Phosphodiester group structure

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. 

Nucleotides are the building blocks of nucleic acids their structures and biochemistry were discussed in chapter 23. When a 5 -phosphomononucleotide is joined by a phosphodiester bond to the 3 -OH group of another mononucleotide, a dinucleotide is formed. The 3 -5 -linked phosphodiester intemucleotide structure of nucleic acids was firmly established by Lord Alexander Todd in 1951. Repetition of this linkage leads to the formation of polydeoxyribonucleotides in DNA or polyribonucleotides in RNA. The structure of a short polydeoxyribonucleotide is shown in figure 25.3. The polymeric structure consists of a sugar phosphate diester backbone with bases attached as distinctive side chains to the sugars. 

Structure of a phosphodiester group. The vertical arrows show the bonds in the phosphodiester group that are free to rotate. The horizontal arrows show the N-glycosidic bond about which the base can rotate freely. A polynucleotide consists of many nucleotides linked together by phosphodiester groups. 

Nucleoproteins, naturally occurring protein conjugates in which the hydroxy group of a Ser, Thr or Tyr residue is linked via a phosphodiester group to the 3 - or 5 -end of a nucleic acid. Nucleoproteins play decisive roles in important biological processes such as viral replication [V. A. Bloomfield et al. (Eds.), Proteins and Nude-oproteins Structure, Dynamics, and Assembly, Rockefeller University Press, 1980 B. A. Juodka, Nucleosides Nucleotides 1984, 3, 445 M. Salas, Annu. Rev. Biochem. 1991, 160, 39 L. Blanco et al., Proc. Natl. Acad. Sci. USA 1994, 91,12198]. 

Ribonucleic acids (RNA) are similar to deoxyribonucleic acids (DNA) in that they, too, consist of long, unbranched chains of nucleotides joined by phosphodiester groups between the 3 -hydroxyl of one pentose and the 5 -hydroxyl of the next. There are, however, three major differences in structure between RNA and DNA ... 

The B - Z transition is Na -dependent and the endpoint corresponds to 2 positive charges per phosphodiester group. The ability to induce this transition is remarkable in view of the fact that normal methods of induction involve high concentrations of salt (2.5M Na ) or ethanol (60% vol/vol). The complex is now used routinely to induce the Z-conformation and as a probe for DNA structure. 

The Raman vibration of the symmetric stretching of the phosphodiester group -5 -CH2-O-PO2-O- appears at 814 cm and is slightly altered on fixation of a metal to the phosphate group.lt has been shown (8) that the intensity of the Raman line at 814 cm is a measure of the conformation in the tRNA backbone.The intensity of the above line undergoes a decrease of about 20% when the Mg " ions are extracted with a chelating agent (EDTA) and suitable dialysis. The backbone structure is... 

Only a few methods other than X-ray fiber dififiaction were attempted to study the structure of DNA in the solid state infrared was one (for example, see Pilet and Brahms, 1972). However, thin films of DNA were used for these studies instead of the fiber samples. On the other hand, P NMR can be measured for the fiber sample, and thus a parallel study of NMR and X-ray fiber diffraction methods can be carried out (Shindo era/., 1980,1981 Shindo and Zimmerman, 1980 Nall et ai, 1981). However, P NMR can only probe phosphodiester groups and requires larger samples than the... 

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