Thymine excision

Abdoul-Carine H, Gohlke S, Fischbach E, Scheike J, lllenberger E (2004) Thymine excision from DNA by subexcitation electrons. Chem Phys Lett 387 267-270 Adams GE, Willson RL (1972) On the mechanism of BUdR sensitization a pulse radiolysis study of one electron transfer in nucleic-acid derivatives. Int J Radiat Biol 22 589-597 Adams GE, Willson RL (1973) Ketyl radicals in aqueous solution. Pulse radiolysis study. J Chem Soc Faraday Trans 1 69 719-729... 

Mismatch Repair. Mispairs that break the normal base-pairing rules can arise spontaneously due to DNA biosynthetic errors, events associated with genetic recombination and the deamination of methylated cytosine (Modrich, 1987). With the latter, when cytosine deaminates to uracil, an endonuclease enzyme, /V-uracil-DNA glycosylase (Lindahl, 1979), excises the uracil residue before it can pair with adenine at the next replication. However, 5-methyl cytosine deaminates to form thymine and will not be excised by a glycosylase. As a result, thymine exits on one strand paired with guanine on the sister strand, that is, a mismatch. This will result in a spontaneous point mutation if left unrepaired. For this reason, methylated cytosines form spontaneous mutation hot-spots (Miller, 1985). The cell is able to repair mismatches by being able to distinguish between the DNA strand that exists before replication and a newly synthesized strand. 

Thymine dimers (Gj) UV radiation Excision endonuclease (deficient in Xeroderma pigmentosum) DNA polymerase DNA ligase... 

Ultraviolet light induces the formation of dimers between adjacent thymines in DNA (also occasionally between other adjacent pyrimidines). The formation of thymine dimers interferes with DNA rephcation and normal gene expression. Thymine dimers are eliminated from DNA by a nucleotide excision-repair mechanism (Figure 1-2-4). 

Figure 1-2-4. Thymine Dimer Formation and Excision-Repair...

An excision endonuclease (excinudease) makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligonucleotide. 

Answer B, Nucleotide excision repair of thymine (pyrimidine) dimers is deficient in XP... 

Xeroderma pigmentosum is caused by a defect in excision repair of thymine dimers, most freguently due to the absence of a UV-specific excinuclease, an enzyme that helps remove thymine dimers. 

The answer is C. Thymine dimers are repaired by the process of nucleotide excision repair, which involves many enzyme activities that recognize the mutated structure, cut the DNA strand on both sides of the mutation, remove (excise) the affected fragment, and then refill the gap. One of the major genes leading to xeroderma pigmentosoum encodes a specific excinuclease. 

Exposure of a cell to ultraviolet light can result in the covalent joining of two adjacent pyrimidines (usually thymines), producing a dimer. These thymine dimers prevent DNA polymerase from replicating the DNA strand beyond the site of dimer formation. Thymine dimers are excised in bacteria as illustrated in Figure 29.27. A similar pathway is present in humans. 

Excision repair. The E. coli mismatch repair is a type of excision repair. However, a different nucleotide excision repair system (NER) is utilized by all organisms from bacteria to human to remove a variety of defects. These include thymine dimers, photohydrates, oxidized bases, adducts of cisplatin (Box 5-B), mutagens derived from polycyclic aromatic compounds,683 and poorly recognized OC mismatched pairs.692 In E. coli this excision repair process depends upon proteins encoded by genes UvrA, B, C, and D and also DNA polymerase I and DNA ligase.693 695a A dimer of protein UvrA forms a complex with helicase UvrB (Eq. 27-22).696 696a... 

One of the lesions removed by nucleotide excision is the thymine photodimer.705 In the fission yeast S. pombe an alternative excision repair system, specialized for removal of thymine dimers and 6-4 photoproducts (Chapter 23), produces two-nucleotide gaps with 3 -OH and 5 -phospho-group ends.702/705a Alternative NER pathways are also employed by bacteria.705b... 

It would appear from these studies that the excision of thymine, and more generally pyrimidine dimers may be a two-step process. The initial single-stranded incision is probably dependent upon the presence of a distorted area in the DNA duplex resulting from the formation of a thymine dimer. Once the initial break has been introduced, a short single-stranded region containing the photoproduct results which is then susceptible to the action of the exonuclease. 

Compare and contrast the excision repair and photoreactivation mechanisms for correction of ultraviolet-induced thymine dimers. 

Pol I also has 5 — 3 -exonuclease activity that is different from the 3 — 5 -exonuclease action. It hydrolyzes DNA from the 5 end of a chain, cleaving a bond in the double-helical region at the terminal phosphodiester bond or a bond several residues distant from the 5 terminus. Either deoxy- or ribonucleotides can be removed. In fact, the main function of the 5 —> 3 exonuclease activity may be to remove ribonucleotide primers (p. 308). This activity can also excise thymine dimers formed by exposure to ultraviolet (UV) light. The three Pol I enzymatic activities are located at distinct sites (domains). 

Is excision repair the only means of removing thymine dimers from DNA ... 

Reardon JT, Sancar A. Recognition and repair of the cyclobutane thymine dimer, a major cause of skin cancers, by the human excision nuclease. Genes Dev. 2003 17(20) 2539-2551. 

Figure 27.49. Excision Repair. Repair of a region of DNA containing a thymine dimer by the sequential action of a...

In humans the cross-linked thymine moieties create a kink in our DNA. An excision enzyme recognizes this kink and that portion of DNA is cut out and repaired. Skin cancer has been linked to the failure of this mechanism. Another repair mechanism is found in some microbes which have an enzyme called DNA photolyase. DNA photolyase functions by recognizing the thymine dimers and un-zipping them (79). We have found methods to use DNA photolyase as an enzyme for regenerating thymine polymer photoresists, allowing re-use of the photoresist systems (20). 

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