Thymine dimer formation

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

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

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. 

Wang Cl, Taylor JS. Site-specific effect of thymine dimer formation on dA dT tract bending and its biological implications. Proc. Natl. Acad. Sci. U.S.A. 1991 88 9072-9076. 

The first step in XJVR-induced skin cancer is UVR-initiated DNA mutation, which causes the transformation of the normal cells to malignant cells. For UVR to initiate a biological reaction, it has to be absorbed by endogenous molecules (chromophores). UVB is absorbed directly by the DNA, and therefore can directly induce DNA mutation (224), in the form of thymine dimer formation (289). Some protein components may also ad as chromophores for UVB (224). UVA is absorbed by the reduced forms of the co-enzymes nicotinamide adenine dinucleotide (NADH) and nicotinamide adenine dinucleotide phosphate (NADPH), tryptophan, riboflavin, and melanin (224,290). UVA-induced DNA damage is believed to be mediated by oxygen reactive species that are released after the absorption of UVA by those endogenous chromophores and results in photooxidation of selected bases... 

Marguet S, Markovitsi D (2005) Time-resolved study of thymine dimer formation. J Am Chem Soc 127 5780-5781... 

Compounds which reduce UV-induced oxidative damage and other symptoms such as skin inflammations and erythema by mediating the prevention of thymine dimer formation and inhibition of matrix metalloproteases. 

In contrast, the photochemistry of uracil, thymine and related bases has a large and detailed literature because most of the adverse effects produced by UV irradiation of tissues seem to result from dimer formation involving adjacent thymine residues in DNA. Three types of reaction are recognizable (i) photohydration of uracil but not thymine (see Section 2.13.2.1.2), (ii) the oxidation of both bases during irradiation and (iii) photodimer formation. 

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. 

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). 

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... 

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

The effect of phase upon the monomer-dimer equilibrium is pronounced. The quantum yields for dimer formation in liquid-aerated water solution are low (from zero for thymine to 10"2 for other pyrimidines) but the quantum yields for dimer formation in frozen aqueous solutions or in single crystals are much higher (reaching unity in frozen water solution for thymine). The quantum yields for monomerization are uniformly high and are about the same in solution or in solid phase. The net result of this phase effect is that even at optimum wavelengths for dimer formation, the yields of dimers are low in solution and high in solid phases, for all the single bases, nucleosides, or nucleotides. 

One obvious reason for the apparent lack of reaction of thymine in water is that the quantum yield for splitting of thymine dimer in solution is 0.5-1.0,28 independent of wavelength, and the probable yield for formation would not be higher, by analogy with other pyrimidines, than... 

The high rate of dimer formation in frozen solution reflects the necessity for a preferred orientation of the two thymine molecules concerned, but it is still considered that water plays an important part. Thymine in dried films,32,34 and on filter paper33 can be converted to dimer by ultraviolet light, but the maximum conversions are much lower, 1732-55%34 (depending upon the humidity34). 

The water lattice may be an important element in forming the ordered thymine structure necessary for dimerization, as pointed out by Beukers and Berends.37 Thymine can crystallize from solution as a monohydrate (a real hydrate)38 in whose crystal lattice one thymine is directly above another. The influence of humidity upon dimer yield in dry films may be connected with monohydrate formation, and monohydrate formation in frozen solutions may be the reason for the almost theoretically maximum quantum yields for dimer formation.31 The possible existence of aggregates in frozen aqueous solutions is supported by a tenfold increase in purine phosphorescence at 44°K produced by the presence of 1% ethanol and by a blue shift of excitation and emission spectra.39... 

Despite the frequent use of photoreversal as a measure of dimer formation in many biological materials, few detailed studies of this phenomenon have been made. The action spectrum for photoreversal of uracil dimer (and thymine dimer) has been reported by Swenson and Setlow,48 and is shown in Figure 1. Purified, crystalline dimer was used in these studies. The quantum yield for dimer breaking was found to be 0.45, one-half of that for monomerization of thymine dimers.49... 

The presence of proflavine protects some viruses against inactivation by ultraviolet radiation and proflavine has been shown to inhibit formation of thymine dimers in DNA.86 (6) The sensitivity of microorganisms to ultraviolet light increases with, but is not proportional to the square of, the thymine content of the DNA.86 (7) Substitution of... 

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... 

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. 

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... 

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