Chem 6440/7440

Computational Studies of the Oxidation of Guanine

Barbara H. MunkComputational Chemistry

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Overview

Background Research Plan Results to date Next Steps Summary

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Background

Oxidation of nucleobases and nucleotides followed by strand scission of the DNA/RNA is a major pathway in mutagenesis, carcinogenesis, aging and cell death

Burrows, C.J.; Muller, J.G.; Oxidative Nucleobase Modifications Leading to Strand Scission; Chem. Rev. 1998, 98, 1109-1151.

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Background

Burrows, C.J.; Muller, J.G.; Oxidative Nucleobase Modifications Leading to Strand Scission; Chem. Rev. 1998, 98, 1109-1151.

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Background Guanine has a lower redox potential than

other nucleobases and chemical oxidation of this base is observed experimentally

Oxidants include reactive oxygen species, ionizing radiation, and transition metal complexes

Reactive oxygen species include: HO·, RO·, ROO·, and O2·

Baik, M.H.; Silverman, J.S.; Yang, I.V.; Ropp, P.A.; Szalai, V.A.; Yang, W.; and Thorp, W.H.; Using Density Functional Theory to Design DNA Base Analogues with Low Oxidation Potentials; J. Phys. Chem. B.; 2001, 105, 6437-6444

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Background

Nucleobase and Nucleoside Numbering Schemes

Burrows, C.J.; Muller, J.G.; Oxidative Nucleobase Modifications Leading to Strand Scission; Chem. Rev. 1998, 98, 1109-1151.

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Background

Oxidation of guanine can

occur at three sites

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Background

Products formed by attack at C-4 and C-5 revert to guanine

Oxidation at C-8 leads to two forms of DNA damage

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Background

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Research Plan Use a minimally substituted guanine

structure

Evaluate oxidation at C-4, C-5 and C-8 positions with ·OH, ·OCH3, and ·OOH

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Research Plan Calculate the enthalpy and free energy of reaction,

and forward and reverse barrier heights using Gaussian (Development Version) on Linux operating system

Electron correlation important Use Density Functional Theory – B3LYP

Basis set – 6-31G(d) Works well for organic molecules Polarization functions give molecular

flexibilityPrat, F.; Houk, K.N.; Foote, C.S.; Effect of Guanine Stacking on the Oxidation of 8-Oxoguanine in B-DNA. J. Am. Chem. Soc. 1998, 120, 845-846.Sugiyama, H.; Saito, I.; Theoretical Studies of GG-Specific Photocleavage of DNA via Electron Transfer: Significant Loweering of Ionization potential and 5’ Localization of HOMO of Stacked GG Bases in B-Form DNA. J. Am. Chem. Soc. 1996, 118, 7063-7068.

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Results to Date

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Reactions with ·OHEnthalpy

of Reaction (Kcal/mol)

Barrier Height

Forward (Kcal/mol)

Barrier Height

Reverse (Kcal/mol)

Free Energy of Reaction (Kcal/mol)

Barrier Height

Forward (Kcal/mol)

Barrier Height

Reverse (Kcal/mol)

4-hydroxyguanine -18.26 -1.62 16.64 -8.19 8.28 16.47

5-hydroxyguanine -13.67 -4.33 9.34 -3.98 5.41 9.37

8-hydroxyguanine -33.06 * * -23.61 * *

* To be determined

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Guanine 4-Hydroxyguanine radical

4-Hydroxyguanine transition state

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Guanine5-Hydroxyguanine

radical

5-Hydroxyguanine transition state

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Guanine 8-hydroxyguanine radical

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Reactions with ·OCH3

Enthalpy of

Reaction (Kcal/mol)

Barrier Height

Forward (Kcal/mol)

Barrier Height

Reverse (Kcal/mol)

Free Energy of Reaction (Kcal/mol)

Barrier Height

Forward (Kcal/mol)

Barrier Height

Reverse (Kcal/mol)

4-methoxyguanine -2.86 10.37 13.23 8.76 21.56 12.80

5-methoxyguanine 0.62 6.88 6.26 12.22 18.63 6.41

8-methoxyguanine -18.98 1.09 20.07 -7.34 12.13 19.47

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Guanine 4-Methoxyguanine radical

4-Methoxyguanine transition state

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Guanine5-Methoxyguanine

radical

5-Methoxyguanine transition state

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Guanine

8-Methoxyguanine transition state

8-Methoxyguanine radical

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Reactions with ·OOH

Enthalpy of

Reaction (Kcal/mol)

Barrier Height

Forward (Kcal/mol)

Barrier Height

Reverse (Kcal/mol)

Free Energy of Reaction (Kcal/mol)

Barrier Height

Forward (Kcal/mol)

Barrier Height

Reverse (Kcal/mol)

4-hydroperoxy

guanine complex

11.46 13.29 1.83 23.03 25.30 2.27

4-epoxyguanine 15.95 * * 18.44 * *

* To be determined

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Guanine

4-Hydroperoxyguanine complex

4-Epoxyguanine

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Reactions with ·OOHEnthalpy

of Reaction (Kcal/mol)

Barrier Height

Forward (Kcal/mol)

Barrier Height

Reverse (Kcal/mol)

Free Energy of Reaction (Kcal/mol)

Barrier Height

Forward (Kcal/mol)

Barrier Height

Reverse (Kcal/mol)

5-hydroperoxy

guanine complex

13.94 * * 25.60 * *

5-epoxyguanine 15.95 * * 18.44 * *

* To be determined

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Guanine 5-Epoxyguanine

5-Hydroperoxyguanine complex

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Reactions with ·OOHEnthalpy

of Reaction (Kcal/mol)

Barrier Height

Forward (Kcal/mol)

Barrier Height

Reverse (Kcal/mol)

Free Energy of Reaction (Kcal/mol)

Barrier Height

Forward (Kcal/mol)

Barrier Height

Reverse (Kcal/mol)

8-hydroperoxy

guanine complex

-5.94 * * 5.80

8-oxo-guanine * * * *

2,6-diamino-5-formamido-4-

hydroxy pyrimidine

0.71 * * 0.49 * *

* To be determined

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Guanine 2,6-Diamino-5-formamido-4-

hydroxy pyrimidine

8-Hydroperoxyguanine complex

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Next Steps

Identify transition states for8-hydroxyguanine4, 5, and 8 hydroperoxyguanine4 and 5 epoxyguanine8-oxo-guanine 2, 6-diamino-5-formamido-4-hydroxy

pyrimidine (FAPy-G)

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Summary Oxidation by ·OH and ·OCH3 at the C-8

position appears to be thermodynamically more favorable than oxidation at C-4 and C-5

Oxidation by ·OOH appears to be a multistep process

Oxidation at the C-4 and C-5 positions may proceed through an epoxide intermediate

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Acknowledgements Dr. H.B. Schlegel Schlegel Group

Dr. Smriti AnandDr. Hrant HratchianJie LiStan Smith

Funding Dept. of Chemistry, WSU

NSF

Gaussian Inc.

Computer Time NCSA

WSU- C&IT

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Reactions Generating ·OH

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Supplemental Material

Alkoxyl radicals RO· can be generated via radical ring opening of epoxides with a nickel catalyst or via hydroperoxides

ROO· are generated in vivo, as lipid hydroperoxides are produced as a consequence of cellular exposure to oxidative stress