Thymine 6-4 photoproduct

A number of studies on photochemistry of the nucleic acid bases in aqueous solutions demonstrated that while uracil undergoes reversible hydration under exposure to UV irradiation, the other bases (thymine, adenine, and guanine) were stable [41,42], However, the sensitivity of dissolved thymine to UV irradiation can be significantly increased if the solution is rapidly frozen [43]. In 1960 the thymine photoproduct was isolated from irradiated frozen aqueous solution of thymine. Elemental analysis, molecular weight measurements, powder X-ray diffraction, NMR and IR spectroscopy confirmed that the most likely photoproduct is a thymine dimer [20]. Similar photoproduct was obtained by hydrolysis of irradiated DNA. Its formation was attributed to reaction between two adjacent thymine groups on the same DNA chain [44], Independently an identical compound was isolated from DNA of UV-irradiated bacteria [45]. 

One of the most interesting nucleobases in which to study the excited-state structural dynamics is thymine, as thymine photoproducts account for >95% of the lesions found in DNA upon either UVB or UVC irradiation [59], Excited-state structural... 

Mutagenesis studies showed that this type of mutation induced a -1 frameshift. A further report describes the incorporation of an (adjacent) cis-syn cyclobutane dimer site specifically into a nucleosome The templating properties of the thymine photoproducts, including the Dewar photoproduct (176), have been examined using the pyrene C-nucleoside triphosphate. The pyrene nucleotide was inserted in preference to dATP opposite the 3 -T of the photoproducts in all cases except for a trans,syn photoproduct, whereas dATP was preferentially incorporated opposite the 5 -T in all cases. This suggests that the incorporation opposite the 3 -end of the photoproduct takes place via a transient abasic site-like intermediate. 

Szymkowski, D.E., Lawrence, C.W., and Wood, R.D. (1993) Repair by human cell extracts of single (6-4) and cyclobutane thymine-thymine photoproducts in DNA. Proc. Natl. 

The cytotoxicity derived from UVA photolysis of DNA containing 4-thiothymidine has been shown to be due to the thietane (37) which is structurally related to the thymine dimer (38). Cells defective in repairing the 6 4 thymine photoproduct were found to be extremely sensitive to 4-thiothymidine-containing DNA under photolytic conditions. 

Donnellan, J.E. and Setlow, R.B., Thymine photoproducts but not thymine dimers found in ultraviolet-irradiated bacterial spores. Science, 149, 308, 1965. 

Very important information concerning the photochemistry of the nucleic acids was furnished by the report of Beukers and Berends that irradiation of frozen solutions of thymine produces a stable photoproduct corresponding to dimerization of the thymine/58 This photoproduct has been subsequently identified as a cis-syn-cis dimer ... 

These results seem to suggest that by irradiation in alkylamines DNA (single stranded) can undergo a selective release of thymine, accompanied by strand scission. This has indeed experimentally been verified. Irradiation of calf thymus DNA in 5% aqueous n-butylamine gave a photoproduct that on heating yields 1-n-butylthymine (81MI1). 

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]. 

A particular dimer of thymine was the first heat-stable photoproduct isolated from photolysis of nucleic acid derivatives, and still appears to be the principal isolable product from photolysis of most examples of biologically active DNA.8,10 Investigation of this product has drawn much attention in recent years. Most of this work has been carried out on polynucleotides and nucleic acids and will be dealt with in those sections. The remaining work has been largely carried out with... 

The maximum conversion of thymine to photoproducts in frozen aqueous solutions is 83-90%31 in samples subjected to alternate cycles of freezing and thawing, and 48-50% in samples continuously frozen during irradiation. This difference is attributed to depletion of thymine in the thymine crystallites of the continuously frozen solutions. The existence of a maximum at less than 100% in the conversion may reflect either the equilibrium always present between monomer and dimer, or... 

The existence of photoreversible, but not of heat-reversible, absorbance change in irradiated poly dI dC was taken to prove that the photoproducts are entirely dimers (in contrast to those in poly C irradiations where the product is almost entirely the hydrate82a). It was possible to detect dimers of uracil as well as those of cytosine, by means of the much slower photoreversal of uracil dimers. In the acid hydrolysates of irradiated dl-dC, both uracil dimers and uracil could be identified. Enzymatic hydrolysis (snake venom phosphodiesterase) does not split pyrimidine dimers, and the products of such hydrolysis of irradiated tritium-labeled poly dl dC contained trinucleotides shown by radioactivity to contain cytosine dimers. Thymine dimers were formed in the photolysis of the poly dA dT, and were detected and assayed by the same methods. The yield of thymine dimers in irradiated poly... 

