Thymine pyrimidine structure

Nitrogenous base plus sugar moiety are called nucleosides. Ribonucleic acids (RNA) resemble DNA in that nucleoside monophosphates are joined through phosphodiester bonds. RNAs differ in that the sugars are p-D-ribose units and the pyrimidine uracil is found in place of thymine. Molecular structures and nomenclature for nitrogenous bases, nucleosides, and nucleotides are delineated in Table 2.2. 

The major bases found in nucleic acids are adenine and guanine (purines) and uracil, cytosine, and thymine (pyrimidines). Thymine is found primarily in DNA, uracil in RNA, and the others in both DNA and RNA. Their structures, along with their chemical parent compounds, purine and pyrimidine, are shown in Figure 10.1, which also indicates other biologically important purines that are not components of nucleic acids. Hypoxanthine, orotic acid, and xanthine are biosynthetic and/or degradation intermediates of purine and pyrimidine bases, whereas xanthine derivatives—caffeine, theophylline, and theobromine—are alkaloids from plant sources. Caffeine is a component of coffee beans and tea, and its effects on metabolism are mentioned in Chapter 16. Theophylline is found in tea and is used therapeutically in asthma, because it is a smooth muscle relaxant. Theobromine is found in chocolate. It is a diuretic, heart stimulant, and vasodilator. 

Each nucleoside is constructed from two components—a deoxyribose sugar and a base. The sugar is the same in all four nucleosides and only the base is different. The four possible bases are two bicyclic purines (adenine and guanine), and two smaller pyrimidine structures (cytosine and thymine) (Fig. 6.2). 

As described above, the bases of DNA are composed of four structures, namely adenine and guanine (purine bases) and cytosine and thymine (pyrimidine bases). On the other hand, in the case of RNA, one of the four bases, uracil, is utilized instead of thymine of DNA within the four kinds of bases. Uracil possesses a structure in which the fifth methyl group of thymine is replaced with a hydrogen atom. 

Nucleotides can be linked together into oligonucleotides through a phosphate bridge at the 5 position of one ribose unit and the 3 position of another. The purine bases, adenine and guanine, have two heterocyclic rings, while the pyrimidines cytosine, thymine, and uracil have one. The structure of adenosine monophosphate is shown in Figure 11. 

Figure 11-6. Structures of representative conical intersections Sj/Sq in the pyrimidine bases, uracil, thymine, and cytosine. Uracil structures (a,d) are taken from Ref. [147, 210]. Thymine structures (b,e) are taken from Ref. [152], Cytosine structures (c,f) are taken from Ref. [157]...

Incorporation of a flavin electron donor and a thymine dimer acceptor into DNA double strands was achieved as depicted in Scheme 5 using a complex phosphoramidite/H-phosphonate/phosphoramidite DNA synthesis protocol. For the preparation of a flavin-base, which fits well into a DNA double strand structure, riboflavin was reacted with benzaldehyde-dimethylacetale to rigidify the ribityl-chain as a part of a 1,3-dioxane substructure [49]. The benzacetal-protected flavin was finally converted into the 5 -dimethoxytri-tyl-protected-3 -H-phosphonate ready for the incorporation into DNA using machine assisted DNA synthesis (Scheme 5a). For the cyclobutane pyrimidine dimer acceptor, a formacetal-linked thymine dimer phosphoramidite was prepared, which was found to be accessible in large quantities [50]. Both the flavin base and the formacetal-linked thymidine dimer, were finally incorporated into DNA strands like 7-12 (Scheme 5c). As depicted in... 

Figure 1.43 indicates major sites of reactivity within the ring structures for nucleophilic displacement reactions. Cytosine, thymine, and uracil all react toward nucleophilic attack at the same two sites, the C-4 and C-6 positions. The presence of powerful nucleophiles, even at neutral pH, can lead to significant base modification or cleavage with pyrimidine residues (Debye, 1947). For instance, hydrazine spontaneously adds to the 5,6-double bond, initiating further ring reactions,... 

As in the case of pyrimidine bases discussed previously, adenine and guanine are subject to nucleophilic displacement reactions at particular sites on their ring structures (Figure 1.50). Both compounds are reactive with nucleophiles at C-2, C-6, and C-8, with C-8 being the most common target for modification. However, the purines are much less reactive to nucleophiles than the pyrimidines. Hydrazine, hydroxylamine, and bisulfite—all important reactive species with cytosine, thymine, and uracil—are almost unreactive with guanine and adenine. 

Platination of the N3 position in 1-substituted uracil and thymine derivatives requires proton abstraction and usually occurs only at high pH, but the Pt-N3 bond, once formed, is thermodynamically stable (log K 9.6) [7]. Platinum binding to N3 increases the basicity of 04, which becomes an additional binding site leading to di- and trinuclear complexes. A list of X-ray structurally characterized species is given by Lippert [7]. Pt complexes of uracil and thymine can form intensely colored adducts (e.g. platinum pyrimidine blues), which show anticar-cinogenic activity analogously to the monomeric species [7]. 

There are five common bases found in nucleic acids. Adenine (A), guanine (G) and cytosine (C) are found in both DNA and RNA. Uracil (U) is found only in RNA and thymine (T) only in DNA. The structures of these bases are shown in Figure 13.2. Adenine and guanine are purine bases while uracil, thymine and cytosine are the pyrimidine bases. 

Pyrimidines A family of 6-membered heterocyclic compounds occurring in nature in a wide variety of forms. They include several nudeic add constituents (cytosine, thymine, and uracil) and form the basic structure of the barbiturates. [NIH]... 

The nitrogen-containing bases that occur in DNA and RNA fall into two structural categories the purines and the pyrimidines. The former contain a five-membered ring fused to a six-membered ring, while the latter contain a six-membered ring only. The two purines are common to both DNA and RNA adenine (A) and guanine (G). The pyrimidine cytosine (C) occurs in both DNA and RNA. The other pyrimidine is thymine (T) in DNA but uracil (U) in RNA. 

The first evidence of the special structure of DNA was the observation that the amounts of adenine and thymine are almost equal in every type of DNA. The same applies to guanine and cytosine. The model of DNA structure formulated in 1953 explains these constant base ratios intact DNA consists of two polydeoxynucleotide molecules ( strands ). Each base in one strand is linked to a complementary base in the other strand by H-bonds. Adenine is complementary to thymine, and guanine is complementary to cytosine. One purine base and one pyrimidine base are thus involved in each base pair. 

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. 

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