Thymine cycloaddition

Other reactions characterized for pyrimidine residues include mercuration at C-5 of cytosine or uracil (Hopman et al., 1986), cycloaddition to the 5,6-double bond of thymine and uracil (Cimino et al., 1985), and thiolation at the C-4 amino group of cytosine (Malcom and Nicolas, 1984). 

Psoralens can react by two different routes upon photoactivation (Parsons, 1980 Pathak, 1984). The first route is through the well-known photoreaction mechanism that principally involves intercalation within double-stranded DNA or RNA with the formation of adducts with adjacent thymine bases. The furan-side and pyrone-side rings in psoralen both can form cycloaddition products with the 5,6-double bond of thymine to create a crosslink between two DNA strands (Reaction 57) or to a lesser extent, within double-strand regions of RNA. 

Phosphonated A.G-nucleosides (659) and (660), containing thymine (a), N -acetyleytosine (d) and fluorouracil (c) have been synthesized in good yields by the 1,3-dipolar cycloaddition methodology (Scheme 2.287) (152). 

An efficient synthesis of the l-aUyl-6-(l, 2, 3 -triazolyl) analogue 170 of 1-[2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (KEPT), an anti-human immunodeficiency virus (HIV) reverse transcriptase inhibitor, was reported using an intermolecular 1,3-dipolar cycloaddition of the azide 169 with acetylenes (35) (Scheme 9.35). Azidouracil (169), when refluxed with an acetylene in equimolar proportions in toluene, gave the corresponding triazoles (170) in excellent yield. 

In a fluid environment the photodimerization of thymine and its derivatives involves cycloaddition at the 5,6-double bond to form one or more of the four possible stereoisomers of the cyclobutane dimer shown... 

Study of the photoreaction of psoralene78 with nucleic acids (DNA) (UV rays, 365 nm) shows that cycloaddition occurs with thymine,... 

An interesting and significant outcome is the finding that the pyrimidine bases of nucleic acids (uracil, thymine, and cytosine) are photoreactive and undergo [2 + 2] cycloadditions on irradiation with ultraviolet light. Thymine, for example, gives a dimer of structure 7 ... 

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]. 

Exposure of DNA to ultraviolet light induces a [2 + 2] cycloaddition reaction between the double bonds of adjacent thymines. The resulting thymine dimer, containing a cyclobutane ring, prevents DNA reproduction and can lead to the development of skin cancer. 

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. 

A [3+2] cycloaddition of fV-3-thymine-substituted enamine 64 with ethoxycarbonyl nitrile oxide, generated in situ from ethyl chloro(hydroxyimino)acetate, gave the dihydroisoxazole 65. Subsequent aromatization and ester-to-amide... 

Bicyclic A(0-Mti-homonucleoside analogues such as 591 were synthesized through 1,3-dipolar cycloaddition of an enantiopure 3-hydroxy-l-pyrroline A -oxide and protected allyl alcohol and subsequent introduction of thymine by a Mitsunobu reaction <2003T5231>. Furthermore, isoxazole, isoxazoline, and isoxazolidine analogues of (7-nucleo-sides such as 592-594 were synthesized by 1,3-dipolar cycloaddition of nitrile oxides and nitrones derived from uracil-5-carbaldehydes with suitable dipolarophiles <2003T4733, 2006T1494>. 

Problem 4.10. The thymine dimer shown in the preceding example is produced by a [2 + 2] cycloaddition of two C=C bonds. A different, perhaps more mutagenic thymine dimer is produced by a different [2 + 2] cycloaddition. Draw a detailed mechanism for the formation of the second type of thymine dimer. 

Single crystals of thymine derivatives with long alkyl-chain substituents are photochemically reactive and undergo (2 + 2) photodimerisation to yield solely the trans-anti dimer. In solution, however, the photoreaction affords the usual four cycloadducts. Irradiation of the bis-thymine PNA dimer (142) brings about intramolecular cycloaddition to give the adduct (143) in 50% yield. The reaction is carried out in water using irradiation at 254 nm. The results from a study of the photochemical cycloaddition within the thymidilyl system (144) has been reported. Photoadducts have been obtained from the... 

Intramolecular photocycloaddition occurs with thymine derivatives and related compounds. Thus, the bis thymine dimer (116) is formed on irradiation at 254 nm of (117). Zinc complexes of 1,4,7,10-tetraazacyclododecane inhibit the intramolecular photodimerisation of the thymidilyl thymidine (118) and the same complexes are active in cleaving cyclobutane systems (119). Conventional (2+2)-cycloaddition does not occur on irradiation of (120) but instead the main product is the cytosine hydrate accompanied by the (6-4)-photoproduct (121). Dimerisation is reported to occur on irradiation in an acidic medium. 

Acetone-sensitized irradiation of uracil (107) with ethene affords the adduct (108) in 75% yield. This compound can be transformed into the cyclobutane derivative (109) in an overall yield of 52%. The intramolecular cyclization of the dinucleotide model (110) has been investigated. The reaction affords the cycloadduct (111) by irradiation using wavelengths > 300 nm. The use of an anionic template for photochemical dimerization of a thymine system has been demonstrated. The thymine forms an assembly (112) with pyrophosphate. Irradiation of this brings about syn- 2 + 2)-cycloaddition of the thymine units. ... 

A biologically significant dimerization of the same type is the (2 + 2)-cycloaddition of pyrimidine bases in deoxyribonucleic acids, which is considered to be at least partly responsible for their observed deactivation upon irradiation with UV light.19 It has been reported that irradiation of thymine yields a (2 + 2)-cycloadduct (133).140 Other thymine and also uracil derivatives behaved similarly.141... 

Exposure to ultraviolet light causes skin cancer. This is one of the reasons why many scientists are concerned about the thinning ozone layer. The ozone layer absorbs ultraviolet radiation high in the atmosphere, protecting organisms on Earth s surface (Section 9.9). One cause of skin cancer is the formation of thymine dimers. At any point in DNA where there are two adjacent thymine residues (Section 27.1), a [2 -f 2] cycloaddition reaction can occur, resulting in the formation of a thymine dimer. Because [2 -I- 2] cycloaddition reactions take place only under photochemical conditions, the reaction takes place only in the presence of ultraviolet light. 

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