DNA free radicals

Dilly O, loemJ B, Vos A, Munch JC (2004) Bacterial diversity in agricultural soils during litter decomposition. Appl Environ Microbiol 70 468-474 Dizdaroglu M (1991) Chemical determination of free radical-induced damage to DNA. Free Radical Biol Med 10 225-242 Eaton RW, Ribbons DW (1982) Metabolism of dimethylphthalate by Micrococcus sp. strain 12B. JBacteriol 151 465-467... 

Breen AP, Murphy JA. Reactions of oxyl radicals with DNA. Free Radic Biol Med 1995 18(6) 1033-1077. 

Cells have two defense systems to cope with free-radical DNA damage that work on very different time scales the fast chemical repair by thiols that occurs at the stage of DNA free-radicals and the slow enzymatic repair that only sets in once the damage is fully set. The present book deals in some detail with the chemical repair. To discuss the even more important enzymatic repair would have exceeded the space allocated to this book, and enzymatic repair is only briefly touched on. 

Thus, in most OH-induced oxidations short-lived adducts must be considered as intermediates. A case in point in the realm of DNA free-radical chemistry is the oxidation of guanine. From the above, it is evident that OH, despite its high reduction potential, cannot be directly used for the study of one-electron oxidation reactions. However, one can make use of its high reduction potential by producing other reactive intermediates [e.g Tl(II) Chap. 10], which no longer undergo an addition to double bonds or H-abstraction. 

In rare cases, the one-electron oxidized products are also readily oxidized, and the three-electron oxidized product is observed. A case in point is the oxidation of the 4-chlorobenzyl radicals by Fe(CN)63 to the corresponding benzaldehyde. The 4-chlorobenzylalcohol is not the intermediate that is further oxidized by Fe(CN)63, and thus the mechanism of the formation of 4-chlorobenzaldehyde is rather complex (Merga et al. 1996). Since Fe(CN)63 is commonly used as a simple and effective oxidant also in DNA free-radical chemistry, such potential complexities have to be kept in mind. 

In DNA free-radical chemistry, N-centered radicals are generated from some nucleobases upon one-electron oxidation (followed by II+ loss). They are also considered as important intermediates in the purine free-radical chemistry. It is, therefore, worthwhile to address very briefly some of the chemistry of N- centered radicals that were encountered in amines and amino acids. 

In DNA free-radical chemistry allylperoxyl radicals play a major role in the free-radical-induced oxidation of Thy. Thus far, this kind of rearrangement has not yet been observed (but also not especially looked for) in this system. 

Competitive scavenging of reactive free radicals, such as OH, by DNA and other substrates, is a very important aspect of DNA free-radical chemistry. This situation has been modeled by various approaches (van Rijn et al. 1985 Lafleur and Loman 1986 Verberne et al. 1987). The most recent model has been developed by Udovicic et al. (1991). 

The reduction and oxidation of radicals are discussed in Chapter. 6.3-6.5. That in the case of radicals derived from charged polymers the special effect of repulsion can play a dramatic role was mentioned above, when the reduction of poly(U)-derived base radicals by thiols was discussed. Beyond the common oxidation and reduction of radicals by transition metal ions, an unexpected effect of very low concentrations of iron ions was observed in the case of poly(acrylic acid) (Ulanski et al. 1996c). Radical-induced chain scission yields were poorly reproducible, but when the glass ware had been washed with EDTA to eliminate traces of transition metal ions, notably iron, from its surface, results became reproducible. In fact, the addition of 1 x 10 6 mol dm3 Fe2+ reduces in a pulse radiolysis experiment the amplitude of conductivity increase (a measure of the yield of chain scission Chap. 13.3) more than tenfold and also causes a significant increase in the rate of the chain-breaking process. In further experiments, this dramatic effect of low iron concentrations was confirmed by measuring the chain scission yields by a different method. At present, the underlying reactions are not yet understood. These data are, however, of some potential relevance to DNA free-radical chemistry, since the presence of adventitious transition metal ions is difficult to avoid. 

Thus the rate of HO2 -elimination must be considerably slower (nearer to 1 s 1), but still fast enough to play a role in DNA free-radical chemistry. Reaction (172) is reminescent of the H02--elimination from 3-hydroxycyclohexadienylperoxyl radicals (derived from the reaction of OH with benzene in the presence of 02 Chap. 8.4). In this system, the reaction is much faster (k = 800 s 1 Pan et al. 1993b) possibly due to the gain in energy in the course of the re-aromatiza-tion]. 

These reactions are only trivial as far as their chemistry is concerned (recombination of radicals and subsequent water elimination). This does not mean, however, that these reactions are of little importance in cellular-DNA free-radical chemistry. 

The photolysis of 5BrUra-substituted DNA has been widely used as tool to study certain aspects of DNA free-radical chemistry. The basic reactions that occur on the nucleobase to nucleotide level are discussed in Chapter 10.7. Some of the primary reactions seem to be different on going from the nucleotide level to dsDNA (Chap. 12.6). Experiments with ssODNs are quite limited. 

