Nucleic acid polymerase cofactors

Some typical biological interactions, frequently used in affinity chromatography are enzyme to substrate analogue, inhibitor, or cofactor antibody to antigen, virus, or cell lectin to polysaccharide, glycoprotein, cell surface receptor, or cell nucleic acid to complementary base sequence, histones, or nucleic acid polymerase hormone or vitamin to receptor, or carrier protein glutathione to glutathione-S-transferase (GST) or GST fusion proteins and metal ions to poly (His) fusion proteins, or native proteins with histidine, cysteine and/or tryptophan residues on their surfaces. 

Classical approaches to plant DNA isolation aim to produce large quantities of highly purified DNA. However, smaller quantities of crudely extracted plant DNA are often acceptable for PCR analysis. Another efficient method for preparation of plant DNA for PCR is a single-step protocol that involves heating a small amount of plant tissue in a simple solution. Several factors influence nucleic acid release from tissue salt, EDTA, pH, incubation time and temperature. These factors must be optimized for different sample substrates. EDTA in the sample solution binds the Mg + cofactor required by the Taq polymerase in the PCR, so the EDTA concentration in the solution, or the Mg + concentration in the PCR, must be carefully optimized. 

The Li+-induced inhibition of the production of the HSV virus may be related to its actions upon viral DNA polymerase production and activity. Li+ reduces both the synthesis of DNA polymerase in tissue culture and the activity of DNA polymerase in vitro, each by about 50%. It has been proposed that Li+ reduces the biosynthesis of viral polypeptides and nucleic acids, and hence inhibits viral DNA replication by competition with Mg2+, a cofactor of many enzymes [243]. However, the inhibitory effect of Li+ on HSV replication in tissue culture is not affected by Mg2+ levels. A more likely hypothesis is the alteration of the intracellular K+ levels, possibly modifying levels of the high-energy phosphate compounds by replacement of either Na+ or K+ in Na+/K+-ATPase [244]. In tissue culture, HSV replication has been shown to be affected by the... 

Nucleic acid is more rigid and stacked, while protein can assume a number of tertiary conformations so that many different surfaces can accommodate different molecular species. The various ribonucleotides that compose RNA can serve as cofactors for enzymatic action (e.g., ATP) and as substrates for polymer formation. For example, ATP can polymerize to poly(A) in the presence of a polynucleotide primer and poly (A) polymerase. Poly (A) polymerase can also function as a poly (A) hydrolase and liberate AMP, ADP, and ATP from poly(A) (Abraham and Jacob, 1978). 

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