Thymine dimers

Finally a few sentences are deserved for the vast area of DNA photochemistry. Thymine dimerization is the most common photochemical reaction with the quantum yield of formation in isolated DNA of all-thymine oligodeoxynucleotides 2-3% [3], Furthermore, a recent study based on femtosecond time-resolved transient absorption spectroscopy showed that thymine dimers are formed in less than 1 ps when the strand has an appropriate conformation [258], The low quantum yield of the reaction in regular DNA is suggested to be due to the infrequency of these appropriate reactive conformations. 

Schreier WJ, Schrader TE, Roller FO, Gilch P, Crespo-Hernandez CE, Swaminathan VN, Carell T, Zinth W, Kohler B (2007) Thymine dimerization in DNA is an ultrafast photoreaction. Science 315 625-629... 

Durbeej B, Eriksson LA (2002) Reaction mechanism of thymine dimer formation in DNA induced by UV light. Photochem Photobiol A 152 95-101... 

Boggio-Pasqua M, Groenhof G, Schafer LV, Bmbmiiller H, Robb MA (2007) Ultrafast deactivation channel for thymine dimerization. J Am Chem Soc 129 10996-10997... 

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. 

Incorporation of a flavin electron donor and a thymine dimer acceptor into DNA double strands was achieved as depicted in Scheme 5 using a complex phosphoramidite/H-phosphonate/phosphoramidite DNA synthesis protocol. For the preparation of a flavin-base, which fits well into a DNA double strand structure, riboflavin was reacted with benzaldehyde-dimethylacetale to rigidify the ribityl-chain as a part of a 1,3-dioxane substructure [49]. The benzacetal-protected flavin was finally converted into the 5 -dimethoxytri-tyl-protected-3 -H-phosphonate ready for the incorporation into DNA using machine assisted DNA synthesis (Scheme 5a). For the cyclobutane pyrimidine dimer acceptor, a formacetal-linked thymine dimer phosphoramidite was prepared, which was found to be accessible in large quantities [50]. Both the flavin base and the formacetal-linked thymidine dimer, were finally incorporated into DNA strands like 7-12 (Scheme 5c). As depicted in... 

Scheme 5 a Flavin-H-phosphonate and formacetal-linked thymine dimer phospho-ramidite used for the synthesis of the flavin and dimer containing DNA-strands 7-12. b Representation of a reduced flavin- and formacetal-linked cyclobutane pyrimidine dimer containing DNA strand, which upon irradiation (hv) and electron transfer (ET) performs a cycloreversion (CR) of the dimer unit, c Depiction of the investigated oligonucleotides... 

In order to gain a more detailed insight into how the flavin and thymine dimer orientation may influence the excess electron transfer process, rigid... 

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.

J.C. Sutherland and Griffin incorporated tritium-labelled thymine into DNA and irradiated it with 313 nm light in buffered saline in the presence of p-aminobenzoic acid for up to 12 min. After separation of the products by TLC, the radioactivity was associated with a fraction which had the characteristic RF of dimers. When the hydrolysate from a 313 nm irradiated sample was re-irradiated at 254 nm and then chromatographed, the radioactivity had the mobility of thymine monomer. This is characteristic of pyrimidine cyclobutyl dimers which were known to be photosynthesized at 313 nm and photodegrad-ed to monomers at 254 nm. Although not degraded itself, the p-aminobenzoic acid clearly acted as a photosensitizer for the DNA-damaging thymine dimerization [40]. 

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. 

The ultraviolet irradiation of DNA produces two photoproducts from thymine. The major product is identical with thymine ice-dimer (cis-syn, LXXVa), and accounts for 91 per cent of the DNA-derived photoproducts [541, 542]. A uracil-thymine dimer is also obtained in smaller quantity, which arises from deamination of a cytosine-thymine dimer [543, 544]. 

The cis-syn thymine dimer from DNA is believed to be formed from intra-strand dimerization of adjacent thymine residues. Photoaddition of two unsaturated molecules in the solid state can arise only if they are initially located in proximity in the crystal lattice [545, 546]. The formation of interstrand dimers would require gross distortion of the helical structure of DNA in order for the bases to approach the limiting distance (c. 4 A.) Hence, such dimers would be formed in only very small amount. However, the composition of the photoproducts may differ under varying experimental conditions [547-550]. 

Biological, chemical. X-ray diffraction, infrared absorption, e.s.r., n.m.r., luminescence, and quantum studies show that dimer formation is universally observed in irradiated frozen solutions of thymine, thymidine, uridine, thymidylic acid and related compounds, and in DNA [560—576]. The purines of DNA, on the other hand, are little affected [577, 578]. Thymine dimers obtained in frozen solution can be converted to the original monomers by ultraviolet... 

Thymine dimers can be removed by photoreactivation (2). A specific photolyase binds at the defect and, when illuminated, cleaves the dimer to yield two single bases again. 

Ultraviolet l fyt causes neighboring thymine bases to form thymine dimers that block replication and gene expression. 

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