Pyrimidine bases, photochemical

Reeve, A. E., and Hopkins, T. R., 1980, Photochemical reaction between protein and nucleic acids photoaddltlon of tryptophan to pyrimidine bases, Photochem. Photobiol. 31 297. 

It is well known that pyrimidine bases convert to photodimers upon irradiation to UV light near the X max( > 270 nm). This photochemical reaction has a lethal effect in biological systems due to the photochemical transformation of pyrimidine bases of nucleic acids. However the photodimerization is a reversible reaction and the photodimers split to afford the original monomers very efficiently upon irradiation at a shorter wavelengths as shown in Scheme 1(1). 

This knowledge regarding the efficient photochemical dimerization of the pyrimidine bases, led us to study, in detail, both the intramolecular... 

All these bases absorb around 260 nm. Thymine and cytosine are most sensitive to irradiation. Two most important types of photochemical reactions that have been observed for these pyrimidine bases are photohydration and photodimerization. In vivo systems, interactions between protons and nucleic acids can also be initiated by radiations of wavelength dlorter than 300 nm. 

Figure 5.25 The photochemical reaction between 8-methoxypsoralene and a pyrimidine base...

Another type of photochemical reaction involving a pyrimidine base is the addition of a molecule of water across the 5,6 double bond of C to yield a 5,6-dihydro-6-hydroxy derivative called the cytosine hydrate. The quantum yield for the formation of cytosine hydrates in UV-irradiated DNA is greater in single-stranded than in duplex-DNA (45). Hydrates of cytosine, deoxycytidine, CMP, or dCMP are unstable, readily reverting to the parent form by rehydration (45). However, their half-life is dramatically increased in DNA, and cytosine hydrate may be the major nondimer C photoproduct. Cytosine hydrate can undergo deamination and dehydration to yield uracil (1). The hydrate of 5-methylcytosine may undergo deamination to yield 5-thymine hydrate, which can convert to thymine upon dehydration (1). 

The photophysical behaviour of a series of methylated angelicins has been recorded using flash photochemical techniques. Irradiation of the complex formed between 4,6-dimethyltetrahydrobenzoangelicin and DNA results in the formation of cycloadducts. These arise by addition between the pyrimidine bases, thymine and cytosine and the furan ring of the angelicin. 

Cimino and co-workers (C4, 12) developed a post-PCR photochemical procedure for the inactivation of polynucleotides. The procedure is based upon the blockage of Tag DNA polymerase when it encounters a photochemically modified base in a polynucleotide strand. Isopsoralen reagents that are added to a reaction mixture prior to amplification tolerate the thermal cycles, are photoactivated after amplification, and form cyclobutane adducts with pyrimidine bases in the DNA. 

Many natural products contain the coumarin structure [28]. Aesculetin 15 is extracted from horse chestnuts and psoralen 16 from the Indian plant Psoralea corylifolia. Furocoumarins such as 16 are photochemically active. On UV irradiation, they induce processes in the cell which lead to an increase in skin pigmentation and inhibition of cell division. This is due to the formation of cyclobutane with the pyrimidine bases of nucleic acids. Psoralens are used in the treatment of psoriasis. 

Scheme 1.12 Pathways of photochemical damage to pyrimidine bases fonnation of a thymine-thymine adducts b thymine-cytosine adducts...

When DNA is exposed to radiation at wavelengths of about 260 nm, adjacent pyrimidines become covalently linked by the formation of a four-member ring structure resulting from the saturation of their respective C5, C6 double bonds. The structure formed by this photochemical cycloaddition is referred to as a pyrimidine dimer. The pyrimidine bases in DNA are thymine and cytosine. 

Pyrimidine bases such as uracil and thymine are known to form photodimers with ejqmsure to UV light (2). It seemed interesting to e]q>lore the photochemical reaction of the pyrimidine bases to the photolithographic process in microelectronics fabrication technology. 

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. 

Photochemical reactions of the pyrimidine polymers in solution were studied to determine the quantum yields of the intramolecular photodimerization of the pyrimidine units along the polymer chains. Photoreactions of the polymers were carried out in very dilute solutions to avoid an intermolecular(interchain) photodimerization. Quantum yields determined at 280 nm for the polymers (1-6 in Figure 1) are listed in Table I. The quantum yield of the 5-bromouracil polymer [poly(MAOU-5Br)] could not be determined because of side reactions of the base during the irradiation. 

An unusual photochemical reaction of 2-pyridones, 2-aminopyridinium salts and pyran-2-ones is photodimerization to give the so-called butterfly dimers. These transformations are outlined in equations (13) and (14). Photodimerization by [2+2] cyclization is also a common and important reaction with these compounds. It has been the subject of particular study in pyrimidines, especially thymine, as irradiation of nucleic acids at ca. 260 nm effects photodimerization (e.g. equation 15) this in turn changes the regular hydrogen bonding pattern between bases on two chains and hence part of the double helix structure is disrupted. The dimerization is reversed if the DNA binds to an enzyme and this enzyme-DNA complex is irradiated at 300-500 nm. Many other examples of [2+2] photodimerization are known and it has recently been shown that 1,4-dithiin behaves similarly (equation 16) (82TL2651). 

Gajewski E, Fuciarelli AF, Dizdaroglu M (1988) Structure of hydroxyl radical-induced DNA-protein crosslinks in calf thymus nucleohistone in vitro. Int J Radiat Biol 54 445-459 Gajewski E, Rao G, Nackerdien Z, Dizdaroglu M (1990) Modification of DNA bases in mammalian chromatin by radiation-generated free radicals. Biochemistry 29 7876-7882 Garner A, Scholes G (1985) Mechanism of the photohydration of pyrimidines a flash photolysis study. Photochem Photobiol 41 259-265... 

The photochemical stability of the nucleic acid bases under UV irradiation is no longer a major concern after the formation of the ozone layer, and the role of the state in the form of modern life is significantly reduced. However, Kohler s group suspects that the tt state might still be involved in the formation of photohydrates and pyrimidine/pyrimidine photoproducts, while the formation of... 

The DNA bases involved in reproduction have short S excited state lifetimes of the order of one picosecond or less [13, 15, 19, 23, 73-75], It has been argued that this phenomenon serves to protect these bases against photochemical damage, because following excitation they do not cross to the reactive triplet state, but instead they rapidly internally convert to the electronic ground state [76], This may have been particularly significant under the conditions of the early earth when purines and pyrimidines presumably were assembled into the first macromolecular structures, producing RNA. 

An example of direct repair is the photochemical cleavage of pyrimidine dimers. Nearly all cells contain a photoreactivating enzyme called DNA photolyase. The E. coli enzyme, a 35-kd protein that contains bound N lO-methenyltetrahydrofolate and flavin adenine dinucleotide cofactors, binds to the distorted region of DNA. The enzyme uses light energy—specifically, the absorption of a photon by the N, N lO-methenyltetrahydrofolate coenzyme—to form an excited state that cleaves the dimer into its original bases. 

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