Thymine photochemistry

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. 

An excellent review on organic photochemistry in organized media, including aqueous solvent, has been reported.178 The quantum efficiency for photodimerization of thymine, uracil, and their derivatives increased considerably in water compared with other organic solvents. The increased quantum efficiency is attributed to the preassociation of the reactants at the ground state. 

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. 

The photochemistry of the polynucleotides has been elucidated primarily by studies of the photochemical behavior of the individual pyrimidine and purine bases (the ribose and phosphate groups would not be expected to undergo photochemical reactions in this wavelength range). These studies have shown the pyrimidines (cytosine and thymine) to be roughly ten times more sensitive to UV than the purines (adenine and guanine.) Thus we would expect most of the photochemistry of the nucleic acids to result from the action of light on the pyrimidines. 

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 ... 

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>. 

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]. 

Molecular mechanisms in nucleic acid photochemistry I. Sensitized photochemical splitting of thymine dimer. J. Amer. chem. Soc. 88, 813 (1966). 

In late 1996, a new family of DNA-mediated ET experiments began to be reported. In these the ET donor is comprised of one or more DNA nucleotides (either G, GG, GGG, or a covalent thymine dimer) while the other is a covalently attached, photoactivated electron acceptor (either anthraquinone, pyrene, or an tris-polypyridyl M(III) complex, where M = Ru or Rh) [74-80]. These experiments have much in common with the kind of experiments outlined immediately above and with the new hairpin studies recently reported. They will be discussed toward the end of this chapter. They differ from the pre-1997 ET kinetics experiments that will be discussed immediately below in that none of them has reported ET rate measurements. Rather, yields of net photochemistry (either DNA strand cleavage or thymine dimer scission) are presented as evidence that photoinduced ET events occurred. For comparison of experimental results with ET theory it is clear that at a minimum ET rates must be measured and at a maximum several rates should be measured for a given D/A pair at a variety of separation distances. 

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

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. 

The UV resonance Raman spectrum of thymine was revisited in 2007, with a slightly different approach, by Yarasi, et al. [119]. Here, the absolute UV resonance Raman cross-sections of thymine were measured and the time-dependent theory was used to experimentally determine the excited-state structural dynamics of thymine. The results indicated that the initial excited-state structural dynamics of thymine occurred along vibrational modes that are coincident with those expected from the observed photochemistry. The similarity in a DFT calculation of the photodimer transition state structure [29] with that predicted from the UV resonance Raman cross-sections demonstrates that combining experimental and computational techniques can be a powerful approach in elucidating the total excited-state dynamics, electronic and vibrational, of complex systems. 

Very few reports of the excited-state structural dynamics of the purine nucleobases have appeared in the literature. This lack of research effort is probably due to a number of factors. The primary factor is the lack of photochemistry seen in the purines. Although adenine can form photoadducts with thymine, and this accounts for 0.2% of the photolesions found upon UVC irradiation of DNA [67], the purines appear to be relatively robust to UV irradiation. This lack of photoreactivity is probably due to the aromatic nature of the purine nucleobases. A practical issue with the purine nucleobases is their insolubility in water. While adenine enjoys reasonable solubility, it is almost an order of magnitude lower than that of thymine and uracil, the two most soluble nucleobases [143], Guanine is almost completely insoluble in water at room temperature [143],... 

Becker RS, Kogan G (1980) Photophysical properties of nucleic acid components. 1. The pyrimidines Thymine, uracil, N,N-dimethyl derivatives, and thymidine. Photochemistry and Photobiology 31 5-13. 

Salet C, Bensasson R (1975) Studies on thymine and uracil triplet excited state in acetonitrile and water. Photochemistry and Photobiology 22 231—235. 

Honnas PI, Steen HB (1970) X-ray- and uv-induced excitation of adenine, thymine, and the related nucleosides and nucleotides in solution at 77.deg.K. Photochemistry and Photobiology 11 67-76. 

Figure 16-3. Global picture of the photochemistry of uracil (U), thymine (T), and cytosine (C) as suggested by the CASPT2 calculations. (Reproduced from Ref. [47] with permission from the American Chemical Society)...

The photochemical response of bacterial DNA and of synthetic polynucleotides to UV, and of the influence thereon of Hg " and Ag have been examined [119, 120], The photochemistry of DNA is altered greatly when these metals are bound, but in different ways. Hg " complexed with bacterial DNA greatly reduces the rate of thymine dimerization, whereas Ag" binding to DNA greatly enhances dimerization. Consequently, biological inactivation is increased in the presence of Ag but reduced with Hg ". 

See also Photoreactivation, Photochemistry, Photosystem Summary, Pyrimidine Dimers, Thymine Dimers, Tetrahydrofolate Coenzymes... 

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