Polymerase, action

Fig. 4. The use of arsonomethyl phosphonate as an analogue of diphosphate by RNA polymerase. The enzyme accepts the analogue in the reverse of polymerase action. Since the product hydrolyzes, the overall effect is that of an exonuclease, producing nucleoside 5 -phosphates (59).

Figure 27-14 Schematic representation of DNA polymerase action on a nicked strand of DNA in which the nick has been enlarged. At the catalytic center new nucleotide units are added at the 3 end of a growing strand. At the 3 -5 exonuclease site the 3 terminal nucleotide may be removed hydrolytically. This will happen to the greatest extent if the nucleotide is poorly paired in the duplex. At the 5 -3 exonuclease site nucleotides are hydrolytically removed from the 5 end of a strand in the chain.265,267...

The biochemical mode of action has been studied by several authors (16, 18). It appears that metalaxyl inhibits RNA synthesis by Interference with template-bound and a -amanitin-insensitive RNA polymerase action (15). 

Nucleotide excision and base removal followed by the action of apurinic-apyrimidine endonucleases (AP endonucleases) are the two types of excision repair that currently are thought to occur. A number of nucleotides are excised from the damaged DNA strand. After excision, the correct complementary bases are replaced by polymerase action, with the intact strand as template. Finally, the new strand is attached covalently to the adjacent undamaged old strand by the enzyme DNA ligase. 

The polymerase chain reaction uses (1) a thermostable DNA polymerase, such as Taq polymerase derived from the bacterial thermophile Thermus aquaticus, (2) a DNA template which is to be amplified, (3) two primers, each typically of around 20 nucleotides, which anneal to distinct parts on the complementary strands of the target and serve as sites for commencing DNA polymerase action, (4) a solution including the four deoxynucleoside triphosphates dATP, dCTP, dGTP and dTTP, Mg2+, salts and pH buffer. 

DNA polymerase needs a primer on which to attach a new nucleotide unit for chain growth. Is a primer obligatory for RNA polymerase action ... 

Daley JM, Laan RL, Suresh A, Wilson TE. DNA joint dependence of pol X family polymerase action in nonhomologous end joining. J. Biol. Chem. 2005 280 29030-29037. 

A second major difference between prokaryotes and eukaryotes is the extent of RNA processing. Although both prokaryotes and eukaryotes modify tRNA and rRNA, eukaryotes very extensively process nascent RNA destined to become mRNA. Primary transcripts (pre-mRNA molecules), the products of RNA polymerase action, acquire a cap at... 

Figure 3-17. Mechanism of DNA synthesis at the replication fork. Two rounds of polymerase action are shown. The number of nucleotides added in each round is much larger than shown in eukaryotes, about 10 ribonucleotides and 200 deoxyribonucleotides are polymerized on the lagging strand. Synthesis on the leading strand is continuous.

Helicases (Figure 24.28)- SSB proteins do not actively denature DNA and cannot actively unwind duplex DNA strands. Nevertheless, unwinding of this kind is essential if single-strand templates are to be exposed for polymerase action. The helicase proteins... 

Kapanidis, A. N., E. Margaret, S. O. Ho, E. Kortkhonjia, S. Weiss, and R. H. Ebright. Initial Transcription by RNA Polymerase Proceeds through a DNA-Scrunching Mechanism. Science 314, 1144-1147 (2006L [Primary research article about using fluorescence to determine the mechanism of polymerase action.]... 

Thiouridine has been incorporated at the 3 -end of the antisense strand of siRNA where it was found to be well tolerated. Both 2-(2-nitrophenyl)propyloxymethyl (NPPOM) and 3-(6-nitropiperonylox-ymethyl) (NPOM) have been used to protect the N3 position of thymine as a photo-labile protecting group which could then be used to control polymerase action during PCR. N3- and 04-carboxymethyl-thymidine have been synthesised as phosphoramidite building blocks and... 

Chamberun, M. and Berg, P. (1964) Mechanism of RNA polymerase action formation of DNA-RNA hybrids with single-stranded templates. J. Molec. Biol. 8,297 characterization of the DNA-de-pendent synthesis of polyadenylic acid. Ibid., p. 708. 

---