DNA radicals

Damage Amplification Reaction of DNA Radical Intermediates with Proximal DNA Bases and Sugars... 

In some circumstances, DNA radical lesions can react with an adjacent base or the sugar residues. In these cases, a single radical hit can be transformed into two adjacent damage sites on the DNA. The resulting tandem lesions may present special challenges to DNA replication and repair systems. ... 

With regard to electron transfer in DNA radical anions (as opposed to HT in the radical cations), the hopping mechanism involves the intermediacy of radical anions of the Cand Tbases which have similar reduction potentials. Since one of these bases is present in each base pair, it is predicted that ET proceeding by the hopping mechanism would not be sequence dependent.1451 This important prediction has yet to be verified. 

Sevilla et al. [49] have simulated the EPR spectrum of whole DNA equilibrated with D2O irradiated and observed at 77 K. The results were 77% Cyt and 23% Thy for the anions and >90% Gua for the cations. The analysis produced a small imbalance in the cations (44%) and anions (56%). It was suggested that some holes remain trapped in the solvation shell. It is also possible that this reflects small errors in the treatment of the basis spectra, or that some DNA radicals are not accounted for because their EPR signal is too broad and poorly resolved. 

Cai et al. [7d] studied the effect of the level of DNA hydration on electron and hole transfer in the MX-DNA system. ESR spectra show that MX radicals decrease relative to the DNA radicals with increasing hydration levels up to r=22 D20/nucleotide. The results further indicate that, as the hydration level increases up to F=22 D20/nucleotide, the interduplex distance D s increases. This results in a substantial decrease in the apparent transfer distances as well as electron and hole transfer rates. Figure 9 shows plots of the transfer rates of electrons, holes, and overall DNA radicals at 77 K vs hydration levels (lower axis) as well as vs the distance between DNA ds s (upper axis). Please note that at hydration levels higher than 22 D20/nucleotide, a... 

Table 2 Results of A(1 )> nd for overall DNA radicals transfer in various...

Scheme 19.—Possible Reactions of One of the Radical Cations Derived from the DNA Radical at C-4. ...

Since DNA is a highly charged polyanion, it is always hydrated by water molecules [in the dry state (under moist air) it contains 12 water molecules per nucleotide subunit]. In a cellular environment, proteins (histones in eukaryotic cells) are always attached to DNA or are at least surrounded by proteins as in viruses. In order to attack DNA, radicals have to be sufficiently mobile in such a partially hydrophilic environment. For this reason, typical lipid radicals confined to the membranes will not be discussed here, although one must keep in mind that small fragments of free-radical nature maybe able to escape the lipid environment and can, in principle, also react with DNA. 

The C-H BDE in peptides is even lower than that of the S-H BDE in thiols as a consequence of the exceptional stability of the radical products due to captoda-tive stabilization (Viehe et al. 1985 Armstrong et al. 1996). Yet, the observed rate constants for the reaction of CH3 and CH2OH with, e.g., alanine anhydride are markedly slower than with a thiol. This behavior has been discussed in terms of the charge and spin polarization in the transition state, as determined by AIM analysis, and in terms of orbital interaction theory (Reid et al. 2003). With respect to the repair of DNA radicals by neighboring proteins, it follows that the reaction must be slow although thermodynamically favorable. 

The (oxidizing) a-carboxyalkyl radicals do not react readily with thiols (Table 6.4). They are, however, rapidly reduced by thiolate ions [reaction (20)]. The reactions of thiols with DNA radicals play a very important role in the chemical repair of DNA radicals in cells (Chaps 12.10 and 12.11). The reversibility of the H-donation of thiols, that is, H-abstraction by thiyl radicals, is discussed in Chapter 7.4. 

The chemistries of nitrogen-centered and sulfur-centered radicals have been reviewed in detail (Alfassi 1997, 1999), and here only some aspects can be discussed that seem pertinent to the formation, reactions and repair of DNA radicals. 

When the amino group is fully deprotonated, the rate of the H-transfer is 1.5 x 10s s4, but also around pH 7 the reaction is still fast, at the ms timescale (for a quantum mechanical study see Rauk et al. 2001). Upon the decay of the amnioal-kyl radicals formed in reaction (35) ammonia as formed in a yield that points to disproportionation as the major process (Zhao et al. 1997). The fact that the ami-noalkyl radical is the thermodynamically favored species does not mean that the repair of DNA radicals by GSH (Chap. 12.11) is not due to its action as a thiol. As with many other examples described in this book, the much faster kinetics that lead to a metastable intermediate (here the formation of the thiyl radical) rather than the thermodynamics as determined by the most stable species (here the aminoalkyl radical) determine the pathway the the reaction. In fact, the C-H BDE of the peptide linkage is lower than the S-H BDE and repair of DNA radicals by peptides, e.g., proteins would be thermodynamically favored over a repair by thiols but this reaction is retarded kinetically (Reid et al. 2003a,b). 

Disulfide radical anions are rather strong reductants (E = -1.7 V Wardman 1989), and it has hence been proposed that in cellular systems these intermediates may contribute to the repair of DNA radicals (Priitz 1989). 

For DNA in cells and in the absence of O2, one has to take into account that the lifetime of the DNA radicals is not determined by their bimolecular decay but rather by their reaction with the cellular thiols, mainly GSH (Chap. 12.11). In the presence of 02, the situation becomes more complex, and the lifetime of the DNA peroxyl radicals is as yet not ascertained. It is expected to be consider-... 

Brustad T, Jones WBG, Nakken KF (1971) On the binding of an organic nitroxide free radical to radiation-induced deoxyribonucleic acid (DNA) radicals under anoxic conditions. Int J Radiat Phys Chem 3 55-61... 

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. 

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