DNA polymerase molecules

A number of different DNA polymerase molecules engage in DNA replication. These share three important properties (1) chain elongation, (2) processivity, and (3) proofreading. Chain elongation accounts for the rate (in nucleotides per second) at which polymerization occurs. Processivity is an expression of the number of nucleotides added to the nascent chain before the polymerase disengages from the template. The proofreading function identifies copying errors and corrects them. In E coli, polymerase III (pol III) functions at the... 

Figure 17.21 Single nanometric aperture for real time single molecule DNA sequencing. A DNA polymerase molecule attached to the bottom surface is used to successively Incorporate fluorescent nucleotides complementary to the DNA strand, causing fluorescence bursts for each incorporation process (see text for details). Image copyright of Pacific Biosciences Inc., reprinted with permission.

Korlach, J., Marks, P.J., Cicero, R.L., Gray, J.J., Murphy, D.L., Roitman, D.B., Pham, T.T., Otto, G.A., Foquet, M., and Turner, S.W (2008). Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc. Natl Acad. Sci. USA 105 1176-1181. 

SaroHnycin (Fig. 1), a streptomycete antibiotic inhibits the DNA polymerase. It prevents the incorporation of thymidine into intact tumour cells, and into DNA primer in cell-free extracts. Sarcomycin probably blocks the thiol groups which are indispensable for the activity of the DNA-polymerase molecule. It is a noncompetitive inhibitor of the enzyme in the same way as iodoacetate or iodo-acetamide. Its action is prevented or reversed by 2-mercaptoethanoL... 

Escherichia coli exonuclease II is part of the DNA polymerase molecule and degrades both single- and double-stranded DNA to deoxyriboside-5 -phosphates, acting from either end of the chain. 

One of the simplest molecules found to inhibit the repHcation of DNA vimses in animals is phosphonoformic acid [4428-95-9] (PEA, 1) CH O P. Both PEA (as the trisodium salt CNa O P, foscamet [63585-09-1] audits homologue phosphono acetic acid [4408-78-0] (PAA, 2) C2H O P, were developed by Astra Pharmaceuticals (6) and show selective inhibition of DNA polymerase in various herpes vimses. 

FIGURE 12.1 DNA replication yields two daughter DNA duplexes identical to the parental DNA molecule. Each original strand of the double helix serves as a template, and the sequence of nucleotides in each of these strands is copied to form a new complementary strand by the enzyme DNA polymerase. By this process, biosynthesis yields two daughter DNA duplexes from the parental double helix. 

DNA polymerase and DNA ligase, resulting in a linear bimolecule, called a concatamer. Continued replication can lead to concatamers of considerable length, but ultimately a cutting enzyme slices each concatamer at a specific site, resulting in the formation of virussized linear molecules with repetitious ends. 

This enzyme is associated with the virions of RNA tumor viruses such as the Rous sarcoma virus (RSV). The enzyme has remarkable enzymatic activity in that it can catalyze several seemingly diverse steps in the synthesis of double-stranded DNA from the single-stranded RNA viral genome. The enzyme uses a tRNA for tryp-tophan as a primer to make a copy of DNA that is complementary to the viral RNA. The resulting RNA-DNA hybrid is converted to a double-stranded DNA molecule by ribon-uclease (RNase)H and DNA-dependent DNA polymerase activities that are intrinsic to reverse transcriptase. 

Enzymatic techniques can employ a variety of DNA or RNA polymerases to add controlled amounts of modified nucleotides to an existing stand. However, the most common procedures utilize either DNA polymerase I or terminal deoxynucleotide transferase. The polymerase is used with a template to add modified nucleoside triphosphates to the end of a DNA molecule or to various sites within the middle of a sequence. The terminal transferase can add modified monomers to the 3 end of a chain without a template. 

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