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DNA DAMAGE AND REPAIR
prepared by David Mitchell
In: A Handbook of Organic Photochemistry and Photobiology,
William Horspool and Pill-Soon Song, Eds., CRC Press, London

The amount of solar ultraviolet radiation (UVR) reaching the earth's surface has increased due to chlorofluorocarbon pollution of the upper atmosphere. The consequences of stratospheric deozonation on the human population are difficult to predict, but may include increased skin cancer and accelerated aging; less direct effects may include deterioration of natural ecosystems and reduction of major food crops (Calkins 1982).

Due to its maximum absorbance at 260 nm, DNA is considered the primary chromophore of UVR. The absorption spectrum of DNA correlates well with photoproduct formation, cell killing, mutation induction, and tumorigenesis. Because UVR induces numerous structural lesions in DNA, sensitive and precise measurements of DNA damage and repair are essential for understanding the cytotoxic and mutagenic effects of specific photoproducts on individual cells and complex organisms.

1. Biological Significance

The sun emits energies at wavelengths that range through 11 orders of magnitude, from 10^(-4) nm to 10^(12) nm (Smith 1977). The vast majority of this energy is biologically irrelevant; ionizing radiations such as high energy particles, X-rays and gamma rays are expended by atomic collisions in the upper atmosphere and long wavelength far infrared, microwaves and radiowaves do not have sufficient energy to influence biochemical reactions. Photodependent biological processes derive their energy from the UV and visible portions of the solar spectrum. UVR is divided into the UVC (240-290 nm), UVB (290-320 nm) and UVA (320-400 nm) regions. Absorption of UVC irradiation by stratospheric ozone greatly attenuates these wavelengths, resulting in very little light shorter than 300 nm reaching the earth's surface. Hence, although comprising only a negligible portion of sunlight, UVB is responsible for most of the sun's pathological effects.
UVR is a potent and ubiquitous carcinogen responsible for much of the skin cancer in the human population today (Cleaver and Kraemer 1989). Tumor incidence and mortality correlate with exposure: basal and squamous cell carcinomas are most prevalent on the face and trunk in men and the face and legs in women; carcinomas increase with decreasing latitude; tumor incidence is increased in individuals working in occupations with high exposure, such as ranchers or fisherman; and the protective action of skin pigmentation results in lower cancer rates in dark-skinned populations compared to lighter-skinned peoples. Genetic diseases that greatly increase the risk of sunlight-induced skin cancer exemplify the importance of UVR damage and its repair in humans. In one such disease, xeroderma pigmentosum, a failure in the DNA repair process is associated with a major increase in the rate of squamous and basal cell carcinoma and melanoma.

The biological effects of DNA photodamage depend on the type of lesion induced and its genomic location, as well as the nature of the target cell and its developmental state. If the photoproduct is repaired correctly, the DNA is restored to its original state and, after some delay, the cell proceeds with its normal activities. If the damage is not repaired, it may interfere with DNA replication or transcription. Should this occur, cell proliferation will cease or, if the block is situated in a gene required for an essential metabolic function, the cell will die. Alternatively, the damage may not block replication. Bypass of the lesion by a DNA polymerase may produce an incorrect complementary base (i.e., a mutation). This mutation can have several outcomes: (1) It may not alter the genetic code and, hence, not effect normal metabolism. (2) It may produce a truncated or partial RNA transcript and manufacture a dysfunctional protein. If this protein is essential, then the mutation is lethal. (3) It may result in activation of an oncogene or inactivation of a tumor suppressor gene, thereby initiating the carcinogenic process (slide 1).

2. DNA Photoproducts

Photon absorption rapidly (10^(-12) sec) converts a pyrimidine base to an excited state. Various pathways are then available for resolution of this unstable electronic configuration (Wang 1976). The major pathway involves rapid dissipation of the energy of the excited base to the ground state (10^(-9) sec) by non-radiative transition or by fluorescence, yielding heat or light in the process. Secondly, the excited base can react with other molecules to form unstable intermediates (i.e. free radicals) or stable photoproducts. Finally, there is a low probability that intersystem crossing, a nonradiative pathway, can transfer a base from the excited singlet state to the excited triplet state. The lifetime of the triplet state is several orders of magnitude longer than the excited singlet state (10^(-3) sec), increasing the chance of photoproduct formation. Cyclobutane dimers form through the excited triplet state. Other photoproducts, such as the pyrimidine(6-4) pyrimidone photoproduct [or (6-4) photoproduct] form by some other mechanism.

