Computational Studies of the Oxidation of Guanine

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Computational Studies of the Oxidation of Guanine

• Barbara H. Munk
• Computational Chemistry
• 6440/7440

2
Overview

• Background
• Research Plan
• Results to date
• Next Steps
• Summary

3
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.
4
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.
7
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 flexibility

Prat, 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 OH
To be determined
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4-Hydroxyguanine transition state
Guanine
4-Hydroxyguanine radical
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5-Hydroxyguanine transition state
5-Hydroxyguanine radical
Guanine
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Guanine
8-hydroxyguanine radical
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Reactions with OCH3
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4-Methoxyguanine transition state
Guanine
4-Methoxyguanine radical
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5-Methoxyguanine transition state
5-Methoxyguanine radical
Guanine
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8-Methoxyguanine transition state
8-Methoxyguanine radical
Guanine
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Reactions with OOH
To be determined
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4-Hydroperoxy guanine complex
Guanine
4-Epoxyguanine
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Reactions with OOH
To be determined
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5-Hydroperoxy guanine complex
Guanine
5-Epoxyguanine
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Reactions with OOH
To be determined
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8-Hydroperoxy guanine complex
2,6-Diamino-5-formamido-4-hydroxy pyrimidine
Guanine
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Next Steps

• Identify transition states for
• 8-hydroxyguanine
• 4, 5, and 8 hydroperoxyguanine
• 4 and 5 epoxyguanine
• 8-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

• Funding
• Dept. of Chemistry, WSU
• NSF
• Gaussian Inc.
• Computer Time
• NCSA
• WSU- CIT

• Dr. H.B. Schlegel
• Schlegel Group
• Dr. Smriti Anand
• Dr. Hrant Hratchian
• Jie Li
• Stan Smith

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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