In cytosine

The authors claim that these associations, which are destroyed in fixed compounds, play an important role in the calculation of Ty.The cases of 1,2,4-triazole-5-thiones 74 [97SA(A)699] and of pyridone dimers 15a-15a and 15a-15b were also studied [96MI(13)65]. (3) The recording of IR spectra in solution at different temperatures to determine the effect of the temperature on Kj-, for instance, in pyrazolinones [83JPR(325)238] and in cytosine-guanine base pairs [92MI(9)881]. (4) The determination of the equilibrium 2-aminopyridine/acetic acid 2-aminopyridinium acetate (see Section III.E) in the acid-base complex was carried out by IR (97NKK100). 

Pyrimidine and imidazole rings are particularly important in biological chemistry. Pyrimidine, for instance, is the parent ring system in cytosine, thymine, and uracil, three of the five heterocyclic amine bases found in nucleic acids An aromatic imidazole ring is present in histidine, one of the twenty amino acids found in proteins. 

Crosslinks result from the reaction of a bifunctional electrophilic species with DNA bases and imply a covalent link between two adjacent DNA strands which inhibits DNA replication. Primary targets within bases are N7 and 06 in guanine and N3 in cytosine. The initial lesions are removed by the suicide enzyme alkyltrans-ferase, whereas nucleotide excision repair is needed for frilly established crosslinks. 

Deamination, the hydrolytic loss of exocyclic amino groups on the DNA bases, is typically a very slow reaction. For example, deamination of cytosine residues in dnplex DNA occnrs with a half-life of about 30,000 years under physiological conditions, and the deamination of adenine residues is still more sluggish. " Alkylation at the N3-position of cytosine (Scheme 8.5) greatly increases the rate of deamination (ty2 = 406 h). Deamination of 3-methyl-2 -deoxycytidine proceeds 4000 times faster than the same reaction in the unalkylated nucleoside. Alkylation of the N3-position in cytosine residues also facilitates deglycosylation (Jy2 = 7700 h, lower pathway in Scheme 8.5), but the deamination reaction is 20 times faster and, therefore, predominates. ... 

Table 11-3. Vertical excitation energies in eV relative to the ground state minimum of the singlet electronic excited states in cytosine...

The dilemma described above, that cytosine-rich matrices lead to (complementary) sequences which are low in cytosine and are themselves ineffective matrices, makes the synthesis of nucleic acids in the absence of enzymes almost impossible. Thus, other models and model experiments must be looked for. 

Sponer, J., J. Leszczynski, and P. Hobza. 1996. Base Staking in Cytosine Dimer. A Comparison of Correlated Ab Initio Calculations with Three Empirical Models and Density Functional Theory Calculations. J. Comp. Chem. 17, 841. 

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. 

Two types of addition to pyrimidine bases appear to exist. The first, the formation of pyrimidine photohydrates, has been the subject of a detailed review.251 Results suggest that two reactive species may be involved in the photohydration of 1,3-dimethyluracil.252 A recent example of this type of addition is to be found in 6-azacytosine (308) which forms a photohydration product (309) analogous to that found in cytosine.253 The second type of addition proceeds via radical intermediates and is illustrated by the addition of propan-2-ol to the trimethylcytosine 310 to give the alcohol 311 and the dihydro derivative 312.254 The same adduct is formed by a di-tert-butyl peroxide-initiated free radical reaction. Numerous other photoreactions involving the formation by hydrogen abstraction of hydroxyalkyl radicals and their subsequent addition to heterocycles have been reported. Systems studied include 3-aminopyrido[4,3-c]us-triazine,255 02,2 -anhydrouri-dine,256 and sym-triazolo[4,3-fe]pyridazine.257 The photoaddition of alcohols to purines is also a well-documented transformation. The stereospecific addition of methanol to the purine 313, for example, is an important step in the synthesis of coformycin.258 These reactions are frequently more... 

Interesting Dimroth rearrangements in cytosine and its derivatives occur when they are allowed to react with acetic anhydride-acetic acid. Cyto-... 

Oxidation of cytosine produces a radical with sites of unpaired spin density at Nl, N3, and C5. The cytosine cation has a pKn<4 and in solution deprotonates at NH2 [22]. In the solid state, Sagstuen et al. [24] assigned the primary oxidation radical observed in cytosine monohydrate as the Nl deprotonated cation, Cyt(Nl—H) . It is known from the ENDOR... 

