Single base damage

Simulation of frank SSBs and base damage as expressed by ALS has been achieved with the RADACK (RADiation attACK) procedure (Begusova et al. 2001b). This takes into account that the various nucleobases and the hydrogens of the sugar moiety react with different rate constants. The effect is shown in Fig. 12.4, where B-DNA is represented in a space-filling model with only the reactive atoms represented, with the same atoms but with sizes according to their OH cross-section or with the non-reactive atoms re-added. It is the last structure that- OH encounters in the RADACK procedure. 

The variations in the probability of damage induction calculated with RADACK are well reflected in the variation of frank SSBs and damaged bases (as expressed by ALS) for different forms of DNA B-DNA (Fig. 12.5), Z-DNA (Tartier et al. 1994 Fig. 12.6) and for a DNA quadruplex (Tartier et al. 1998). The yield of OH-induced frank SSBs of various topoisomers of DNA minicircles is the same (Culard et al. 1994). It has been concluded that the accessibility of H4 is already sufficient in the relaxed topoisomer that an increase in accessibility in the T-2 topoisomer would be without effect. 

Nearly all modifications that have been detected on the model level (Chap. 10) are also found in free-radical damaged DNA. Obviously the DNA-bound lesions are much more difficult to detect, and there is an ongoing discussion as to the best procedure of their excision (Chap. 13.2 for a review on the excision and repair of base lesions in vivo see Wallace, 2002). Mechanistic details concerning the formation of the base lesions have been discussed in Chapters 10 and 11, and only some additional information will be given below and in the section on clustered lesions where the phenomenon of tandem lesions, two damaged bases that are formed side by side, is dealt with. The yields of damaged bases formed upon y-irradiation in aqueous solution, as has been determined by the GC-MS/SIM technique, are compiled in Table 12.5. 

As can be seen from this table, the detectable products amount to 35% of OH at most. Moreover, dsDNA gave rise to markedly lower yields than ssDNA. Whether this is due to incomplete OH scavenging in these systems due to low-molecular-weight impurities is as yet unknown. Obviously, as we know from other studies, there are more products formed such as Iz, Z, cA, cG, 5HmU, 5ForU, Fo and hydantoin lesions (see below) than have been determined in this study. Moreover, there is an attack of OH at the sugar moiety that is generally believed not to exceed 20% by much (see, however, Sect. 12.4.4). Thus, there is a gap in the material balance. The material balance is especially poor in the absence of 02. 

It is noteworthy that some product yields do not change very much whether the solutions were saturated with air or with N2O/O2, despite the fact that the OH yield is halved in air-saturated solutions (cases in point are for ssDNA and in the units of Table 12.5 Cg (37.9), Tg (43.4), 8-oxo-G (62.0) for further values see Fuciarelli et al. 1990). Whether this means that (V- that is an abundant and freely diffusing radical under such conditions plays an important role in the 

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As to the severity of the above lesions, it is important to note that single base damages, SSBs and even DSBs do not necessarily constitute a lethal damage (Table 12.1). 

In regard with NER, at least 32 proteins, forming several complexes, are necessary and sufficient in a successful repair of a bulky lesion. In the case of BER, 5-6 proteins are necessary to reconstitute the entire process on a single base damage [7]. For both systems, the action ofthe proteins or complexes is coordinated and protein interactions allow passing from one step to the next one. Thus, free repair intermediates which could be entry sites for nucleases that would degrade DNA, are avoided. 

The mammalian process of base excision repair (BER) deals with most single base damages and abasic sites and acts on both oxidative and non-oxidative base modifications. The modified bases are removed by a subset of repair proteins called DNA glycosylases. Each DNA glycosylase enzyme is specific for one or a few altered bases in the DNA and catalyzes its removal. 

A common cause of DNA damage results from spontaneous deamination of bases, for example spontaneous deamination of cytosine forms uracil (Fig. 65.2). Remember uracil is found in RNA and is not normally present in DNA. In RNA, uracil pairs with adenine. Also, remember cytosine pairs with guanine so if the cytosine is deami-nated to uracil an incompatible pairing of the uracil with guanine results that distorts the DNAhehx. This type of single base damage is repaired by the base excision repair process. 

Base excision- repair Spontaneous, chemical, or radiation damage to a single base Base removal byN-glycosylase, abasic sugar removal, replacement... 

A. Single-base substitutions may occur as a result of DNA damage, chemical mutagenesis, or unrepaired errors in replication. 

Figure 5 Individual examples of simulated sites of damage induced by 3.2 MeV alpha particles in DNA. In each example, the outer and inner rows represent the sugar-phosphate moieties and the pairs of bases, respectively, with single base pair resolution (dots). An x or H represent energy deposition or reaction of hydroxyl radical leading to induction of a single strand break or base damage. A indicates hit sites that did not lead to strand breaks (SB) or base damage (BD). Nomenclature no strand break (No SB) single strand break (SSB), (SSB ), (2SSB) double strand break (DSB), (DSB+), (DSB + ).

The majority of strand breaks is of simple type containing a single strand break however, if base damage is taken into account, the majority of single strand breaks appears to be complex [81],... 

We have previously studied the dynamics of normal DNA [5-8], Here we present experimental evidence that DNA damage results in specific changes to its dynamics. Two kinds of prototypical DNA damage Eire studied and compared with an equivalent undamaged sequence. An abasic sample reproduces the most common type of in vivo damage to DNA, the loss of a single base. The chain-end sample explores a more severe type of damage, the disruption of the helical structure at the severed end of a DNA chain. 

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