Polynucleotide hydroxyl terminal

The nucleotide bases are flat molecules. Each base pair is parallel to the one below it, with 340 picometers separating the two. There is a rotation of 36° between pairs, giving ten base pairs per complete turn of the helix. The two sugar-phosphate backbone strands wind around these stacked pairs, as shown in Figure 13-29. The two strands of DNA run in opposite directions, with the terminal phosphate end of one polynucleotide matched with the free hydroxyl end of the other. 

A tRNA molecule is specific for a particular amino acid, though there may be several different forms for each amino acid. Although relatively small, the polynucleotide chain may show several loops or arms because of base pairing along the chain. One arm always ends in the sequence cytosine-cytosine-adenosine. The 3 -hydroxyl of this terminal adenosine unit is used to attach the amino acid via an ester linkage. However, it is now a section of the nucleotide sequence that identifies the tRNA-amino acid combination, and not the amino acid itself. A loop in the RNA molecule contains a specific sequence of bases, termed an anticodon, and this sequence allows the tRNA to bind to a complementary sequence of bases, a codon, on mRNA. The synthesis of a protein from the message carried in mRNA is called translation, and a simplified representation of the process as characterized in the bacterium Escherichia coli is shown below. 

It is to be expected that terminal ribofuranose moieties, each having one free primary hydroxyl group, would be converted by oxidation to the corresponding glycosiduronic acids these should be readily decarboxylated and cleaved, thus making possible a stepwise degradation of the polynucleotide chain. 

Fig. 12.19. The regions of eukaryotic mRNA. The wavy line indicates the polynucleotide chain of the mRNA and the As constituting the poly(A) tail. The 5 -cap consists of a guanosine residue linked at its 5 hydroxyl group to three phosphates, which are linked to the 5 -hydroxyl group of the next nucleotide in the RNA chain. The start and stop codons represent where protein synthesis is initiated and terminated from this mRNA.

As soon as a ddNTP is incorporated into the growing polynucleotide, the reaction is terminated, as there is no free 3 -hydroxyl group for further incorporation of a nucleotide. Thus, the addition of ddNTPs leads to a series of tmncated chains, each terminated by the dideoxy analogue in the position of the corresponding base. 

Strand polarity, antiparaUel coirformatioK the polarity of nucleotide chains, with reference to the sequence of 3, 5 -phosphodiester bonds. Polynucleotide chains have a 3 -end (the terminal sugar residue is linked to the preceding residue via its S -hydroxyl, and the 3 -hydroxyl is free or phosphorylated) and a 5 -end (the 5 -hydroxyI is free or phosphorylated). In DNA and other double-stranded nucleic acids, the two strands always lie antiparallel to one another. During replication and transcription, the newly synthesized strand is always antiparallel to its template. The polarity of a nucleotide strand is indicated by 3 5 or 5 -> 3. ... 

In contrast to the polymerization and pyrophos-phorolysis that attack 3 -terminal groups, the hydrolytic property (exonuclease II) of E. coli DNA polymerase can affect both ends of the molecule (3 -OH or 5 -OH and 5 -P04-terminal). However, the exonucleo-lytic attack does not take place when the polynucleotide chain is terminated by the 3 -P04-terminus. DNA polymerase—which is synthesized after E, coli is infected by T4 phage—appears to hydrolyze exclusively from the 3 -hydroxyl terminus and is inhibited by conditions conducive to DNA synthesis. The mode of... 

The specificity of pancreatic ribonuclease has been the subject of many careful studies. It has been found to hydrolyze the intermediate linkage between the 3 -phosphate of a pyrimidine nucleoside and the 5 -hydroxyl of the adjoining purine or pyrimidine nucleoside 162, 163). Thus, when ribonuclease is allowed to act upon yeast or calf liver RNA cytidine 3 -phosphate, uridine 3 -phosphate, and a number of oligonucleotides ( limit polynucleotides ) are formed. The oligonucleotides contain only purine nucleosides with a terminal pyrimidine nucleoside 3 -phosphate residue 164, 166) [Eq. (45)]. 

Selective and preferential acetylation of terminal hydroxyl groups in polynucleotides... 

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