Uracil bases

Z = 8 D, = 1.84 R = 0.059 for 2,587 intensities. In the asymmetrical unit, there are two molecules that have similar conformations. The glycosyl dispositions are anti (45.8°, 40.9°) in both molecules. The D-ribosyl conformation is 2Tj (157.6°, 32.1°) in one molecule, and 2T3 (165.1°, 31.9°) in the other. The exocyclic, C-4 -C-5 bond torsion-angles are gauche+ (51.9°, 53.9°) in both molecules, and the C-5 -0-5 bond torsion-angles are trans (172.5°, 176.6°). The two UDP molecules form a dimer coordinated by three K+ ions. There is no metal-ion or water bridge between the pyrophosphate chain and the uracil base of the same molecule. The three K+ ions are coordinated by oxygen atoms of... 

Shukla MK, Leszczynski J (2002) A theoretical investigation of excited-state properties of die adenine-uracil base pair. J Phys Chem A 106 1011—1018... 

A uracil glycosylase recognizes and removes the uracil base, leaving an apyrimidinic (AP) site in the DNA strand. 

Like RNAs (see p.82), deoxyribonucleic acids (DNAs) are polymeric molecules consisting of nucleotide building blocks. Instead of ribose, however, DNA contains 2 -deoxyribose, and the uracil base in RNA is replaced by thymine. The spatial structure of the two molecules also differs (see p.86). 

The deoxyuracil derivatives-2-hydroxypyrimidine (69) (2-pymoH), 4-hydroxy-pyrimidine (70) (4-pymoH), 4,6-dimethyl-2-hydroxypyrimidine (71) (2-dmpymoH), and pyrimidine (72) (pym), shown here as the minor tautomer, have provided metallacalixarenes having closer resemblance to classical calixarenes, as compared with those obtained from uracil. The reactions of [(en)M(H20)2KN03)2 (M = Pd and Pt ) with 2-pymoH in water gave tetranuclear metallacalixarenes [(en)Pd(2-pymo-N2 N3)]4(N03)4 (73) and [ en)Ft 2-pjmo-Nl N3MN03)2 (74) (2000IC2301). As compared with uracil-based systems, the appearance of one set of resonances for each of pyrimidine PI, in their IT NMR spectra showed fast... 

These ideas have been illustrated in a recent study of the co-crystalline complex of 1-meCyt 5-FUra [19]. Using model calculations, it was shown how the hydrogen-bonding network of the crystal is able to sustain a proton shuttle which leads to the selective formation of certain radicals. Calculations predict that the site of reduction would be the cytosine base, yielding the N3 protonated cytosine anion, Cyt(N3-I-H), while the uracil base would be the site of oxidation, yielding the N1 deprotonated uracil cation, Ura(Nl—H) ... 

The palladium catalysed coupling of trimethylsilylacetylene and the iodopyridone derivative shown in 3.57. led to the formation of the corresponding ethynylpyridine. The absence of the spontaneous ring closure to furo 2,3-/)]pyndinc might be attributed to the preference of the pyridone form over the hydroxypyridine form. Addition of a copper catalyst and base, however, led to the closure of the fiiian ring (3.57.),73 The same approach was utilised in the functionalization of uracil based nucleosides.74... 

Ultraviolet spectroscopy metal in water complexes, 309 Uracil bases... 

M. Meyer et al., Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads. J. Comput. Chem. 26, 352-364 (2005)... 

Activated aromatic compounds are chlorinated readily by (dichloroiodo)benzene. Generally, negligible amounts of ortAo-chloro isomers are produced from diverse aromatic compounds, e.g. salicylic acid gave its 5-chloroderivative (89%) [16]. Exceptions were noted in the chlorination of the triphenyl phosphinimine of aniline which afforded o- and p-products in the ratio 7 3 [17], and of 2-naphthol which gave its 1-chloroderivative (84%) [16]. (Dichloroiodo)benzene was superior for the chlorination of uracil bases and protected nucleosides, e.g. [18] ... 

In abiotic conditions it has been possible to obtain all four RNA bases (adenine, cytosine, guanine and uracil), but not the DNA characteristic base (thymine). In vivo, furthermore, thymine is synthesised from uracil-based precursors. 

The uracil-uracil base-pair configuration UUS2 (Fig. 16.2) is not observed with the monomer bases, but in the modified nucleoside 5-dimethylaminouridine [DMURID], and it has been proposed to occur in the double helix formed by the... 

Similarly, we can write the interaction matrix for the possible hypoxanthine-uracil base pairs ... 

Constitutional Self-Organization of Adenine-Uracil-Based Hybrid Materials... 

Figure 3 Supramolecular dimers, trimers, and oligomers generated by H-bonding self-assembly of (a) adenine, (b) uracil, and (c) adenine-uracil base-pair. (R = sugar, alkyl, etc.)...

How is the other major pyrimidine ribonucleotide, cytidine, formed It is synthesized from the uracil base of UMP, but UMP is converted into UTP before the synthesis can take place. Recall that the diphosphates and triphosphates are the active forms of nucleotides in biosynthesis and energy conversions. Nucleoside monophosphates are converted into nucleoside triphosphates in stages. First, nucleoside monophosphates are converted into diphosphates by specific nucleoside monophosphate kinases that utilize ATP as the phosphoryl-group donor (Section 9.4). For example, UMP is phosphorylated to UDP by UMP kinase. 

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