The previous section outlined the typical e loss and e gain products observed in the nucleic acid bases in the solid state. These studies can be applied to the study of the radiation chemistry of DNA. The relevance of the study of model systems is shown by considering the following remarkable observations. Years ago, Ehrenberg et al. showed the EPR spectra of the 5,6-dihydrothymine-5-yl radical observed in thymine, thymidine, and DNA. The spectra are nearly identical [46]. The reduction product observed in cytosine monohydrate is the N3 protonated anion. In solution, this reduction product gives rise to a 1.4-mT EPR doublet. The same feature is present in irradiated DNA at 77 K. Likewise, the result of e loss in guanine bases is characterized by a broad EPR singlet. The same feature is also evident in the EPR spectrum of DNA irradiated and observed at 77 K. 

Only a confused picture is revealed by these essentially qualitative studies. Many questions are left unanswered. The probable formation of uracil hydrate in cytosine photolysis has not been reported and the question of dimer formation, either in solution or in ice, is still unresolved. There are thus large gaps in our knowledge about the photolysis of cytosine and cytidine. Much more detailed work has been carried out on cytidylic acid and on dinucleotides of cytosine (Sect. XI-C). 

An attempt has been made to apply the Cohen and Reiss theory to dimer and hydrate formation in RNA.158 The results were inconclusive, probably because of a poor choice of example. Application of the theory to RNA was complicated by the necessity of estimating the distribution of uracil residues on the chain. The results are made still more tentative by the fact that Tanaka ignored the probability of dimer formation between cytosine residues, mixed dimers between cytosine and uracil, and hydrate formation in cytosine as well as the resultant deamination phenomena. A better choice of example would have been poly-uridylic acid. 

Some other interesting observations regarding free radicals in these systems are noteworthy. In many instances, multiple conformations of radicals are found at lower but not higher temperatures. This indicates that the radicals exist in shallow energy wells at low temperature this phenomenon was observed very early, in the 4 K ENDOR investigation of radical formation in amino acids.23 Unlike the process in DNA. In which it is well understood that the thymine anion radical protonates at C6 to form T(C6)H-, in the crystalline state there is a not clear link between pyrimidine electron adducts and H-addition radicals. We finally note that a deuterium isotope effect of protonation/deprotonation processes was found in cytosine.HCl and 2 -deoxycytidine.HCl, as evidenced by a lower propensity for these processes to occur in partially deuterated systems than in predated ones. 

Color Plate 29 DNA Sequencing by Capillary Gel Electrophoresis with Fluorescent Labels (Section 26-6) Tall red peaks correspond to chains terminating in cytosine and short red peaks correspond to thymine. Tall blue peaks arise from adenine and short blue peaks indicate guanine. Two different fluorescent labels and two fluorescence wavelengths were required to generate this information. [From M. C. Ruiz-Martinez, J. Berka, A. Belenkii,... 

X-ray crystal results on cytosine itself10 -13 (anhydrous and monohydrate), its complexes with different partners,15-20 cytidine,21 and cytidine 2, 3 -cyclic phosphate22 all indicate its existence in the lactam-amine form (2). In a number of crystals the cytosine ring is protonated, invariably at N-3.23-32 In cytosine 5-acetic acid33 half of the molecules... 

Several methods of quantum chemistry have been applied to calculate the charge distributions in cytosine and some of its derivatives. 

The charge distributions in cytosine have been previously reviewed in several articles and books.1 6-140 170-172 221-227 These include the... 

Fig. 3. Net -charges in cytosine calculated by different methods (from top to bottom tt-HMO, w-SCF MO, EHT, IEHT, CNDO/2, nonempirical calculations). Data taken from Pullman and Pullman1 222,223,220 and from Clementi et al.220 (in parentheses).

Thg IEHT method with a different set of parameters has been applied by Rein et al.212 to calculate the total charge distribution in cytosine and other nucleic acid bases (cf. Fig. 4). The 77-charges have not been indicated. 

Fig. 5. Net total electronic charges in cytosine and fluorocytosine tautomers calculated by the CNDO/2 method. The numbers in parentheses indicate jt-charges.

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... 

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