Phosphodiester group

The HPLC-MS/MS assay was also successfully applied to the measurement of UV-induced dimeric pyrimidine photoproducts [123, 124]. The latter lesions were released from DNA as modified dinucleoside monophosphates due to resistance of the intra-dimer phosphodiester group to the exonuclease activity during the hydrolysis step [125, 126]. The hydrolyzed photoproducts exhibit mass spectrometry and chromatographic features that allow simultaneous quantification of the three main classes of photolesions, namely cyclobutane dimers, (6-4) photoproducts, and Dewar valence isomers, for each of the four possible bipyrimidine sequences. It may be added that these analyses are coupled to UV detection of normal nucleosides in order to correct for the amount of DNA in the sample and obtain a precise ratio of oxidized bases or dimeric photoproducts to normal nucleosides. 

On treatment with hot alkali, most of the phosphodiester groups were... 

The 2-amino-2-deoxy-D-glucosyl phosphate linkage is very labile to acid consequently, the teichoic acid is hydrolyzed under mild conditions to a fragment which is apparently44 (43) or (44). Study of this compound should establish which hydroxyl group of the 2-acetamido-2- deoxy-D-glucose residue bears the phosphodiester group. The alanine ester residues (84a) Unpublished work of the authors with Mr. D. Button. 

All of the ribitol teichoic acids so far examined are composed of chains of ribitol residues joined through phosphodiester groups at C-l and C-5. Each chain is terminated by a phosphomonoester residue, and the ribitol residues bear glycosyl and D-alanine ester substituents. Detailed structures have been proposed for the polymers from Bacillus aubtilis and Lactobacillus arabinosus, and from two strains of Staphylococcus aureus. The structure of the teichoic acid from Bacillus subtilis was the first to be established in detail the other polymers differ mainly in the nature of the glycosyl substituents. 

The production of ribitol diphosphates on acid hydrolysis, and also on alkaline hydrolysis, of the product obtained after oxidation of the teichoic acid with periodate establishes the presence of ribitol phosphate residues joined to each other through phosphodiester groups. On oxidation of the polymer (o-alanine removed) with periodate, many of the ribitol residues were oxidized, and the quantitative data obtained support a structure in which there are 7-8 units in the chain. 

Phosphodiester Linkages The proton noise decoupled lp nmr spectra of the daunomycin poly(dA-dT) complex in 1 M NaCl solution at 67°C have been recorded at 1 antibiotic per 6 base pairs (Nuc/D = 11.8) and 1 antibiotic per A,3 base pairs (Nuc/D = 5.9). Resolved resonances are observed for the complex at both Nuc/D ratios (Figure 32). One of the resonances in the complex exhibits a chemical shift similar to that observed for poly(dA-dT) in 1 M NaCl alone ( 4.1 ppm) at this temperature while the other resonance is shifted downfield by 0.3 ppm in the Nuc/D = 11.8 complex and by 0.45 ppm in the NucD = 5.8 complex (Table XI). The results suggest that daunomycin intercalates at either the dTgdA or dApdT sites, resulting in a downfield shift of the 31p resonance of the corresponding phosphodiester grouping at the intercalation site. 

A second fragmentation pathway has been proposed for type a -B and w ions. This pathway does not require the loss of a nucleic base or the proximity of the charge to the cleavage site. It thus allows observation of these ions to be explained in the absence of adjacent charge. The first step is the direct cleavage of the 3 C—O bond of the phosphodiester group to produce the a and w fragments. The a ions then dissociate by the loss of a nucleic base to yield ions of type a -B . 

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