Thymine moieties

Interestingly, one-electron oxidants partly mimic the effects of OH radicals in their oxidizing reactions with the thymine moiety of nucleosides and DNA. In fact, the main reaction of OH radicals with 1 is addition at C-5 that yields reducing radicals in about 60% yield [34, 38]. The yield of OH radical addition at C-6 is 35% for thymidine (1) whereas the yield of hydrogen abstraction on the methyl group that leads to the formation of 5-methyl-(2 -de-oxyuridylyl) radical (9) is a minor process (5%). Thus, the two major differences in terms of product analysis between the oxidation of dThd by one-electron oxidants and that by the OH radical are the distribution of thymidine 5-hydroxy-6-hydroperoxide diastereomers and the overall percentage of methyl oxidation products. 

Figure 2. NMR spectrum of poly- Aysine having pendant thymin moieties...

Asymmetric synthesis of stavudine and cordycepin, anti-HIV agents, and several 3 -amino-3 -deoxy-P-nudeosides was achieved utilizing this cycloisomerization of 3-butynols to dihydrofuran derivatives [16]. For example, Mo(CO)6-TMNO-promoted cyclization of the optically active alkynyl alcohol 42, prepared utilizing Sharpless asymmetric epoxidation, afforded dihydrofuran 43 in good yield. Iodine-mediated introduction of a thymine moiety followed by dehydroiodination and hydrolysis of the pivaloate gave stavudine in only six steps starting from allyl alcohol (Scheme 5.13). 

An almost complete description of both OH radical-mediated and one-electron oxidation reactions of the thymine moiety (3) of DNA and related model compounds is now possible on the basis of detailed studies of the final oxidation products and their radical precursors. Relevant information on the structure and redox properties of transient pyrimidine radicals is available from pulse radiolysis measurements that in most cases have involved the use of the redox titration technique. It may be noted that most of the rate constants implicating the formation and the fate of the latter radicals have been also assessed. This has been completed by the isolation and characterization of the main thymine and thymidine hydroperoxides that arise from the fate of the pyrimidine radicals in aerated aqueous solutions. Information is also available on the formation of thymine hydroperoxides as the result of initial addition of radiation-induced reductive species including H" atom and solvated electron. 

It was first reported in 1941 that DNA can be damaged by exposure to UV light, which was initially attributed to depolymerization [18,19], Only in the 1960s was it recognized that dimerization of adjacent thymine bases in the DNA strands via photocycloaddition is a major factor in biological inactivation of exposed DNA [17]. As a result of this photoreaction the double carbon-carbon bonds in thymine moieties cyclizes with an adjacent thymine forming so-called cyclobutane thymine dimer as shown in Figure 13.2. The thymine photodimer was first isolated and analyzed in 1960 by Beukers and Berends [20] who experimented with frozen aqueous solutions of thymine. 

The need for an inexpensive, stable and versatile system, which incorporates thymine moieties in the polymer backbone led to design of the vinyl-benzylthymine (VBT) monomer [34]. Its structure is presented in Figure 13.4. This monomer can be synthesized in one step from thymine and vinylbenzyl chloride. The monomer contains several built-in functionalities. 

Poly-9-(f -methacryloyloxyethyl)adenine (polyMAOA, 25 a), poly-l-(fi-methacryloyl-oxyethyl)uracil (polyMAOU, 27 a), -thymine (poly-MAOT, 29 a), poly-9-(f -acryloyl-oxyethyl)adenine (polyAOA, 25b), poly-1 -(fi-acryloyloxyethyl)uracil (polyAOU, 27b) and -thymine (polyAOT, 29 b) were prepared by free-radical polymerization of their corresponding monomers26,27). PolyMAOA and polyAOA are soluble in DMSO, ethylene glycol and acidic aqueous solution (below pH 3), while the polymers having uracil and thymine moieties are soluble in DMSO, DMF and alkaline aqueous solution (above pH 10). 