Symons MCR (1997) Electron movement through proteins and DNA. Free Radical Biol Med 22 1271-1276... 

When talking about research, I must mention Mrs. Rita Wagner, a superb technician that looked after my laboratory and the younger Ph.D. students for about 25 years. Some of her fine work is referred to here. I have often been envied for being so lucky to have had her. It was also very fortunate that Heinz-Peter Schuchmann joined my group soon after my start at the MPI. His competence complemented mine extremely well, and this allowed us to carry out various projects that would not have been possible for either of us on our own. When Dietrich Schulte-Frohlinde was director, DNA free-radical research was the main research topic of the MPI, and our groups collaborated very closely for many years. With Peter Schuchmann and Dietrich Schulte-Frohlinde common interests beyond science led to a continuing friendship. 

Tofigh S, Frenkel K. 1989. Effects of metals on nucleoside hydroperoxide, a product of ionizing radiation in DNA. Free Radic Biol Med 7 131-143. 

Much research has been carried out towards the identification of DNA-derived radicals formed after reaction with OH radicals or other one-electron oxidants. The main features of DNA free radical chemistry have been reasonably well established from studies performed on DNA itself as well as on model systems including nucleobases, sugars, nucleosides and nucleotides, poly-U, poly-A, and DNA oligomers. ... 

Some peroxyl radicals release HO /O spontaneously and/or base-induced [OH and/or buffers cf. reactions (41), (45) and (47)], and nearly all peroxyl radicals give rise in one of their bimole-cular routes (the oxyl radical pathway) to radicals that are capable of undergoing such reactions. For DNA free-radical chemistry, the formation of HO /O/ is an interesting reaction insofar as 0 that dominates at neutral pH [pJdiffusing radical and may react with the much less mobile DNA radicals. 0 is a rather long-lived radical, as in a cellular environment there are only few sinks... 

Box H.C., Dawidzik J.B., Budzinski E.E., Free radical-induced double lesions in DNA, Free Radic. Biol. Med., 2001,31,856-868. 

Debije M.G., Bernhard W.A., Thermally stable sites for electron capture in directly ionized DNA free radicals produced by the net gain of hydrogen a C5/C6 of cytosine and thymine in crystalline oligodeoxynucleotides. J. Phys. Chem. A, 2002,106,4608-4615. 

ESCODD (2002) Inter-laboratory validation of procedures for measuring 8-oxo-7,8-di-hydroguanine/8-oxo-7,8-dihydro-2 -deoxyguanosine in DNA. Free Radic Res 36 239-45 ESCODD (2003) Measurement of DNA oxidation in human cells by chromatographic and enzymic methods. Free Radic Biol Med 34 1089-99... 

Poulsen HE, Loft S (1998) Interpretation of oxidative DNA modification Relation between tissue levels, excretion of urinary repair products and single cell gel electrophoresis (comet assay). In Aruoma 01, Halliwell B (eds) DNA free radicals Techniques, mechanisms and applications. OICA International, London, pp 261-70 Poulsen HE, Loft S, Weimann A (2000) Urinary measurement of 8-oxodG (8-oxo-2 -de-oxyguanosine). In Lunec J, Griffiths HR (eds) Measuring in vivo oxidative damage a practical approach. Wiley, London, pp 69-80... 

The identification of drugs that might overcome the problem of the reduced radiation sensitivity of sub-populations of tumour cells at low oxygen tensions was a triumph of radiation chemistry [9]. Several pieces of evidence pointed to the possibility that the radiosensitizing effect of oxygen involved short-lived DNA free radicals and that chemical substitutes for oxygen could be found that might be therapeutically useful. 

Free radicals seek to combine with electrons from stable compounds and thus produce more free radicals in the process. The cell membrane is one of the most vulnerable structures to free radical damage. Also affected are low-density lipoproteins, other proteins, and DNA. Free radicals alter functions of these molecules or cause mutations in DNA. There are mechanisms in place to repair free radical damage, but the repair is not completely effective and becomes less so with age. The result is heart disease, cancer, arthritis, cataracts, and aged skin (Elson, 2009). 

Braun, A.P. and Schubnan, H. 1995. The multifunctional calcium/calmodulin-dependent protein kinase From form to function. Annu. Rev. Physiol. 57 417-445 Breen, A.P. and Murphy, J.A. 1995. Reactions of oxyl radicals with DNA. Free Radic. Biol. Med. 18 1033-1077... 

Jaruga P, Kirkali G, Dizdaroglu M. Measurement of formamidopyrimidines in DNA. Free Radic Biol Med 2008 45 1601-1609. 

Palit S, Sharma A, Talukder G (1991) Cytotoxic effects of cobalt chloride on mouse bone marrow cells in vivo. Cytobios 68 85-89 Park L-W, Floyd RA (1992) Lipid peroxidation products mediate the formation of 8-hydroxydeoxyguanosine in DNA. Free Radic Biol Med 12 245-250 Peskin AV, Shlyahova L (1986) Cell nuclei generate DNA-nicking superoxide radicals. FEBS Lett 194 317-321... 

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