Thymine repair

Fig. 11 Thymine dimer repair at a distance by DNA-mediated charge transport. Here photoexcitation of intercalated [Rh(phi)2bpy/]3+ tethered to the 3 -end of a DNA duplex oxidizes a remote thymine dimer (>34 A away) within the helix leading to dimer repair. The arrows mark the sites of intercalation of the phi ligand. Adapted from [149]...

Oxidative repair is not a unique feature of our Rh(III) complexes. We also demonstrated efficient long-range repair using a covalently tethered naphthalene diimide intercalator (li /0 1.9 V vs NHE) [151]. An intercalated ethidium derivative was ineffective at dimer repair, consistent with the fact that the reduction potential of Et is significantly below the potential of the dimer. Thymine dimer repair by a series of anthraquinone derivatives was also evaluated [151]. Despite the fact that the excited triplets are of sufficient potential to oxidize the thymine dimer ( 3 -/0 1.9 V vs NHE), the anthraquinone derivatives were unable to effect repair [152]. We attribute the lack of repair by these anthraquinone derivatives to their particularly short-lived singlet states anthraquinone derivatives that do not rapidly interconvert to the excited triplet state are indeed effective at thymine dimer repair [151]. These observations suggest that interaction of the dimer with the singlet state may be essential for repair. 

DNA CT also permits chemistry at a distance. Oxidative DNA damage and thymine dimer repair can proceed in a DNA-mediated reaction initiated from a remote site. These reactions too are sensitive to intervening DNA dynamical structure, and such structures can serve to modulate DNA CT chemistry. The sensitivity of DNA CT to base pair stacking also provides the basis for the design of new DNA diagnostics, tools to detect mutations in DNA and to probe protein-DNA interactions. 

Figure 9.4 Repair of DNA inactivated by ultraviolet light. Light causes die dimerization of adjacent thymine residues that block DNA replication. The four enzymes shown are involved in removal and replacement of a portion of the DNA that contains the dimer.

Figure 2 Double-stranded oligonucleotide photoprobes that simulate modified DNA and intended to cross-link to DNA-binding proteins. (A) Probe modeling interstrand cross-linking by cisplatin Source From Ref. [63], with permission from the American Chemical Society via the Rightslink service (license number 2458870278307 granted June 30, 2010). The benzophenone probe prior to reaction with DNA is shown in the lower part of the panel. (B) Photoaffinity probe for bacterial DNA repair proteins. TT is a simulated thymine dimer intended to be recognized as a site of damage in DNA, and T (two instances) is the diazirine thymine derivative T Source From Ref. [64], with permission from Wiley.

There is always interest in the photochemistry of the pyrimidine nucleic acid bases and related simple pyrimidinones, due to its importance in genetic mutation. In addition to damaging DNA, photo-induced reactions may also repair the damage, as in the reduction, by FADH, of the thymine glycol 64 back to thymine <06JACS10934>. Another report related to repair of DNA involved a model study, by means of the linked dimer 65, of the involvement of tryptophan in the electron-transfer leading to reversion of thymine oxetane adducts <06OBC291>. 

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. 

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...

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

MBD4 Contains MBD domain and a repair domain (T-G mismatch glycosylase) Thymine glycosylase that binds to the product of deamination at methylated CpG sites Co-localizes with heavily methylated satellite DNA in mouse cells expressed in somatic tissues and in ES cells... 

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. 

FIGURE 8.2 Formation of a thymine-thymine dimer by UV-B radiation, and repair by UV-A or blue light-activated photolyase. 

DNA synthesis in irradiated sensitive bacterial cells is permanently inhibited by doses which produce about 5 thymine dimers per single strand of DNA (1000 p.). In the cells of resistant bacteria, DNA synthesis is inhibited only by doses of radiation which produce about 500 dimers per cell. The difference between the two types of bacteria is caused by the presence in the resistant cells of efficient enzymatic mechanisms for repairing the damage done by thymine dimerization. 

Perhaps the best-characterized lesion in DNA associated with uv inactivation and mutagenesis is that involving the intrastrand photodimerization of adjacent thymine residues this lesion is almost wholly repaired by photodissociation of the dimers at shorter wavelengths in the photoreactivation process. Production of the chh dimer in this case, promoted by the configuration of adjacent molecules on the same sugar-phosphate strand, must however involve a rotational displacement of 36°, following the reduction of 0.6 A in molecular separation. 

The molecular basis for the potential carcinogenicity of NTA is still being investigated, but initial results show increased incorporation of thymine into DNA by human lymphocytes performing DNA repair in the presence of NTA [20]. This could feasibly lead to mutagenicity. The biodegradation pathway of NTA is shown in Figure 10.7. 

The deamination of 5-methylcytosine occurs more frequently than that of other bases but the product, thymine, is of course a normal base and therefore will not be recognized by the repair system (Fig. 6.42). This represents a major source of point mutations in DNA. 

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