DNA components

The DNA component deoxythymidine triphosphate (dTTP) is synthesized from UDP in several steps. The base thymine, which only occurs in DNA (see p. 80), is formed by meth-ylation of dUMP at the nucleoside monophosphate level. Thymidylate synthase and its helper enzyme dihydrofolate reductase are important target enzymes for cytostatic drugs (see p. 402). 

Electrophoresis has been used for a long time as one of the most important separation principles in analytical biochemistry. In particular, it has been applied to the separation of DNA and DNA components. Electrophoretical techniques have predominated in this field for decades and will continue to do so in the future. The advent of capillary electrophoresis (CE) has boosted the development of electrophoretic techniques, because it opened access to higher sensitivity, better resolution, and greater speed of separation (1-3). 

Arylnitrenium ions are considered to be key intermediates in carcinogenic DNA damage by metabolically activated amines. The enzymatic activation of amines and the propogation of DNA-amine adducts into mutations and cellular transformations is beyond the specific scope of this chapter. Presented here is an outline of the key mechanistic issues relevant to the interaction of DNA components with various arylnitrenium ions. 

Antimetabolites are analogues of normal DNA components or of coenzymes involved in nucleic acid synthesis. They get incorporated or competitively inhibit utilization of normal substrate to form dysfunctional nucleic acid molecules. 

Hurwitz, J.L., Coleclough, C., Cebra, J.J. (1980). gene rearrangements in IgM-bearing B cells and in the normal splenic DNA component of hybridomas making different isotypes of antibody. Cell 22,349-359. 

Because of the fast rates of [reactions (2) and (6)] in aqueous solutions, reactions of alkoxyl radicals with DNA components can be neglected unless created within the DNA or in its very neighborhood (Chap. 2.4). 

Transition metal ions in their high oxidation state have also been used to oxidize DNA components. These reactions may involve one-electron oxidation steps, i.e., free-radicals may also play a role. Oxoruthenium(IV) complexes oxidize GMP an order of magnitude faster (k = 6.1 -15 dm3 mol-1 s-1) at the base moiety than dCMP (0.24 - 0.47 dm3 mol-1 s-1), where the sugar moiety is attacked (Far-rer and Thorp 2000). 

Mundy CJ, Colvin ME, Quong AA (2002) Irradiated guanine a Car-Parinello molecular dynamics study of dehydrogenation in the presence of an OH radical. J Phys Chem A 106 10063-10071 Murata-Kamiya N, Kamiya H, Muraoka M, Kaji H, Kasai H (1998) Comparison of oxidation products from DNA components byy-irradiation and Fenton-type reactions. J Radiat Res 38 121-131 Nabben FJ, van der Stroom HA, Loman H (1983) Inactivation of biologically active DNA by isopropanol and formate radicals. Int J Radiat Biol 43 495-504 Nakashima M, Hayon E (1979) Rates of reaction of inorganic phosphate radicals in solution. J Phys Chem 74 3290-3291... 

When deciding to study the dynamics of electronic excitation energy transfer in molecular systems by conventional spectroscopic techniques (in contrast to those based on non-linear properties such as photon echo spectroscopy) one has the choice between time-resolved fluorescence and transient absorption. This choice is not inconsequential because the two techniques do not necessarily monitor the same populations. Fluorescence is a very sensitive technique, in the sense that single photons can be detected. In contrast to transient absorption, it monitors solely excited state populations this is the reason for our choice. But, when dealing with DNA components whose quantum yield is as low as 10-4, [3,30] such experiments are far from trivial. 

Figure 28. A condensed schematic diagram of a synthetic Borromean link112 made up of three different circular single-stranded DNA components.

Goemer H (1990) Phosphorescence of nucleic acids and DNA components at 77 DegK. Journal of Photochemistry and Photobiology B Biology 5 359—377. 

While these studies give good estimates for the IPs, it has been shown that the properties of DNA components are affected by the first few waters of hydration which mimic the first hydration shell around the molecule. For example, each water that acts as a net hydrogen bond donor to a base results in an elevation of the IP while each water that acts as a net hydrogen bond acceptor will tend to lower the IP [54], The solvation model, e.g., PCM (polarized continuum model), which takes into account the effect of the bulk solvent on the solute lacks these specific interactions and has the effect of substantially lowering the IP. Nevertheless, these first waters need to be included for a good accounting of IPs and EAs. 

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