Dimerizations between adjacent pyrimidine bases are by far the most prevalent photoreactions resulting from UVC or UVB irradiation of DNA. The relative induction of these photoproducts depends on wavelength, DNA sequence, and protein-DNA interactions. The two major photoproducts are the cyclobutyl pyrimidine dimer and the (6-4) photoproduct (slide 2). The (6-4) photoproduct undergoes a further UVB-dependent conversion to its valence photoisomer, the Dewar pyrimidinone (slide 2). In addition to the major photoproducts, rare dimers may also form, such as the adenine-thymine heterodimer.

In contrast to the direct induction of DNA damage by UVC and UVB light, UVA produces damage indirectly through highly reactive chemical intermediates. Similar to ionizing radiation, UVA radiation generates oxygen and hydroxyl radicals which in turn react with DNA to form monomeric photoproducts, such as cytosine and thymine photohydrates, as well as strand breaks and DNA-protein crosslinks. The relationship between the relative occurrence of these photoproducts and their biological effect depends on the cytotoxic and mutagenic potential of the individual lesion. Hence, even though a photoproduct may occur at a low frequency, its structure and location may elicit a potent biological effect.

3. Detection of DNA Damage

A variety of analytical procedures have been developed to measure UVR damage and repair in DNA (Friedberg and Hanawalt). Many types of photoproducts have been identified and quantified by chromatographic techniques. Since the initial detection of the cyclobutane dimer by 2-dimensional paper chromatography, thin-layer chromatography and high performance liquid chromatography have been adapted to the analysis of this and other types of photodamage. All of these procedures require DNA that has been hydrolyzed to free bases or nucleotides by enzymatic digestion or treatment in strong acid at high temperature.

Many types of photodamage can be converted into single-strand breaks in DNA by enzymatic or biochemical treatment. Frank breaks induced directly in DNA by UVR and breaks produced at sites of photoproducts can be quantified by alkaline gradient centrifugation, alkaline elution, or agarose gel electrophoresis. The sensitivity of these procedures requires maintenance of high molecular weight DNA through the extraction and analytical procedures. UvrABC exinuclease (slide 3), a partial excision repair complex purified from Escherichia coli cleaves DNA on either side of damage produced by exposure to UVR (slide 4). Cleavage of specific photoproducts has been achieved by using purified enzymes that combine a glycolsylase that cuts the base from the sugar leaving an abasic (AP) site, and an apurinic/apyrimidinic endonuclease which cleaves the phosphodiester backbone on either side of the AP site. Nonenzymatic cleavage of alkali-labile sites, such as AP sites or Dewar pyrimidinones, also produces quantifiable strand breaks for analysis of induction and repair.

These techniques have recently been adapted to the analysis of UV photoproduct induction and repair at the gene and base sequence levels. Photodamage at the sequence level can be mapped as strand breaks in DNA fragments irradiated with high fluences of UVC and UVB light and at the gene level using Southern blot hybridization of DNA fragments separated by agarose gel electrophoresis. Recently, the distribution of photoproducts at the sequence level in a gene promoter irradiated in vivo with low UV fluences was analyzed by ligation-mediated polymerase chain reaction.

Polyclonal and monoclonal antibodies recognize and bind a variety of photoproducts, including the cyclobutane dimer, (6-4) photoproduct, Dewar pyrimidinone, and thymine glycol (slide 5). Techniques such as immunoprecipitation, enzyme-linked immuoassays, radioimmunoassays, quantitative immunofluorescence, and immuno-electron microspcopy are powerful analytical tools; each has its own unique attributes and applications. Unlike chromatography, immunological assays do not require chemical or enzymatic degradation of DNA before analysis; unlike assays that require strand scission, sensitivity does not depend on the molecular weight or purity of sample DNA.

4. DNA Repair

The total number of photoproducts remaining in cellular DNA at any time depends on the amount of UVR absorbed and the amount of damage repaired. Damage tolerance strategies are complex and vary greatly among organisms. Nearly all organisms have behaviors or natural features that mitigate exposure of DNA to solar UVR and reduce the amount of photodamage. In addition to habitat selection, avoidance responses, and physical morphologies which attenuate the transmission of UVR to sensitive, internal areas of cells, many organisms have evolved biochemical mechanisms to protect themselves. UVR absorbing compounds such as melanin and anthocyanin are produced in human skin and in plants; colorless UV-absorbing compounds, such as flavenoids in terrestrial plants, mycosporine amino acids in fungi and mycosporine-like compounds in marine organisms, have also been identified as possible UV-protective chemicals.

