Computational Studies of the Oxidation
of Guanine
Barbara H. Munk
Computational Chemistry
6440/7440
Chem 6440/7440
Overview
Background
 Research Plan
 Results to date
 Next Steps
 Summary

Chem 6440/7440
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.
Chem 6440/7440
Background
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Burrows, C.J.; Muller, J.G.; Oxidative Nucleobase Modifications
Leading to Strand Scission; Chem. Rev. 1998, 98, 1109-1151.
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·
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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
Background
Nucleobase and Nucleoside
Numbering Schemes
Chem 6440/7440
Burrows, C.J.; Muller, J.G.; Oxidative Nucleobase Modifications
Leading to Strand Scission; Chem. Rev. 1998, 98, 1109-1151.
Background
Oxidation of
guanine can
occur at three
sites
Chem 6440/7440
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
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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.
Results to Date
Chem 6440/7440
Reactions with ·OH
Enthalpy Barrier
of
Height
Reaction Forward
Barrier
Height
Reverse
Free
Energy of
Reaction
Barrier
Height
Forward
Barrier
Height
Reverse
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(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
*
*
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* To be determined
4-Hydroxyguanine
transition state
Guanine
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4-Hydroxyguanine
radical
5-Hydroxyguanine
transition state
Guanine
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5-Hydroxyguanine
radical
Guanine
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8-hydroxyguanine
radical
Reactions with ·OCH3
Enthalpy Barrier
of
Height
Reaction Forward
Barrier
Height
Reverse
Free
Energy of
Reaction
Barrier
Height
Forward
Barrier
Height
Reverse
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(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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4-Methoxyguanine
transition state
Guanine
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4-Methoxyguanine
radical
5-Methoxyguanine
transition state
Guanine
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5-Methoxyguanine
radical
8-Methoxyguanine
transition state
Guanine
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8-Methoxyguanine
radical
Reactions with ·OOH
Enthalpy Barrier
of
Height
Reaction Forward
Barrier
Height
Reverse
Free
Energy of
Reaction
Barrier
Height
Forward
Barrier
Height
Reverse
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
4-hydroperoxy
guanine complex
11.46
13.29
1.83
23.03
25.30
2.27
4-epoxyguanine
15.95
*
*
18.44
*
*
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* To be determined
4-Hydroperoxy
guanine
complex
Guanine
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4-Epoxyguanine
Reactions with ·OOH
Enthalpy Barrier
of
Height
Reaction Forward
Barrier
Height
Reverse
Free
Energy of
Reaction
Barrier
Height
Forward
Barrier
Height
Reverse
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
5-hydroperoxy
guanine complex
13.94
*
*
25.60
*
*
5-epoxyguanine
15.95
*
*
18.44
*
*
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* To be determined
5-Hydroperoxy
guanine
complex
Guanine
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5-Epoxyguanine
Reactions with ·OOH
8-hydroperoxy
guanine complex
Enthalpy Barrier
of
Height
Reaction Forward
Barrier
Height
Reverse
Free
Energy of
Reaction
Barrier
Height
Forward
Barrier
Height
Reverse
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
(Kcal/mol)
-5.94
*
*
5.80
*
*
*
*
*
*
*
*
8-oxo-guanine
2,6-diamino-5formamido-4hydroxy
pyrimidine
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0.71
* To be determined
0.49
8-Hydroperoxy
guanine
complex
Guanine
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2,6-Diamino-5formamido-4hydroxy pyrimidine
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
Chem 6440/7440
Acknowledgements


Dr. H.B. Schlegel
Schlegel Group
 Dr. Smriti Anand
 Dr. Hrant Hratchian
 Jie Li
 Stan Smith


Funding

Dept. of Chemistry, WSU

NSF

Gaussian Inc.
Computer Time
 NCSA

Chem 6440/7440
WSU- C&IT
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
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