Nucleobase radical cations

In the direct effect of ionizing radiation on DNA, radical cations are the primary products (Chap. 12). For this reason, their reactions are of considerable interest. Obviously, photoionization (e.g., at 193 nm) and laser multi-photon excitation leads to such species (e.g., Candeias and Steenken 1992b Malone et al. 1995 Chap. 2.2). Base radical cation electron pairs have been proposed to be the first observable intermediates with a lifetime of 10 ps for Ade and four times longer for the other nucleobases (Reuther et al. 2000). Radical cations are also assumed to be intermediates in the reactions of photosensitization reactions with qui-nones, benzophenone, phthalocyanine and riboflavin (Cadet et al. 1983a Decar-roz et al. 1987 Krishna et al. 1987 Ravanat et al. 1991, 1992 Buchko et al. 1993 Douki and Cadet 1999 Ma et al. 2000). Nucleobase radical cations may be produced by electrochemical oxidation (Nishimoto et al. 1992 Hatta et al. 2001) or with strongly oxidizing radicals (for a compilation of their reduction potentials see Chap. 5.3). Rate constants are compiled in Table 10.3. 

Usually, radical cations have much lower pfCa values than their parent compounds. A typical examples is phenol, whose pfCa value is at 10 while that of its radical cation is at -2 (Dixon and Murphy 1976). Thus in this case, ionization causes an increase in acidity by 12 orders of magnitude. It is hence expected that also the nucleobase radical cations should be much stronger acids than their parents. This has indeed been found in all systems where equilibrium conditions are established, and the consequences for DNA base pairs have been discussed (Steenken 1992). 

Photooxidation of purine nucleosides and also of Cyt by pyrimido[5,4-g]pteridine N-oxide under argon affords in high yields the 5 -0,8-cyclopurine nucleosides and 5 -0,6-cyclocytidne, whereby the N-oxidc is reduced (Sako et al. 1986). Nucleobase radical cations are believed to be the intermediates in this surprising oxidation reaction. 

The effect of other inorganic radicals on the nucleobases, apart from the water radicals mentioned above, has repeatedly been studied, for instance the sulfate radical which has been used to generate nucleobase radical cations with the aim to mimic the direct effect of ionizing radiation on DNA. Carbon-centred... 

In this context, in the narrow sense the term nucleobase radical cation signifies a species identical to that which is produced upon one-electron oxidation of the base. Its deprotonation leads to a radical whose unpaired spin is largely heteroatom-sited. Reprotonation of this radical could in principle give rise to radical cations that are not identical but tautomeric to the original radical cation. 

Direct hydrogen atom abstraction occurs less frequently from the nucle-obases, despite the expected modest carbon—hydrogen bond dissociation energy of the carbon—hydrogen bonds in the methyl groups of thymidine and 5-methyl-2 -deoxycytidine due to resonance stabilization of the incipient radicals. The respective radicals are also formed by deprotonation of the nucleobase radical cations, intermediates involved in electron transfer that are produced via one-electron oxidation. Amine radicals are also postulated as intermediates produced from the spontaneous decomposition of chloramines that arise from reactions of nucleosides with hypochlorous acid." " However, the majority of nucleobase radical intermediates arise from the... 

Only the first deprotonation product of the cationic nucleobase radical needed to be considered to obtain the appropriate trends in potential, which were verified by testing whether electrocatalytic oxidation was observed with metal complexes of appropriate potential. 

Major emphasis has been on the isolation and identification of the main decomposition products arising from one electron oxidation reactions with the pyrimidine and purine bases of isolated DNA and related model compounds13,14D. In recent years, major interest has been devoted on the delineation of the mechanistic features of charge transfer within double stranded DNA. This is mostly achieved using defined-sequence oligonucleotides in which radical cations are generated in most cases by photo-ionization of selected nucleobases and 2-deoxyribose. For more information on these systems, the reader is encouraged to read the recent review article by Cadet et al.134 and other references mentioned there in. 

Similar effects are observed with the nucleobase-derived radical cations (Chap. 10.2). 

Gua has the lowest reduction potential among the four nucleobases (Table 10.2), and hence it is preferentially oxidized to its radical cation (for the calculation of ionization potentials of the DNA bases see Close 2004 Crespo-Hernandez et al. 2004), and this property makes Gua and its derivatives to stick out of the other nucleobases with respect to its different free-radical chemistry. In contrast, Thy and Cyt are good electron acceptors, while the purines are only poor ones in comparison (for the calculation of electron affinities, see Richardson et al. 2004). This is of special importance in the effects caused by the absorption of ionizing radiation by DNA. 

