Uracils, formation

Figure 1.45 Reaction of bisulfite with cytosine bases is an important route of derivatization. It can lead to uracil formation or, in the presence of an amine (or hydrazide) containing compound, transamination can occur, resulting in covalent modification.

Figure 27.2 Treatment of cytosine bases with bisulfite results in a multi-step deamination reaction, ultimately leading to uracil formation.

Since the site of modification on cytosine bases is at a hydrogen bonding position in double helix formation, the degree of bisulfite derivatization should be carefully controlled. Reaction conditions such as pH, diamine concentration, and incubation time and temperature affect the yield and type of products formed during the transamination process. At low concentrations of diamine, deamination and uracil formation dramatically exceed transamination. At high concentrations of diamine (3M), transamination can approach 100 percent yield (Draper and Gold, 1980). Ideally, only about 30-40 bases should be modified per 1,000 bases to assure hybridization ability after derivatization. 

W-Cyclopent[c]isoxazoles, 3a,4,5,6-tetrahydro-, 56, 264, 60, 310, 311 Cyclopropa-fused uracils, formation and rearrangement, 55, 196 Cyclopropanation, of... 

The synthesis of Saflufenacil (294) is similar to Benzfendizone synthesis, but on the key step of uracile formation instead of isocyanate corresponding urethane 316 was used in basic conditions. Starting amine 315 was obtained in 3 steps from acid... 

The mode of action has been a subject for research for a number of years. While it was originally thought that maleic hydrazide replaced uracil in the RNA sequence, it has been deterrnined that the molecule may be a pyrimidine or purine analogue and therefore base-pair formation is possible with uracil and thymine and there exists the probabiHty of base-pair formation with adenine however, if maleic hydrazide occurs in an in vivo system as the diketo species, then there remains the possibiHty of base-pairing with guanine (50). Whatever the mechanism, it is apparent that the inhibitory effects are the result of a shutdown of the de novo synthesis of protein. 

The direct formation of dipyrimidin-5-yl sulfides occurs on treatment of appropriate 5-unsubstituted pyrimidine substrates with sulfur mono- or di-chloride. Thus, reaction of uracil (83 R = H) with sulfur monochloride in boiling formic acid gives diuracil-5-yl sulfide in good yield sulfur dichloride gives a poor yield. Simple derivatives of uracil and barbituric acid undergo similar reactions but not cytosine, isocytosine, 2,4-bismethylthiopyrimidine or pyrimidine-4,6-dione (59). The mechanism is unknown (72AJC2275). 

In contrast, the photochemistry of uracil, thymine and related bases has a large and detailed literature because most of the adverse effects produced by UV irradiation of tissues seem to result from dimer formation involving adjacent thymine residues in DNA. Three types of reaction are recognizable (i) photohydration of uracil but not thymine (see Section 2.13.2.1.2), (ii) the oxidation of both bases during irradiation and (iii) photodimer formation. 

There are CN/CC replacements reported which involve the participation of a two-carbon side-chain, present as substituent in the pyrimidine system. An example is the formation of 4-alkylaminopyridin-2-ones on alkaline hydrolysis of 6-[2-(dimethylamino)vinyl]uracils (R = Me, Ph, CH2Ph ... 

This four-atom replacement was observed in some reactions of uracil derivatives, containing at position 5 a substituent with the CCCN moiety. Treatment of the Z-isomer 5-(2-carbamoylvinyl)-l,3-dialkyluracil with ethanolic sodium ethoxide gave in good yield 3-ethoxycarbonylpyridin-6(lf/)-one (84%) together with 3-A-methylcarbamoyl)pyridin-6-(l7 )-one (10%) (85JOC1513) (Scheme 26). The reaction involves an initial attack of the terminal amino group of the side-chain on position 6 of the uracil molecule. C-6-N-1 bond fission and N-C bond formation yield the pyridin-6(l//)-one. A subsequent attack of the ethoxide ion on the carbonyl groups of the side-chain yields both pyridin-2-one derivatives (Scheme 26). Similar results were obtained with the -isomer. 

Another ring-enlargement method for the formation of 1,3-diazocines employs the [2+2] photocycloadducts 3 of uracil derivatives and alkynes.4-5... 

Pd(0)-catalyzed substitution reaction, a novel, mild reduction of a-nitro ester to an amino acid ester with TiCl3, and an improved procedure for uracil ring formation. 

The same problem, the stability of the nucleobases, was taken up by Levi and Miller (1998). They wanted to show that a synthesis of these compounds at high temperatures is unrealistic, and thus they took a critical look at the high temperature biogenesis theories, such as the formation of biomolecules at hydrothermal vents (see Sect. 7.2). The half-life of adenine and guanine at 373 K is about a year, that of uracil about 12 years and of the labile cytosine only 19 days. Such temperatures could have easily been reached when planetoids impacted the primeval ocean. 

Partly saturated pyrazino[l,2-r-]pyrimidines were prepared by formation of the pyrazine ring. 2-Substituted-8-hydroxy-3,4-dihydro-177,277-pyrazino[l,2-r-]pyrimidin-l-ones were prepared by a [6+0] synthesis involving cyclization of 6-hydroxy-pyrimidine-4-(fV-hydroxyethyl)carboxamides <2005W02005/087766>. The 2/7-pyra-zino[l,2-c]pyrimidine-3-carboxamide 164 (Y = NH) was formed from [5+1] atom fragments via the uracil derivative 163 (Y = NH) and DMF-dimethyl acetal. Compounds 163 were prepared from 6-chloromethyluracil and glycine methyl ester 162 (Y = NH) (Scheme 20) <2004W02004/014354>. 

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