Once DNA damage is present, its removal may proceed in whole or in part by at least two well-studied mechanisms, photoenzymatic repair (PER)(slide 6) or excision repair (Friedberg 1984). PER involves specific recognition and binding of a small enzyme called a photolyase to a cyclobutane dimer. This enzyme catalyzes the direct reversal of the dimer upon absorption of a photon within the UVA/visible range of light. Photoreactivation occurs widely throughout the plant and animal kingdoms. Its presence and operation in placental mammals, particularly in human skin, is a matter of some controversy.

Organisms that display reduced PER, often have a greater capacity for excision repair. The excision repair mechanism utilized by the cell depends on the type of damage encountered and the location of the damage in chromatin. The excision repair pathway begins with the search and recognition of the lesion as a structural distortion in the DNA helix. DNA at the site of damage is unwound or otherwise disassociated from nucleosomal proteins to provide accessibility to repair enzymes. The DNA backbone is then incised at or near the site of the lesion allowing its excision and concomitant resynthesis of the DNA around the damaged site. Finally, the single-strand gap remaining after disengagement of the DNA polymerase complex is ligated.

Base excision repair is initiated by enzymatic recognition of the lesion and scission of the bond between the damaged base and its associated deoxyribose sugar, a process called aglycosylation. Examples of n-glycosylases include endonuclease III from E. coli which repairs photohydrates and endonuclease V from T4 phage which recognizes cyclobutane dimers. In the latter case, cleavage of the n-glycosyl bond of the 5' pyrimidine base leaves an abasic site which is subsequently recognized by an AP endonuclease that cleaves the phosphodiester bond 3' to the abasic site. The remaining abasic site is digested with a 5' AP endonuclease or 3'6 5' exonuclease associated with DNA polymerase. The damaged strand is removed and resynthesized by a DNA polymerase complex and the remaining gap is ligated.

In contrast to base excision repair, nucleotide excision repair recognizes a broad spectrum of DNA damage, including UVR-induced photoproducts. This process has been well studied in E. coli (slide 7) and is thought to be an important excision repair pathway in eukaryotes as well (slide 8). As with base excision repair, the nucleotide excision repair process is initiated by enzymes that recognize and bind the helical distortion created at the damaged site. A repair complex is assembled and cleaves the DNA a few bases to either side of the lesion, leaving a gap. This gap is filled by a DNA polymerase and the strand is ligated to restore the DNA duplex to its original integrity.

5. Summary

The clinical effects of defective DNA repair can include increased risk of skin cancer and accelerated aging, as well as neurological and growth disorders. This phenotypic heterogeneity belies the complexity of the excision repair process and presents a formidable task in defining the functions of the various proteins involved in DNA repair. Recent advances in cloning the genes involved in DNA repair in mammals, yeast and Drosophila melanogaster have greatly increased our understanding of the DNA repair process. In addition to defining the components of an ancient and essential molecular process, future studies in DNA repair may help direct the prevention and clinical treatment of sunlight-induced skin cancer and lessen the impact of stratospheric deozonation on the human population.

Links

Survival curves and target theory
Arena, Victor (1971) Ionizing Radiation and Life, C.V. Mosby Co., Saint Louis, MO,
pp 363-368.

UV-induced DNA damage and repair: a review
Sinha and Hader, 2002. Photochem. Photobiol. Sci. pp 225-236.

References
1. J. Calkins (Ed.), The Role of Solar Ultraviolet Radiation in Marine Ecosystems, NATO Conference Series IV: Marine Sciences, Vol. 7, Plenum Press, New York, 1982.
2. Smith, K. C. (Ed.), The Science of Photobiology. Plenum Press, New York (1977).
3. Cleaver, J. E. and Kraemer, K. H., Xeroderma pigmentosum, in: The Metabolic Basis of Inherited Disease, Vol. II, 6th Ed. (C.R. Scriver, A.L. Beaudet, W.S. Sly, and D. Valle, eds.), McGraw-Hill, 1989, pp. 2949-2971.
4. Wang, S. Y. (Ed.), Photochemistry and Photobiology of Nucleic Acids, Vols. I and II. Academic Press, New York, 1976.
5. Friedberg, E. C. and Hanawalt, P. C. (Eds.), DNA Repair: A Laboratory Manual of Research Procedures, Vols. 1-3. Marcel Dekker, Inc., New York.
6. Friedberg, E. C., DNA Repair, W.H. Freeman and Co., New York, 1984

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

last modified on Feb 3, 2009