Pyrimidine 5-methylcytosine

Primary synthesis has limited application in making pyrimidine-carboxylic acids or even their esters. However, some pyrimidine-4(and 5)-carboxylic acids can be effectively so made. For example, bromomucic acid (785) reacts as an aidehydo ketone with S-methyl-thiourea to give 5-bromo-2-methylthiopyrimidine-4-carboxylic acid (786) directly (53JCS3129) while the Whitehead synthesis (Section 2.13.3.1.2<7) can give, for instance, 3-methylcytosine-5-carboxylic acid (787) (55MI21300). 

As is well-known, nucleic acids consist of a polymeric chain of monotonously reiterating molecules of phosphoric acid and a sugar. In ribonucleic acid, the sugar component is represented by n-ribose, in deoxyribonucleic acid by D-2-deoxyribose. To this chain pyrimidine and purine derivatives are bound at the sugar moieties, these derivatives being conventionally, even if inaccurately, termed as pyrimidine and purine bases. The bases in question are uracil (in ribonucleic acids) or thymine (in deoxyribonucleic acids), cytosine, adenine, guanine, in some cases 5-methylcytosine and 5-hydroxymethylcyto-sine. In addition to these, a number of the so-called odd bases occurring in small amounts in some ribonucleic acid fractions have been isolated. 

Among the simplest compounds of this series are l-(2-deoxy-2-fluoro- -D-arabinofuranosyl)thymine (758, FMAU) and 1-(2-deoxy-2-fluoro-)S-D-arabinofuranosyl)-5-methylcytosine (749, FMAC). Later FIAU (757) and FMAU (758) were prepared in high yields (>95% the ratio of Plot an-omers being 7/1 and 4/1, respectively) by condensation using 743 and 2,4-bis(0-trimethylsilyl)-5-iodouracil (769), and 743 and 2,4-bis(0-trimethylsi-lyl)thymine (770), respectively. Likewise, 753, 757, 758, and 765 (this was described later) were prepared in high yields using pyrimidine derivatives... 

Small quantities of additional purines and pyrimidines occur in DNA and RNAs. Examples include 5-methyl-cytosine of bacterial and human DNA, 5-hydroxy-methylcytosine of bacterial and viral nucleic acids, and mono- and di-N-methylated adenine and guanine of... 

For various reasons, the generalizations mentioned above must be regarded as strictly provisional. Analyses utilizing formic acid indicate the presence of more than one phosphorus atom per purine or pyrimidine residue. This discrepancy, it is pointed out, could equally well result from an apparent deficiency of bases, due to error in the analytical technique.160 It is also necessary to consider that some nucleic acids are now known to contain more bases than was previously realized. Thus, 5-(hydroxymethyl)-cytosine is present in various viruses,181-182 and 5-methylcytosine occurs in various animal and plant deoxyribonucleic acids but is absent from those of microbial origin.17-160-1M- 184- 186 Certain microbial deoxyribonucleic acids also contain 6-methylaminopurine.186a Various bacteriophage deoxyribonucleic acids have been found to contain a component which is believed to consist of a D-glucoside186b of 5 -(hydroxymethyl)cytidylic acid. 

The most important pyrimidine derivatives are those upon which biological organisms depend. Cytosine 1018 and uracil 1019 are found in ribonucleic acid (RNA) in the form of their ribonucleotides, cytidine 1020 and uridine 1021, while in deoxyribonucleic acid (DNA), cytosine and thymine 1022 are found in the form of their 2 -deoxyribonucleotides, 2 -deoxycytidine 1023 and thymidine 1024. 5-Methylcytosine 1025 is also found to a small extent (c. 5%) in human DNA in the form of its 2 -deoxyriboside 1026, and 5-(hydroxymethyl)cytosine-2 -deoxyriboside 1027 has also been detected in smaller amounts <2005CBI1>. Many variants of cytosine and uracil can be found in RNA including orotic acid 1028 in the form of its ribonucleotide orotidine 1029. Other pyrimidine derivatives to have been isolated from various biological sources include 2 -deoxyuridine 1030, alloxan 1031, and toxopyrimidine (pyramine) 1032 (Figure 2). 

The 15N magnetic resonance studies of the pyrimidine bases or their derivatives are scarce. Roberts et al.BB have measured the 1H and 15N magnetic resonance spectra of a number of pyrimidines including uracil and 1-methylcytosine. The most important result of this study was the elucidation of the dominant tautomeric structures of uracil and proto-nated 1-methylcytosine as the diketo, 32, and keto-amine form, 7, respectively (cf. Sections II and IV and the spectrum of 1-methylcytosine hydrochloride labeled only in the amino group62). In the case of uracil,85 the two 15N-bonded protons gave two doublets centered at 10.78 and 10.96 ppm (measured downfield from internal tetramethyl-... 

Much coordination chemistry has been carried out with simple pyrimidines and the nucleic acid bases. The crystal structure566 of tetrakis(l-methyl-pyrimidine-2-thione)zinc(II) perchlorate bis(propanone) demonstrates unidentate coordination by the non-methylated (N-3) nitrogen atom, with r(Zn—N) at 2.058 and 2.060 A. The structure of dichlorobis(l-methylcytosine)cadraium(II)567 involves two Cd—Q bonds (2.497 and 2.485 A) and two Cd—N(3) bonds (2.281 and 2.296 A) with approximately tetrahedral stereochemistry. 

