. (2012) Structures of (5′S)-8,5′-cyclo-2′-deoxyguanosine mismatched with dA or dT Chem. Res. Toxicol. 25, 478-490
17. Pullman, A. and Pullman, B. (1981) Molecular electrostatic potential of the nucleic acids Q. Rev. Biophys. 14, 289-380
18. Suzuki, T., Ohsumi, S., and Makino, K. (1994) Mechanistic studies on depurination and apurinic site chain breakage in oligodeoxyribonucleotides Nucleic Acids Res. 22, 4997-5003
19. Rios-Font, R., Rodriguez-Santiago, L., Bertran, J., and Sodupe, M. (2007) Influence of N7 protonation on the mechanism of the N-glycosidic bond hydrolysis in 2 ′-deoxyguanosine. A theoretical study J. Phys. Chem. B 111, 6071-6077
20. Przybylski, J. L. and Wetmore, S. D. (2010) Modeling the dissociative hydrolysis of the natural DNA nucleosides J. Phys. Chem. B 114, 1104-1113
21. Guthrie, R. D. and Jencks, W. P. (1989) IUPAC recommendations for the representation of reaction-mechanisms Acc. Chem. Res. 22, 343-349
22. Theruvathu, J. A., Jaruga, P., Dizdaroglu, M., and Brooks, P. J. (2007) The oxidatively induced DNA lesions 8,5′-cyclo-2′-deoxyadenosine and 8-hydroxy-2′-deoxyadenosine are strongly resistant to acid-induced hydrolysis of the glycosidic bond Mech. Ageing Dev. 128, 494-502
23. Romieu, A., Gasparutto, D., and Cadet, J. (1999) Synthesis and characterization of oligonucleotides containing 5′,8-cyclopurine 2′-deoxyribonucleosides: (5′R)-5′,8-cyclo-2′- deoxyadenosine, (5′S)-5′,8-cyclo-2′-deoxyguanosine, and (5′R)-5′,8-cyclo-2′-deoxyguanosine Chem. Res. Toxicol. 12, 412-421
24. Kohda, K., Tsunomoto, H., Minoura, Y., Tanabe, K., and Shibutani, S. (1996) Synthesis, miscoding specificity, and thermodynamic stability of oligodeoxynucleotide containing 8-methyl-2′-deoxyguanosine Chem. Res. Toxicol. 9, 1278-1284
25. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J. A., Jr., Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C., Iyengar, S. S., Tomasi, J., Cossi, M., Rega, N., Millam, J. M., Klene, M., Knox, J. E., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Martin, R. L., Morokuma, K., Zakrzewski, V. G., Voth, G. A., Salvador, P., Dannenberg, J. J., Dapprich, S., Daniels, A. D., Farkas, Ö., Foresman, J. B., Ortiz, J. V., Cioslowski, J., and Fox, D. J. (2009) Gaussian 09, Gaussian Inc., Wallingford, CT.
26. Becke, A. D. (1993) Density-functional thermochemistry 0.3. The role of exact exchange J. Chem. Phys. 98, 5648-5652
27. Lee, C. T., Yang, W. T., and Parr, R. G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density Phys. Rev. B 37, 785-789
28. Cossi, M., Barone, V., Cammi, R., and Tomasi, J. (1996) Ab initio study of solvated molecules: A new implementation of the polarizable continuum model Chem. Phys. Lett. 255, 327-335
29. Peng, C. Y. and Schlegel, H. B. (1993) Combining synchronous transit and quasi-Newton methods to find transition-states Israel J. Chem 33, 449-454
