Phosphodiester linkages

Two new strands form as nucleotides that are complementary to those of the original strands are joined by phosphodiester linkages The sources of the new bases are dATP dGTP dCTP and dTTP already present in the cell... 

Section 28 6 Many important compounds contain two or more nucleotides joined together by a phosphodiester linkage The best known are those m which the phosphodiester joins the 5 oxygen of one nucleotide to the 3 oxygen of the other... 

The other important feature of the primary stmcture of RNA is the presence of the 2 -hydroxyl group in ribose. Although this hydroxyl group is never involved in phosphodiester linkages, it does impose restrictions on the heHcal conformations accessible to double-stranded RNA. 

Phosphorothioates. All three synthetic approaches appHcable to unmodified oligonucleotides can be adapted for synthesis of phosphorothioates (11) (33,46). If all of the phosphodiester linkages in an oligonucleotide are to be replaced with phosphorothioates, the ff-phosphonate method for coupling, followed by oxidation with Sg in carbon disulfide and triethylamine in the final step, is the most straightforward method. 

Fig. 19.1. Structure of phosphorylcholine (PC). PC is involved in phosphodiester linkage to carbohydrate in a number of lower organisms, including filarial nematodes (linking sugar appears to be A/-acetylglucosamine on species examined to date).

The result was quite disappointing, as instead of the required 3 -5 -phosphodiester linkage, which is found in nucleic acids today, the main products obtained were those with the unnatural 2 -5 -bond between the nucleotides. Further experiments showed that the presence of divalent metal ions had a clear positive effect on the matrix-dependent polycondensation. The addition of l-10mMPb2+ to 100 mM of poly(U) as the matrix and 50 mM of ImpA monomer caused the yield of oligomeric product (pentamers and longer) to increase by a factor of four (Sleeper et al., 1979). 

Figure 8.5 (a) Structural detail of the 2 -5 oligonucleotides (2 -5 A ) generated by 2 -5 A synthetase. Compare the 2 -5 phosphodiester linkages with the 3 -5 linkages characteristic of normal cellular oligonucleotides such as mRNA (b)... 

Figure 14.15 Major types of modification potentially made to an oligo s phosphodiester linkage in order to increase their stability or enhance some other functional characteristic. The native phosphodiester link is shown to the left...

Because of its unusual active site and its potential as a model for mammalian PC-PLC enzymes, there has been considerable interest in the mechanism of the PLC5c catalyzed hydrolysis of phospholipids. The few mechanistic points that are commonly accepted are that a water must be activated for attack on the phosphodiester linkage, the leaving group must be protonated, and the products must leave the enzyme active site (Fig. 11). These issues will now be examined. 

The heterodinucleoside duplex drugs ara-C-NOAC [arabinocytidylyl-(5 —>5 )-N -octadecyl-l-p-D-arabinofuranosylcytosine, mol. wt. 801g/mol], 5-FdU-NOAC [2 -deoxy-5-fluorouridylyl-(5 5 ) -N -octadecyl-l-p-o-ara-binofuranosylcytosine, mol. wt. 804g/mol] and NOAC-ETC [3 -C-ethynyl-cytidylyl-(5 —>5 ) -N -octadecyl-l-p-o-arabinofuranosylcytosine, mol. wt. 825g/mol] were synthesized by condensation of NOAC via a 5 5 phosphodiester linkage to ara-C, 5-FdU or ETC, respectively, using the method as described (45,52). 

The enzymes catalysing the synthesis of RNA, using DNA as a template, are known as DNA-dependent RNA polymerases. The term dependency indicates a requirement for a template. The RNA polymerases synthesise RNA in the 5 to 3 direction in formation of the phosphodiester linkage. This requires that the DNA template is read in the 5 to 3 direction (see below for explanation). 

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