Michael M. Cox Jennifer A.

Doudna Michael ODonnell

Molecular Biology
Principles and Practice

DNA Mutation and Repair

Copyright 2012 by W. H. Freeman and Company

Lesion v.s. mutation

Lesion: site of DNA damage Mutation: permanent base change bad - result in amino acid change that makes protein non-functional good - evolution (rare) silent mutation - no functional impact

Sources of DNA damage

Endogenous damages: internal agents from normal metabolic byproducts
Reactive oxygen species

Exogenous damages: external agents

UV radiation from the sun X-rays and gamma rays Hydrolysis or thermal disruption Plant toxins Man-made mutagenic chemicals Viruses
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UV-induced DNA damages

UV light
UV-A: 320-400 nm
majority of UV light reaching earth does little DNA damage

UV-B: 295-320 nm
~10% of UV light reaching earth responsible for most of DNA damage in skin

UV-C: 100-295 nm
includes wavelength of maximum DNA absorbance (260 nm) little reaches earth's surface due to ozone layer

Two pathways for UV-induced DNA damage

both involve dimer formation between adjacent pyrimidine rings on same strand cyclobutane pyrimidine dimer (CPD)
accounts for 75% of UV induced damage

(6-4) photoproducts
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UV-induced cyclobutane pyrimidine dimer formation

thymine-thymine dimers are most common cytosine-thymine and cytosine-cytosine dimers also form at slower rates
Adapted from Friedberg, E. C., et al. DNA Repair and Mutagenesis, 2/3. ASM Press, 2005.

UV-induced (6-4) photoproduct formation

Adapted from Friedberg, E. C., et al. DNA Repair and Mutagenesis, 2/3. ASM Press, 2005.

Cyclobutane pyrimidine dimers produce a kink in DNA

Reproduced from Park, H., et al., Proc. Natl. Acad. Sci. USA 99 (2002): 1596515970. Copyright 2002, National Academy of Sciences, USA. Photo courtesy of ChulHee Kang, Washington State University.

Other DNA damages

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DNA has three types of bonds susceptible to hydrolytic cleavage

phosphodiester bonds, N-glycosylic bonds, and bonds linking exocyclic amine groups to bases are susceptible

Adapted from Doetsch, P. W. Encyclopedia of Life Sciences. John Wiley & Sons, Ltd., April 2001. [doi: 10.1038/npg.els.0000557].

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AP site formation by N-glycosyl bond cleavage

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Water-mediated deamination

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Transition and transversion mutations caused by deamination

Transition

Transversion

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DNA damage by hydroxyl radical

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8-oxoguanine base pairs with C or A

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Alkylating agents damage DNA

transfer methyl, ethyl, or larger alkyl groups to DNA alkylation takes place at:
nitrogen and oxygen atoms external to the base ring systems nitrogen atoms in the base ring systems except those linked to deoxyribose non-bridging oxygen atoms in phosphate groups
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Methylation results in mutation of GC pair to AT

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Summary What I learned in this lecture.

Mutations: Permanent base changes Sources of DNA damage: Endogenous (reactive o2 species) or exogenous (external agents: UV rays, X-RAYS, gamma rays, hydrolysis or thermal disruption, plant toxins, chemicals, viruses) UV: two pathways for UV-induced DNA damage both involve dimer formation btwn adjacent pyrimidine rings on same strand cyclobutane pyrimidine dimer (CPD) (6-4 photoproducts) --cyclobutane pyrimidine dimer produces a kink in DNA Other DNA damages DNA has three types of bonds susceptible to hydrolytic cleavage. WHAT ARE THEY 1)phosphodiester bonds 2)N-glycosylic bonds 3)exocyclic amine groups to bases -When DOES AN AP SITE FORM? When the N-glycosylic bond in cleaved, this will lead us to an opening of the ribose ring! -Water also cleaves the exocylic amine (the amine groups on the bases). WHAT are the RESULTS of this EXOCYCLIC AMINE BONDs BREAKING? Transition and transversion mutations! TRANSITION AND TRANSVERSION MUTATIONS ARE CAUSE BY DEAMINATION! -SIDE BAR: DNA DAMAGE can also occur by hydroxyl radical. Ex: guanine 8-oxoguanine. -8-OXOGUANINE base pairs with C or A (GAC) GAGA AND CHRISTINE -Alkylating agents damage DNA! Where does alkylation take place? N and O external to ring system, N in base ring system except those linked to deoxyribose, non-bridging oxygen atoms in phosphate groups -METHYLATION RESULTS IN MUTATION FROM GC pair to AT!

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