Nucleic acids depolymerization

Although some depolymerases act processively in cleaving their polymeric substrates, others act by what can be described as multiple attack which results in nonselective scission or random scission. The analysis of cleavage products during the course of enzyme-catalyzed depolymerization can provide important clues about the nature of the reaction. With random scission, the rate of bond scission must be proportional to the total number of unbroken bonds present in the solution. Thomas measured the rate of base addition in a pH-Stat (a device with an automated feedback servomotor that expels ti-trant from a syringe to maintain pH) to follow the kinetics of DNA bond scission by DNase. The number of bonds cleaved was linear with time, and this was indicative of random scission. In other cases, one may apply the template challenge method to assess the processivity of nucleic acid polymerases. See Processivity... 

Water is not just the solvent in which the chemical reactions of living cells occur it is very often a direct participant in those reactions. The formation of ATP from ADP and inorganic phosphate is an example of a condensation reaction in which the elements of water are eliminated (Fig. 2-22a). The reverse of this reaction— cleavage accompanied by the addition of the elements of water—is a hydrolysis reaction. Hydrolysis reactions are also responsible for the enzymatic depolymerization of proteins, carbohydrates, and nucleic acids. Hydrolysis reactions, catalyzed by enzymes called... 

Melling and Atkinson29 investigated nuclease treatment as a method for the removal of nucleic acids from bacterial suspensions. Two strains of E. coli were used and for both the strains the nuclease treatment was effective in depolymerizing nucleic acids and, hence, in recovery of supernatant after centrifugation to remove cell debris from disrupted cells. The nucleotide content in the supernatant was found to be 15-20% of total proteins and nucleic acids. The nucleotide content in the supernatant was reduced to a very low level by ammonium sulfate precipitation followed by dialysis of the redissolved precipitate. As stated earlier, direct precipitation of nucleotides resulted in significant residual nucleotides in the proteins. 

Metal ions are usually required to promote and stabilize functionally active or native conformations of nucleic acids, as well as to mediate nucleic acid-protein interactions. However, metal ions can also cause structural transformation of nncleic acids, or denature their native structures. In addition to structural roles, some metal compounds can indnce cleavage (i.e. scission, fragmentation, or depolymerization) and modification (withont cleavage) of nucleic acids. Metal-nucleic acid interactions can be either nonspecific or dependent on the chemical nature of nucleotide residues, nucleic acid sequence, or secondary and/or tertiary structure of nucleic acids. The specificity of these interactions is dependent... 

It should be pointed out that these depolymerization reactions are carried out at elevated temperatures. At low temperatures RNA, like DNA, is stabilized by metal ions through the charge neutralization effect 18, 29). We have thus seen that coordination of metal ions with the phosphate group produces two strikingly different results with nucleic acid. At low temperatures the conformation of the macromolecules is stabilized by a charge neutralization mechanism, and at high temperatures RNA and the polyribonucleotides are depolymerized. 

Antimicrotubule agents represent a unique class of compounds in so far as their taiget does not involve nucleic acid synthesis or int ity. Antimicrotubule agents basically exploit the dynamic character the most prominent features of all microtubules (except stable microtubules of cilia and flagella) i.e., the rapid exchange of subunits between polymers and a soluble tubulin pool. This dynamic ins ility is described by four parameters the rates of polymerization and depolymerization, and the fiequendes of catastrophe (the transition from polymerization to depolymerization) and rescue (the transition from depolymerization to... 

This depolymerization of RNA by zinc thus is also quite analogous to the destabilization of thiophenal-ethylenediamine by copper ions. We shall see later that zinc ions binding to phosphate can also stabilize the nucleic acid structure, just as copper ions can stabilize, as well as labilize, a Schiff base. 

It should be noted that even though the same metal can influence nucleic acid molecules in three different ways, these different influences take place under quite different conditions. The stabilization through neutralization of the charge on the phosphate occurs at relatively low temperature, in RNA below temperatures required for cleavage and in DNA below temperatures required for strand separation. The depolymerization occurs only with RNA, because of the requirement of the 2 -hydroxyl group, and the unwinding-rewinding phenomenon can occur only with molecules like DNA that have ordered structures that can be unwound. It is not confined to DNA, but works also with polyribonucleotides with helical properties. 

AA is known to Inactivate viruses (Murata and Uike, 1976) and antltumorlc reductones like AA depolymerIzed nucleic acids and alter the priming action of DNA for DNA—polymerase (Omura et al., 1975 1978). 

The probability is very strong that complete depolymerization of nucleic acids to the stage of nucleotides requires the intervention of more than one enzyme. Studies on the distribution of nucleolytic activity have shown it to be common among diverse cells. 

The two hydrolyzable bonds in nucleotides are the N-ribosidic link and the phosphoester link at C3 or at Cs in muscle adenylic acid. Repeated work has shown that phosphatases can split the phosphate from free nucleotides. It is a controversial issue, however, whether there exist phosphatases which can cleave free phosphate from nucleic acids without the preliminary intervention of a depolymerizing enzyme... 

Scope of data. This chapter covers metal ion interactions with DNA, RNA and polynucleotides. A few related data involving oligonucleotides are included when necessary and appropriate. Oligomers when crystallized for X-ray analysis resemble polymers and are treated as such. The subject matter is limited to direct effects of metal binding, e.g. metal association constants and binding characteristics, metal binding effects on conformation, and metal-catalyzed depolymerization. There are of course many other phenomena that could be included, but are deemed unsuitable for tabulation. The effects of metal binding to DNA and RNA that involve interaction with proteins are covered only when the primary effect is on the nucleic acid moiety. 

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