The use of supramolecular interactions to bind a pharmaceutically active drug noncovalently to a polymer in order to achieve slow release was presented by Puskas et al. [96]. Here, a side-chain functionahzed poly(styrene) bearing thymine moieties (Fig. 20) was prepared and complexed with phenol as a complexing agent. The release of the bound phenol was studied in aqueous buffer solution, revealing a slow desorption within 4.5 hours from the polymer. Thus, this system is adaptable for slow release of drugs from polymeric matrices. 

In humans the cross-linked thymine moieties create a kink in our DNA. An excision enzyme recognizes this kink and that portion of DNA is cut out and repaired. Skin cancer has been linked to the failure of this mechanism. Another repair mechanism is found in some microbes which have an enzyme called DNA photolyase. DNA photolyase functions by recognizing the thymine dimers and un-zipping them (79). We have found methods to use DNA photolyase as an enzyme for regenerating thymine polymer photoresists, allowing re-use of the photoresist systems (20). 

Figure 3.2 Hydroxyl radical-mediated oxidation of the thymine moiety in DNA.

Superficial comparison of the thymidine transient spectra with the deoxyribose and thymine transient spectra, all at pH 7, suggests that both pentose and base transients may contribute to the observed spectra. The peak in the thymidine spectrum at 400 n.m. is at the same wavelength as the thymine transient peak, and the short wavelength absorption is similar to the deoxyribose transient absorption. However, thymine itself gives a transient spectrum at pH 10.6 which is similar to that of thymidine at pH 7 (cf. Figure 2), and the similarity in decay rates of the thymidine transient absorption at 320 to that at 390 n.m. indicates that both absorptions may be caused by the same transient species. If so, the transient probably involves the thymine moiety. At pH 12.2 the spectra and decay of the thymidine transient are consistent with formation of transients on both the pentose and base parts of the molecules. 

Silver also has been demonstrated to be reactive in solution systems. Thus, silver perchlorate has been shown to influence the photochemical reactivity of stilbene in acetonitrile and methanol. The fluorescence of the stilbene is quenched on addition of the perchlorate and this is good evidence for the enhancement of the So-Ti crossing induced by the heavy ion Ag+. It seems likely that an Ag+/stilbene complex is formed. The perturbation of the system is better in methanol than in acetonitrile. However, cis.trans isomerism of the stilbene is reduced within the excited Ag+/stilbene complex since it is difficult for the geometrical isomerism to occur. Enhanced isomerism is observed with the Ag+/azobenzene system. In this complex there are steiic problems encountered in the nitrogen rehybridization process that is operative in the isomerism . Enhanced So-T crossing is also seen in the Ag+/1 1 complex with tryptophan where the fluorescence is quenched and there is a threefold increase in phosphorescence . Complexes between Ag+ and polynucleotides and DNA cause quenching of the fluorescence. Enhancement of phosphorescence and a 20-fold increase in the dimerization of thymine moieties has also been observed when silver ions are added to the reaction system . ... 

Another type of dimeric lesions are pyrimidine-pyrimidone (Pyr[6-4]Pyr) dimers formed by a Paterno-Biichi-type reaction at dipyrimidine sites between the C(5)=C(6) double bond of the first pyrimidine and the C(4)=0 carbonyl group of the second base. This kind of dimerization is demonstrated in Scheme 8.2 for the case of adjacent thymine moieties. 

Scheme 8.1 Dimerization of adjacent thymine moieties in DNA by [In+ln] cycloaddition.

Figure 22.1 Fluorescence quenching efficiencies of thymine functionalized fx>lytbiophene (PTT) in the presence of various metal Ions. From Y. Tang, F. He, M. Yu, F. Feng, L. An, H. Sun, S. Wang, Y. Li and D. Zhu, A reversible and highly selective fluorescent sensor for mercury(ll) using poly(thiophene)s that contain thymine moieties, Macromol. Rapid Commun., 27, 389-392 (2006). Copyright Wiley-VCH Verlag GmbH Co. KCaA.

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