Double-Stranded Polynucleotides

Morphologists postulated for many years that the transfer of information from DNA to protein involves a form of nuclear RNA that migrates from nucleus to cytoplasm. This hypothesis found some concrete support as molecular biology developed. At first, it was found that a small fraction of bacterial RNA has a base composition identical to DNA in bacteria infected with T phage. The synthesis of DNA-depend-ent RNA was demonstrated in bacterial preparations and in mammalian nuclei. Triphosphate ribosides (UTP, GTP, CTP, and ATP) are required precursors for the synthesis of the new polynucleotide. Double-stranded DNA serves as a template in the reaction, and an RNA polymerase catalyzing the polymerization of the ribonucleotide was partially purified from both the bacterial and mammalian systems. 

The double stranded DNA shown m Figure 28 14(a) contains the polynucleotide sequence (the target region) we wish to amplify The DNA is denatured by heating to... 

Polynucleotides. Polynucleotides are potent interferon inducers. A mismatched, double-stranded synthetic polyribonucleotide ampligen and the double-stranded acids, polyadenylic-polyuridylic acid and polyinosinic-polycytidylic acids have been widely studied for cancer therapy(ii). Although these materials elicit excellent activity with murine rodents, therapeutic effects are dramatically decreased within primates. 

Watson and Crick showed in 1953, using X-ray diffraction data of hydrated DNA fibres [26], that B-DNA, the most commonly encountered form, corresponds to a right-handed double-stranded helix (Fig. 4). Two polynucleotide... 

The question of energy transfer is introduced also by the fact that polynucleotides frequently exist not only in single-strand forms but also entirely or partially as double-strand helices in which pyrimidine residues on one chain are hydrogen bonded to purine residues on the other chain. The reactivity of the pyrimidine residue can be strongly affected by the presence of its purine partner. An example of this will be found further on. 

Nucleic Acid. A nucleic acid is a natural polynucleotide. It is a sugar-phosphate chain with purine and pyrimidine bases attached to it, as shown in Chart 10. If the sugar is deoxyribose and the pyrimidine bases are cytosine and thymine, the nucleic acid is deoxyribonucleic acid, DNA if the sugar is ribose, and the pyrimidine bases are (mostly) cytosine and uracil, the nucleic acid is ribonucleic acid, RNA. The sequence of bases may appear arbitrary and random, but it constitutes a meaningful code (see Code Word). In double-stranded nucleic acids,... 

A few measmements of direct electrical transport were also performed on single bundles. Other measurements were done on networks formed of either double-stranded DNA [67] or alternative polynucleotides [68]. All the reported measurements showed current flowing through the bundles. We will show a few examples here. 

The purines and pyrimidines are relatively stable compounds with considerable aromatic character. Nevertheless, they react with many different reagents and, under some relatively mild conditions, can be completely degraded to smaller molecules. The chemistry of these reactions is complex and is made more so by the fact that a reaction at one site on the ring may enhance the reactivity at other sites. The reactions of nucleic acids are largely the same as those of the individual nucleosides or nucleotides, the rates of reaction are often influenced by the position in the polynucleotide chain and by whether the nucleic acid is single or double stranded. The reactions of nucleosides and nucleotides are best understood in terms of the electronic properties of the various positions in the bases.26 33 Most of the chemical reactions are nucleophilic addition or displacement reactions of types that are discussed in Chapters 12 and 13. 

A few recent NMR investigations of polynucleotides include studies of triple-helical DNA,689 Holliday junctions,290 double-stranded oligonucleotides containing adducts of carcinogens,690 691 of hairpin loops with sheared A A and G G pairs,692 and of proton exchange in both imino and amino groups.693... 

Finally, it should be noted that exonuclease III possesses an intrinsic DNA-phosphatase activity which specifically removes 3 -phosphoryl groups from double-stranded polynucleotides. This enzyme when acting on a 3 -phosphoryl-terminated DNA, first removes the 3 -phosphoryl group as inorganic phosphate, then proceeds as an exonuclease with the stepwise release of deoxynucleoside 5 -monophosphates (9). 

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