The formation of dimers other than thymine dimer in irradiated DNA has been recently reported by Setlow and Carrier,87 using E. coli DNA containing either labeled thymine (14C or tritium) or labeled cytosine (tritium). Three photoproducts could be isolated by chromatography of the acid hydrolysates of the irradiated DNA and were... 

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. 

Matsufuji H, Shibamoto T (2004) The role of EDTA in malonaldehyde formation from DNA oxidized by Fenton reagent systems. J Agric Food Chem 52 3136-3140 Matsunga T, Hieda K, Nikaido O (1991) Wavelength dependent formation of thymine dimers and (6-4)photoproducts in DNA by monochromatic ultraviolet light ranging from 150 to 365 nm. Photochem Photobiol 54 403-410... 

Yamada H, Hieda K (1992) Wavelength dependence (150-290 nm) of the formation of the cyclobutane dimer and the (6-4) photoproduct of thymine. Photochem Photobiol 55 541-548 Yan M, Becker D, Summerfield S, Renke P, Sevilla MD (1992) Relative abundance and reactivity of primary ion radicals in y-irradiated DNA at low temperatures. 2. Single- vs double-stranded DNA. J Phys Chem 96 1983-1989... 

It should be noted here that thymine photodimerization may occur by a non-concerted mechanism, involving free radical intermediates. Indeed, photoproducts other than cis-syn dimer, such as the next most abundant thymine dimer, so-called 6 4 adduct, were observed in irradiated DNA. However, the quantum yield of cis-syn photodimer formation (r/j 0.02) is more than an order of magnitude higher than that of the 6 4 adduct ( 0.0013) which in turn is an order of magnitude higher than the quantum yields for other thymine isomers [68]. This specificity can lead to the conclusion that the thymine photodimerization occurs predominantly via concerted 2 + 2 cycloaddition mechanism. A time-resolved study of thymine dimer formation demonstrated that thymine cyclobutane dimers are formed on a timescale of less than 200 nsec, while the 6 4 adduct is formed on a timescale of few milliseconds [69]. The delay in the formation of the latter was attributed to the mechanism of its formation through a reactive intermediate. 

Thymidine cyclobutane dimers are important photoproducts formed by short-wave UV irradiation (2 = 290-320 nm) of DNA, by [2 + 2] cycloaddition between two adjacent thymine nucleobases in the same oligonucleotide strand (Scheme 4.5.1) [1]. They lead to profound biological effects in vivo, including mutation, cancer, and cell death [2] (Box 21). In a wide range of organisms the repair of these lesions in DNA is accomplished by enzymes (the photolyases), which regenerate undamaged thymidines by means of a photoinduced electron-transfer process [3]. 

Photochemistry of Pyrimidone-2 Dimer Reduction Product 141 III. 1.2 Tetrameric Photoproduct of Thymine and Pyrimidone-2. 141... 

Of additional, and particular, interest is the finding that the dimer reduction product of pyrimidone-2 is an integral component of a tetrameric photoproduct resulting from the photodimerization of a photoadduct of thymine and pyrimidone-2 77), as shown in Scheme 3. This tetrameric photoproduct has, furthermore, been isolated from an irradiated frozen aqueous solution of cytosine and thymine 8), and, more... 

The pyrimidine nucleobases have the highest quantum yields for photoreactivity, with thymine uracil > cytosine. The purine nucleobases have much lower quantum yields for photochemistry, but can be quite reactive in the presence of oxygen. As can be seen from Figure 9-3, thymine forms primarily cyclobutyl photodimers (ToT) via a [2ir + 2tt cycloaddition, with the cis-syn photodimer most prevalent in DNA. This is the lesion which is found most often in DNA and has been directly-linked to the suntan response in humans [65]. A [2Tr + 2Tr] cycloaddition reaction between the double bond in thymine and the carbonyl or the imino of an adjacent pyrimidine nucleobase can eventually yield the pyrimidine pyrimidinone [6 1]-photoproduct via spontaneous rearrangement of the initially formed oxetane or azetidine. This photoproduct has a much lower quantum yield than the photodimer in both dinucleoside monophosphates and in DNA. Finally, thymine can also form the photohydrate via photocatalytic addition of water across the C5 = C6 bond. 

Uracil has a similar photoreactivity to thymine, but in RNA. Although the rate of photoreaction is similar, the photoproduct partitioning is different. While uracil forms the cyclobutyl photodimer and photohydrate, there is no evidence that it forms the pyrimidine-pyrimidinone [6 1] photoproduct. Also, the major photoproduct in... 

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