Guanine, aromaticity

Another property of pyrimidines and purines is their strong absorbance of ultraviolet (UV) light, which is also a consequence of the aromaticity of their heterocyclic ring structures. Figure 11.8 shows characteristic absorption spectra of several of the common bases of nucleic acids—adenine, uracil, cytosine, and guanine—in their nucleotide forms AMP, UMP, CMP, and GMP (see Section 11.4). This property is particularly useful in quantitative and qualitative analysis of nucleotides and nucleic acids. 

Because aromatic purines and purine nucleosides and free purines such as hypo-xanthine and guanine 242 are readily silylated-aminated [64] (cf Scheme 4.24), it is obvious that 6-membered hydroxy-N-heterocycles are analogously silylated-aminated, with reactivity in the order given in Scheme 4.25 [73] X=OTf is the best leaving group and X=NHSiMe3 (cf the transamination as discussed in Section 4.2.4) is the weakest. 

The bases are monocyclic pyrimidines (see Box 11.5) or bicyclic purines (see Section 11.9.1), and all are aromatic. The two purine bases are adenine (A) and guanine (G), and the three pyrimidines are cytosine (C), thymine (T) and uracil (U). Uracil is found only in RNA, and thymine is found only in DNA. The other three bases are common to both DNA and RNA. The heterocyclic bases are capable of existing in more than one tautomeric form (see Sections 11.6.2 and 11.9.1). The forms shown here are found to predominate in nucleic acids. Thus, the oxygen substituents are in keto form, and the nitrogen substituents exist as amino groups. 

Aromatic amines (anilines) may become activated in vivo to form reactive amines. These are nucleophiles and may attack DNA, forming covalent modifications. Aromatic nitro compounds can be metabolised to also form reactive amines. A-nitroso compounds result in the alkylation of oxygen sites in DNA bases (0-6 in guanine and 0-4 in thymidine) [8,10]. 

The bases that occur in nucleic acids are aromatic heterocyclic compounds derived from either pyrimidine or purine. Five of these bases are the main components of nucleic acids in all living creatures. The purine bases adenine (abbreviation Ade, not A ) and guanine (Gua) and the pyrimidine base cytosine (Cyt) are present in both RNA and DNA. In contrast, uracil (Ura) is only found in RNA. In DNA, uracil is replaced by thymine (Thy), the 5-methyl derivative of uracil. 5-methylcyto-sine also occurs in small amounts in the DNA of the higher animals. A large number of other modified bases occur in tRNA (see p. 82) and in other types of RNA. 

Figure 6.40 Sites of electrophilic attack on guanine. PAHs are polycyclic aromatic hydrocarbons such as benzo(a)pyrene.

Because the chemical shifts of the nonexchangeable nucleobase proton signals are sensitive to (de)protonations of the aromatic structure, the absence of certain protonation shifts, or alterations in the expected pKa values, can give valuable information about the sites where platinum is bound. So, in N7-platinated guanine, no N7 protonation shift around pH 2 is observed, whereas the pKa of the N1 protonation decreases from 9.5 to 8.5 (54). 

A complete understanding of the biochemical functions of DNA requires a clear picture of its structural and physical characteristics. DNA has significant absorption in the UV range because of the presence of the aromatic bases adenine, guanine, cytosine, and thymine. This provides a useful probe into DNA structure because structural changes such as helix unwinding affect the extent of absorption. In addition, absorption measurements are used as an indication of DNA purity. The major absorption band for purified DNA peaks at about 260 nm. Protein material, the primary contaminant in DNA, has a peak absorption at 280 nm. The ratio A26(j/A2m is often used as a relative measure of the nucleic acid/protein content of a DNA sample. The typical A260/Am for isolated DNA is about 1.8. A smaller ratio indicates increased contamination by protein. 

Unlike phenols (Section 26-l), structural analysis of many of the hydroxy-substituted aza-aromatic compounds is complicated by isomerism of the keto-enol type, sometimes called lactim-lactam isomerism. For 2-hydro xypyrimidine, 19, these isomers are 19a and 19b, and the lactam form is more stable, as also is true for cytosine, 15, thymine, 16, and the pyrimidine ring of guanine, 18. 

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