30. Jaguar (2011) Schrödinger LLC, New York.
31. Schindler, M. (1988) Magnetic-properties in terms of localized quantities 0.9. The DNA bases and the protonation of adenine J. Am. Chem. Soc. 110, 6623-6630
32. Seckarova, P., Marek, R., Malinakova, K., Kolehmainen, E., Hockova, D., Hocek, M., and Sklenar, V. (2004) Direct determination of tautomerism in purine derivatives by low-temperature NMR spectroscopy Tetrahedron Lett. 45, 6259-6263
33. Zheng, Y., Xue, Y., and Yan, S. G. (2008) The effects of oxidation and protonation on the N-glycosidic bond stability of 8-oxo-2 ′- deoxyguanosine: DFT study J. Mol. Struct.-Theochem. 860, 52-57
34. Greisch, J. F., Leyh, B., and De Pauw, E. (2009) Collision induced dissociation of deuterium enriched protonated 2′-deoxyguanosine Eur. Phys. J. D 51, 89-96
35. Lipscomb, L. A., Peek, M. E., Morningstar, M. L., Verghis, S. M., Miller, E. M., Rich, A., Essigmann, J. M., and Williams, L. D. (1995) X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine Proc. Natl. Acad. Sci. U.S.A. 92, 719-723
36. Xu, Y., Ikeda, R., and Sugiyama, H. (2003) 8-Methylguanosine: a powerful Z-DNA stabilizer J. Am. Chem. Soc. 125, 13519-13524
37. Jang, Y. H., Goddard, W. A., 3rd, Noyes, K. T., Sowers, L. C., Hwang, S., and Chung, D. S. (2002) First principles calculations of the tautomers and pK(a) values of 8-oxoguanine: implications for mutagenicity and repair Chem. Res. Toxicol. 15, 1023-1035
38. Gorenstein, D. G. (1987) Stereoelectronic effects in biomolecules Chem. Rev. 87, 1047-1077
39. Haromy, T. P., Raleigh, J., and Sundaralingam, M. (1980) Enzyme-bound conformations of nucleotide substrates. X-ray structure and absolute configuration of 8,5′-cycloadenosine monohydrate Biochemistry 19, 1718-1722
40. Stivers, J. T. and Jiang, Y. L. (2003) A mechanistic perspective on the chemistry of DNA repair glycosylases Chem. Rev. 103, 2729-2759
41. Zoltewicz, J. A., Clark, D. F., Sharpless, T. W., and Grahe, G. (1970) Kinetics and mechanism of the acid-catalyzed hydrolysis of some purine nucleosides J. Am. Chem. Soc. 92, 1741-1749
42. Baik, M. H., Friesner, R. A., and Lippard, S. J. (2002) Theoretical study on the stability of N-glycosyl bonds: why does N7-platination not promote depurination? J. Am. Chem. Soc. 124, 4495-4503
43. Hevesi, L., Wolfson-Davidson, E., Nagy, J. B., Nagy, O. B., and Bruylants, A. (1972) Contribution to the mechanism of the acid-catalyzed hydrolysis of purine nucleosides J. Am. Chem. Soc. 94, 4715-4720
44. Kampf, G., Kapinos, L. E., Griesser, R., Lippert, B., and Sigel, H. (2002) Comparison of the acid-base properties of purine derivatives in aqueous solution. Determination of intrinsic proton affinities of various basic sites J. Chem. Soc. Perkin Trans. 2, 1320-1327
45. Karwowski, B. T. (2010) The difference in stability between 5 ′ R and 5 ′ S diastereomers of 5 ′,8-cyclopurine-2 ′- deoxynucleosides. DFT study in gaseous and aqueous phase Cent. Eur. J. Chem. 8, 134-141
46. Wilde, J. A., Bolton, P. H., Mazumder, A., Manoharan, M., and Gerlt, J. A. (1989) Characterization of the equilibrating forms of the aldehydic abasic site in duplex DNA by 17O-NMR J. Am. Chem. Soc. 111, 1894-1896
47. Pierce, J., Serianni, A. S., and Barker, R. (1985) Anomerization of furanose sugars and sugar phosphates J. Am. Chem. Soc. 107, 2448-2456
48. Pande, P., Das, R. S., Sheppard, C., Kow, Y. W., and Basu, A. K. (2012) Repair efficiency of (5′S)-8,5′-cyclo-2′-deoxyguanosine and (5′S)-8,5′-cyclo-2′-deoxyadenosine depends on the complementary base DNA Repair in press