Lesions nucleobase

The negative selective pressure imposed by lesion nucleobases has driven the evolution of repair pathways dedicated to recognition and removal of base lesions, followed by restoration of the original DNA sequence-(Lindahl, 1993). The major pathway for this type of repair (Fig. 1) is initiated by the excision of a damaged base and is therefore known as base excision DNA repair (BER). Another repair pathway, nucleotide excision repair (NER), can also repair some lesion nucleobases that severely distort the DNA helix. The NER pathway is discussed in Chapter 2. 

Under low oxygen conditions, C5 -sugar radicals can react with the base residue on the same nucleotide. In purine nucleotides, the carbon-centered radical 91 can add to the C8-position of the nucleobase (Scheme 8.31). Oxidation of the intermediate nucleobase radical 92 yields the 8,5 -cyclo-2 -deoxypurine lesion 93197,224,225,230-233 Similarly, in pyrimidine nucleotides, the C5 -radical can add to the C6-position of nucleobase. Reduction of the resulting radical intermediate yields the 5, 6-cyclo-5,6-dihydro-2 -deoxypyrimidine lesion 94,234-236... 

Electron donation to nucleobases is a fundamental process exploited by nature to achieve the efficient repair of UV induced lesions in DNA [27, 28]. Nature developed to this end two enzymes, CPD photolyases and (6-4) photolyases, which both inject electrons into the UV damaged DNA bases [29, 30]. Both enzymes are, in many species, including plants, essential for the repair of the UV-light induced DNA lesions depicted in Scheme 1 [31]. 

Although the reduction potentials of DNA bases and UV induced DNA lesions inside a DNA double strand or inside the active site of a DNA photolyase, together with the reduction potential of the photoexcited FADH- in the photolyases, are not known, currently available redox potentials indicate that the single electron reduction of a nucleobase or a UV induced dimer lesion by a reduced and deprotonated flavin coenzyme is a weakly exothermic process. The reduced and deprotonated FADH- in its photoexcited state is... 

In general, reduction potentials of nucleobases have been studied much less than their oxidation potentials, and in particular water-based data are rather lacking [2, 35]. We therefore listed the available polarographic potentials measured in dimethylformamide and data obtained from pulse radiolysis studies or fluorescence quenching measurements. From the data in Table 1, it is evident that the pyrimidine bases are most easily reduced. The reduction potential of the T=T CPD lesion is close to the estimated value of the undamaged thymine base [34, 36]. 

The conversion of the monofunctional adducts into bifunctional lesions depends drastically on the structure of the Pt drug. Obviously, Pt compounds exhibiting trans geometry form different bisadducts than cisplatin and hence, a different spectrum of antitumor activity is expected. Mechanistically, the formation and possible isomerization of bisadducts are not well understood. The assumption that hydrolysis of the second leaving group controls the formation of bisadduct may be an oversimplification. Studies with model compounds as well as with oligonucleotides have indicated that a certain nucleobase may be a powerful nucleophile toward Pt(II) if spatially in a correct position. Unfortunately, our knowledge on these interactions is at present very limited. 

A number of studies are concerned with the free-radical reactions of typical nucleobase lesions. For example, the cyclobutane-type Thy dimer can be split by one-electron reduction [Heelis et al. 1992 reactions (307) and (308)], a process that is relevant to the repair of this typical UV-damage by the photoreactivating enzyme (photolyase, for a review see Carrell et al. 2001, for the energetics of the complex reaction sequence, see Popovic et al. 2002). At 77 K, the dimer radical anion is sufficiently long-lived to be detectable by EPR (Pezeshk et al. 1996). 

Besides inducing a Fenton-type (i.e., free-radical) chemistry, H2O2 (at high concentrations) can oxidize nucleobases, and in the case of Ade and its derivatives the formation of the N7-oxide has been reported (Rhaese 1968), and further reactions seem to occur as well. This lesion, now attributed to the N1-oxide [reaction (50)], has been detected by the 32P-postlabelling technique (Mouret et al. 1990) and polyclonal antibodies have been raised to detect this lesion in oxidized DNA (Signorini et al. 1998). 

As mentioned briefly above, the enzymatic excision of damaged nucleobases may cause some problems. A case in point is the action of nuclease PI. While a single 8-oxo-G lesion is excised as the damaged nucleoside, the clustered 8-oxo-G/Fo lesion is only obtained as modified dinucleotide (Maccubbin et al. 1992). Another example is the hydrolysis of dG pC which severely inhibits the action of bovine spleen phosphodiesterase, while HMUrapA shows only very little inhibition (Maccubbin et al. 1991). Enzymatic hydrolysis of DNA is, in fact, the recommended method for the determination of HMUra (Teebor et al. 1984 Frenkel et al. 1985). It is recalled that mammalian cells cope with this DNA lesion with the help of a hydroxymethyluracil glycosylase (Hollstein et al. 1984). 

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]. 

Because of the complex structure of DNA various damage pathways are possible. The most important lesions are caused by radical species or UV irradiation, which can affect the sugar backbone, the nucleobases, or both. These lesions, if not repaired, can contribute to mutagenesis, carcinogenesis, aging, inherited disease, and cell death. 

Pt-NMR chemical shifts in the -3000 ppm region, indicative of a [N3S] mixed-donor environment of platinum, confirm the monofunctional nature of the above Pt-nucleobase adducts. This ultimately prevents the formation of a bifunctional (cytotoxic) lesion on target DNA, in accordance with the lack of in vitro cytotoxicity found in L1210 leukemia cells (7DW >... 

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. 

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... 

Many other guanosine lesions have been investigated, the majority of which are those derived from polyaromatic hydrocarbons (PAHs), though adducts with smaller reactive species are also reported. Reaction with aldehydes, such as acrolein and crotonaldehyde leads to the formation of propano-dG adducts such as (86) and its a- and y-hydroxy derivatives as well as ring-opened derivatives like (87). Derivatives (87) can further react with other nucleobases, particularly guanine, leading to crosslinking. The reaction with aldehydes is... 

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