DNA and RNA also contain minor amounts of other bases. Among the minor purines are 1-methylguanine, 6-methylaminopurine (primarily amino group of adenine is methylated), 6-dimethylaminopurine, and 7-methylguanine. Among the minor pyrimidines are 3- or 5-methylcytosine and 5-hydroxymethylcytosine. 

BSA was effective for the derivatization of purine and pyrimidine bases [456] and nucleosides [457]. Bases were silylated by heating at 150°C with BSA—acetonitrile (1 3) for 45 min. It was stated that under these conditions the TMS derivative of guanine can be prepared reproducibly, but both cytosine and 5-methylcytosine provided two peaks. Silylation of nucleosides, including pseudouridine, was carried out by heating at 120°C with a 100-fold excess of BSA for 2 h. With the use of OV-17 as the stationary phase, this procedure was adopted for the determination of the composition of ribonucleic acids. 

Another type of photochemical reaction involving a pyrimidine base is the addition of a molecule of water across the 5,6 double bond of C to yield a 5,6-dihydro-6-hydroxy derivative called the cytosine hydrate. The quantum yield for the formation of cytosine hydrates in UV-irradiated DNA is greater in single-stranded than in duplex-DNA (45). Hydrates of cytosine, deoxycytidine, CMP, or dCMP are unstable, readily reverting to the parent form by rehydration (45). However, their half-life is dramatically increased in DNA, and cytosine hydrate may be the major nondimer C photoproduct. Cytosine hydrate can undergo deamination and dehydration to yield uracil (1). The hydrate of 5-methylcytosine may undergo deamination to yield 5-thymine hydrate, which can convert to thymine upon dehydration (1). 

MO methods have calculated that the bond order of the C(5)-C(6) bond in the first triplet of a series of pyrimidines is lower than in the first excited singlets of the corresponding molecules, and have concluded that dimerization of the bases occurs via the triplet state. They divided the pyrimidines into three groups the pyrimidines which are known to be easily dimerizable (uracil, 6-methyluracil, thymine, orotic acid—for these molecules the Pse values in their T state are of the order of 0.09-0.12), those which dimerize not so easily (5-aminouracil, cytosine, 5-methylcytosine—Pge 0.13-0.17), and the bases which do not dimerize at all or only with considerable difficulty (2-thiothymine, Pgg = 0.31 isocytosine, Pgg = 0.39 and 5-nitrouracil). The relative distribution of the bases within groups leads sometimes to only limited agreement with available experimental data. For instance, as the Pgg = 0.085 in T of uracil is lower than Pgg = 0.106 in T of thymine, uracil should dimerize more easily than thymine, a conclusion in disagreement with experiment. ... 

Singlet-singlet transition energies of the minor pyrimidine bases have been calculated in a few papers (tt-SCF MO Cl calculations isocytosine 104,156,188,189 jjg anioii and cation, 2-thiothymine, - 2-(S -methylcytosine and 4-jS-methylisocytosine and anions of thio-oytosine and isothiocytosine, 2-thio, 4-thio, 2,4-dithiouracil, thiocytosine, and isothiocytosine and several methyl derivatives of rare pyrimidines and their anions ). 

This formulation is confirmed by the fact that, on deamination, " it retains its tetranucleotide structure and pentabasicity, and hence contains no phosphoamide links. Bredereck and collaborators completely methylated thymonucleic acid, obtaining a product possessing seven A -methyl and three methoxyl groups to each four phosphorus atoms. On stepwise hydrolysis, this material gave 1,6-dimethyladenine, 1,6-di-methylcytosine, and 1-methylthymine. This confirms the previously-mentioned conclusion, that the sugar is attached to position 9 of the adenine and to position 3 of the pyrimidines. 

The bases found in DNA are adenine and guanine which contain the purine ring system, and cytosine, thymine, and S-methylcytosine, which contain the pyrimidine ring system. RNA contains adenine, guanine, cytosine, and uracil. (See Fig. 37.6.)... 

Applications to cis-bis(pyrimidine)Ft(II) Complexes. Considerably less stereochemical data are presently available for cis-bis(pyrimidine)Pt(II) complexes from X-ray diffraction studies (20, 33, 40-42). Of these, we have chosen to present conformational drawings in Figure 4 for the cis-[Pt(NH )9(l-methylcyto-sine)2] cation (33), the mixed base cation cis-[Pt(NH3)o(l-methylcytosine)(N(l)-deprotonated thymine monoanion)(41) and the [Pt(en)(7,9-dimethylhypoxanthine)2] cation (20). In the latter complex, the nucleobases are actually modified purines however, since the pyrimidine ring site N(l) of the purine base is bound to the Pt(II) center, this complex is included in the present series. 

Preliminary data obtained with 5-methylcytosine indicate that at pH 12.1 it gives a spectrum similar to that given by thymine. In contrast, Figures 6 C and 6 D show that the spectra resulting from reaction of OH with uracil are not altered greatly by pH changes. Thus, the conclusions of stationary state studies that as the pH is increased the site of attack on pyrimidine bases shifts if a 5-methyl group is available are confirmed. 

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