Cytosine, in DNA

Methylated bases occur in small amounts in deoxyribonucleotides. The role of methylation, especially of cytosine in DNA, is discussed below and in Chapter 15. 

There are two types of nucleic acid RNA and DNA The nucleotides in RNA contain ribose, and the common pyrimidine bases are uracil and cytosine. In DNA, the nucleotides contain 2 -deoxyribose, and the common pyrimidine bases are thymine and cytosine. The primary purines are adenine and guanine in both RNA and DNA... 

Several nucleotide bases undergo spontaneous loss of their exocyclic amino groups (deamination) (Fig. 8-33a). For example, under typical cellular conditions, deamination of cytosine (in DNA) to uracil occurs in about one of every 107 cytidine residues in 24 hours. This corresponds to about 100 spontaneous events per day, on average, in a mammalian cell. Deamination of adenine and guanine occurs at about l/100th this rate. 

DNA Repair Mechanisms Vertebrate and plant cells often methylate cytosine in DNA to form 5-methylcytosine (see Fig. 8-5a). In these same cells, a specialized repair system recognizes G-T mismatches and repairs them to G=C base pairs. How might this repair system be advantageous to the cell (Explain in terms of the presence of 5-methylcytosine in the DNA.)... 

The study of the nucleic acid bases is interesting because they possess many possible sites of protonation or electrophilic attack. Isopotential maps have been constructed for adenine, cytosine, and thymine.244 They may be used to study theoretically the proton affinities of the different atoms in these molecules. It is well known that protonation of cytosine, its nucleotide or nucleoside, occurs at N-394,245-247 (cf. Section II) alkylation also occurs at N-3.103-248-249 Nevertheless protonation of the oxygen of cytosine in DNA has been reported.250 The basic pA of cytosine is higher than that of adenine. The isopotential map in the molecular plane of cytosine (Tig. 8) shows that the potential well is deeper for N-3 than for 0 and the minimum for N-3 in cytosine is deeper than for any nitrogen in adenine. These maps, and their confrontation with the experimental facts have been discussed228-244... 

Finally, a similar approach was undertaken to evaluate the origin of factor 3 in Fig. 15.3c whose score image reveals several small-localized pockets in the epidermis. The loading from factor 3 (Fig. 15.3b) depicts one broad feature at 1090cm 1 not present in the other factor loadings. Based on both the position of this particular band and the spatial distribution of the factor score, the band probably arises from a phosphodiester mode of DNA [30, 31] present in the nuclei of keratinocytes or other cells. An additional feature at 780 cm 1 in both spectra and factors (not shown) arises from cytosine in DNA [32] and is consistent with this interpretation. 

Since an oxidation product on cytosine in DNA could not deprotonated at Nl, it may be more relevant to look at oxidation in a nucleotide. In 5 -dCMP (with N3-H in the native molecule) oxidation produces the N3 deprotonated cation with p(Nl) = 0.30 and p(C5) = 0.60 [43],... 

Naturally, the next application was aimed at the quantitation of this relationship. The ratio of 5-methylcytosine cytosine in DNA was determined by mass spectrometry, using multiple selected ions monitoring, for (/)-174 DNA as well as for DNA originating from calf thymus, salmon sperm, and several other sources. It must be noted however, that these GC-MS data were obtained from hydrolysates of the whole DNA. 

A common mutagenic event is the deamination of cytosine in DNA to form uracil. If the damaged strand is replicated, a CG base pair in DNA will be converted to a... 

If cytosine in DNA is deaminated, the uracil residue that results may be removed by... 

From the experimental point of view, protonation of cytosine, its nucleoside and nucleotide, occurs on N3 33 40> and so does alkylation 38>41>, both reactions being easier in cytosine than in adenine. In DNA, where the N3 position is involved in hydrogen bonding, the reactivity of cytosine towards methylation is much reduced or even suppressed, depending on the reagent 38>. A protonation of the oxygen of cytosine in DNA 42> has been reported. 

C-methylation reaction is the methylation of the C-5 position of cytosine in DNA. In this case, the carbon C-5 of cytosine cannot directly act as a nucleophile. The electron withdrawal by N-3 and the carbonyl, however, makes the C-5—C-6 double bond electron deficient and prone to attack by nucleophiles in a reaction that is similar to a Michael reaction. In DNA methyltransferases (DNMTs), this nucleophile is the thio-late from a Cys residue. The addition product is nucleophilic and reacts with SAM via an Si,j2-like mechanism to capture the methyl group. The resulting intermediate then eliminates the Cys of DNMT to give the methylated cytosine product (Figure 1.9). The methylation of C-5 of cytosine is an example of converting an electron-deficient methyl acceptor to a nucleophile for the methyl-transfer reaction by addition of an active site Cys thiolate. 

The parent substance of several nitrogenous cxtmpounds found in nucleic acids. The principal pyrimidines found in RNA are uracil and cytosine in DNA they are thymine and cytosine. 

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