I - cytosine

Base composition- Proportion of the total bases consisting of guanine plus cytosine or thymine plus adenine base pairs. Usually expressed as a guanine -I- cytosine (G -I- C) value, e.g. 60% G-l-C. 

AG values of adduct III and TV with that of adduct II, sufficient data for adduct II is not available. Yet the similar solvent KIE is a strong evidence to say that the a,p-dihydroxyethyl radical (I lO CI ICH,OH) is a good model for the 6-methyluracil-6-yl and 6-methyl-i-cytosine-6-yl radices when their adducts III and IV lead to similar transition states on their way to the products. And adducts II, III and IV differ with adducts I and V where former set have an OH group in p position as shown in their structures above. The strong difference in KIE between the two sets of adducts I and... 

The primary stmcture of DNA is based on repeating nucleotide units, where each nucleotide is made up of the sugar, ie, 2 -deoxyribose, a phosphate, and a heterocycHc base, N. The most common DNA bases are the purines, adenine (A) and guanine (G), and the pyrimidines, thymine (T) and cytosine (C) (Fig. 1). The base, N, is bound at the I -position of the ribose unit through a heterocycHc nitrogen. 

Cytosine was isolated from hydrolysis of calf thymus in 1894 and by 1903 its structure was known and it had been synthesized from 2-ethylthiopyrimidin-4(3H)-one. The acid hydrolysis of ribonucleic acid gives nucleotides, among which are two cytidylic acids, 2 -and 3 -phosphates of cytidine further hydrolysis gives cytidine itself, i.e. the 1-/3-D-ribofuranoside of cytosine, and thence cytosine. The deoxyribonucleic acids likewise yield deoxyribonucleotides, including cytosine deoxyribose-5 -phosphate, from which the phosphate may be removed to give cytosine deoxyriboside and thence cytosine. 

Scott et al. [12] provided some experimental evidence supporting equation (27). The mixture contained uracil, hypoxanthine, guanine and cytosine, each present in the mobile phase at a concentration of 14 mg/1. The column employed was Im long, 1.5 mm I.D., packed with a pellicular cation exchange resin and operated at a flow rate of 0.3 ml/min. 

B-i = Benzylated Adenine, B2 = Thymine Bi = Benzylated Cytosine, B2 = Thymine Z = Dimethyl Triptophan, B- = B2 = Thymine... 

Barton and coworkers have shown that proteins can in fact modulate the DNA electron transfer [168]. Methyltransferases are enzymes that recognize distinct DNA sequences, e.g., 5 -G CGC-3, and effect methylation by extrading the target base cytosine ( C) completely out of the DNA duplex while the remainder of the double helix is left intact. The methyltransferase Hha 1-DNA complex is a well-characterized example, revealing that the structure of the DNA is significantly but locally distorted [169,170]. In a recent study, Raj ski et al. used DNA duplex 20 containing the M.Hha I binding site between two oxidizable 5 -GG-3 sites [168] (Fig. 20). The duplex contains a complementary strand, selectively 5 -modified with a Rh intercalator that can function as a photooxidant. Upon... 

C]-FlAC was synthesized from [2- C]cytosine in the general manner used for unlabeled 748 (FIAC), and its metabolic fate in mice was studied. The compound (after i.v. injection) was deaminated by cytosine nucleoside deaminase and appeared as [2- C]-FIAU in plasma, as confirmed by experiments on rats having a very low level of the deaminase, and by treatment with tetrahydrouridine, a nucleoside deaminase inhibitor. This was further confirmed by the use of purified human deoxycytidine deaminase. It was... 

Lalezari, J. P etal. (1995). (S)-l-[3-Hydroxy-2-(phosphonylmethosy)propyl]cytosine (cidofovir) Results of a phase I/n study of a novel antiviral nucleotide analogue. J. Infect. Dis. 171,788-798. 

Solvatochromic shifts for cytosine have also been calculated with a variety of methods (see Table 11-7). Shukla and Lesczynski [215] studied clusters of cytosine and three water molecules with CIS and TDDFT methods to obtain solvatochromic shifts. More sophisticated calculations have appeared recently. Valiev and Kowalski used a coupled cluster and classical molecular dynamics approach to calculate the solvatochromic shifts of the excited states of cytosine in the native DNA environment. Blancafort and coworkers [216] used a CASPT2 approach combined with the conductor version of the polarizable continuous (CPCM) model. All of these methods predict that the first three excited states are blue-shifted. S i, which is a nn state, is blue-shifted by 0.1-0.2 eV in water and 0.25 eV in native DNA. S2 and S3 are both rnt states and, as expected, the shift is bigger, 0.4-0.6eV for S2 and 0.3-0.8 eV for S3. S2 is predicted to be blue-shifted by 0.54 eV in native DNA. 

Hall, R. J., N. A. Burton, I. H. Hiller, and P. E. Young. 1994. Tautomeric equilibria in 2-hydroxypyridine and in cytosine. An assessment of density functional methods, including gradient corrections. Chem. Phys. Lett. 220,129. 

The interstrand cross-link also induces DNA bending.72 X-ray and NMR studies on this adduct show that platinum is located in the minor groove and the cytosines of the d(GC) base pair involved in interstrand cross-link formation are flipped out of the helix stack and a localized Z-form DNA is observed.83-85 This is a highly unusual structure and very distorting—implications for differential repair of the two adducts have been addressed. Alternatively, the interstrand cross-link of the antitumor inactive trans-DDP is formed between a guanine (G) and its complementary cytosine (C) on the same base p a i r.86,87/ nms- D D P is sterically incapable of producing 1,2-intrastrand adducts and this feature has been cited as a dominant structural reason for its lack of antitumor efficacy. It is clear that the structural distortions induced on the DNA are very different and likely to induce distinctly different biological consequences. 

Prepare bisulfite modification solution consisting of 3 M concentration of a diamine (i.e., ethylenediamine), 1M sodium bisulfite, pH 6. The use of the dihydrochloride form of the diamine avoids having to adjust the pH down from the severe alkaline pH of the free-base form. Note The optimum pH for transaminating biotin-hydrazide to cytosine residues using bisulfite is 4.5 (see Section 2.3, this chapter). 

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