Short-lived adducts may be formed as intermediates in the reactions of the oxidizing inorganic radicals with the nucleobases, and it is therefore not always fully excluded that processes observed at very short times and attributed to the reactions of radical cations are in fact due to such intermediates. It may be mentioned that, for example, a long-lived S04 -adduct is observed in the reaction of S04, with maleic acid (Norman et al. 1970). It has been suggested that S04, in its reactions with the pyrimidines forms only an adduct and does not give rise to radical cations (Lomoth et al. 1999). The observation of heteroatom-centered radicals by EPR from the nucleobases Ura, Thy and Cyt (Catterall et al. 1992) as well as dCyd (Hildenbrand et al. 1989) (see below) has been taken as evidence that in the reaction of S04 with pyrimidines radical cations are likely, albeit... 

The radical anions may be formed by reacting the nucleobases with eaq which may be either generated radiolytically or in a two-step reaction, e.g in the laser flash photolysis of anthraquinonedisulfonate in the presence of pyrimidines (yielding the pyrimidine radical cation and an anthraquinonedisulfonate radical anion) and subsequent photoionization of the anthraquinonedisulfonate radical anion (Lii et al. 2001). The latter approach, combined with Fourier transform EPR spectroscopy, yielded detailed information as to the conformation of the radical anions of Ura and Thy in aqueous solution (for a discussion see Close 2002 Naumov and Beckert 2002). Similarly valuable EPR information has been obtained from y-irradiated single crystals (cf. Box and Budzinski 1975 Boxet al. 1975 Sagstuen et al. 1998). 

Deeble DJ, Schuchmann MN, Steenken S, von Sonntag C (1990) Direct evidence for the formation of thymine radical cations from the reaction of SO/" with thymine derivatives a pulse radiolysis study with optical and conductance detection. J Phys Chem 94 8186-8192 DeFelippis MR, Murthy CP, Faraggi M, Klapper MH (1989) Pulse radiolytic measurement of redox potentials the tyrosine and tryptophan radicals. Biochemistry 28 4847-4853 Delatour T, Douki T, D Ham C, Cadet J (1998) Photosensitization of thymine nucleobase by benzo-phenone through energy transfer, hydrogen abstraction and one-electron oxidation. J Photo-chem Photobiol 44 191-198... 

The OH-adduct radicals can become deprotonated at nitrogen. As a consequence of this, water is eliminated from the adduct. This reaction results in the formation of a heteroatom-centered, oxidizing radical e.g. reaction (11)] this may also be formed directly from the deprotonated nucleobase at higher pH [reaction (10)]. At high pH, this radical can undergo a second deprotonation [reaction (12)]. However, this radical anion is not the thermodynamically favoured species under these conditions, and is subsequently reprotonated at carbon (i.e. the heteroatom-protonated acid has a lower p a value than its carbon-protonated isomer) [reaction (14)]. The hydroxyl group can also be eliminated by acid catalysis, which gives rise to a radical cation. These reactions will be discussed below in a separate section. 

The observation of heteroatom-centered radicals by EPR from the nucleobases uracil, thymine [cf. reactions (94) and (95)], cytosine [23, 99] as well as 2 -deoxycytidine [21, 99] is evidence that a radical cation is indeed a likely intermediate in the reaction of the sulfate radical with pyrimidines. 

Some of these activated species like HO Cu -hydroperoxo, or Cu -hydroxo have been also proposed in the case of the oxidations of the DNA nucleobases (55). Various mechanisms like HO addition on a double-bound, hydrogen abstraction on the methyl groups or electron transfer induce nucleobases oxidations and copper complexes are oxidant enough to perform them, but, in the presence of excess of reductants, such as in the conditions often used during DNA oxidation by copper complexes, oxidized nucleobases (base radicals and radical cations) may be reduced back to undamaged species. Thus the ability of copper complexes to oxidize nucleobases could be underestimated. 

Fig. 4.1 Spin densities of a guanine-cytosine dimer radical cation, (GC)j. a KS-DFT supramole-cular calculation using PW91 functional, b FDE calculation considering two subsystems where the left side subsystems blue contour) is positively charged and c FDE calculation for four subsystems with one subsystems blue contour) is positively charged. The nucleobases structures and spin densities were taken from Ref. [48]...

Laser flash photolysis of tetrachloroquinone at 355 nm produces the triplet state, which is highly reactive towards thymine or uracil. Hydrogen abstraction competes with electron transfer, leading to the ketyl radical and the radical anion, respectively. The concomitantly produced nucleobase radicals and radical cations are expected to induce oxidative or strand cleavage damage to DNA. ... 

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