O the 3 end of the primer strand moves from the

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o The 3' end of the primer strand moves from the polymerase active site to the 3'->5' exonuclease active site. o The 3' residue is removed as a 5' mononucleotide, regenerating the 3' end that was used in the reaction cycle in which the error occured. o This event creates a paired primer 3' end which is rebound to the polymerase active site, minus the misincorporated residue. o A polymerization cycle procedes to try once again to incorporate the correct triphosphate. o Approximately 3% of correct incorporation events are also removed, suggesting this activity is not simply stimulated by the presence of mispairing.
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* The 5'->3' exonuclease removes paired DNA (and unpaired single strands) from in front of the enzyme. o The 5'->3' exonuclease is active on the same DNA at the same time as the polymerase activity. o The exonuclease can clear damaged DNA or RNA that might block the polymerase on the template strand. o The newly synthesized strand can be laid down as the old strand is cleared away. o The nuclease only removes paired residues, but can do so even if a string of unpaired residues is in the way. o The removed pieces can be mononucleotides or oligonucleotides.
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* DNA polymerase I is not the main replication polymerase in the E. coli cell. o Mutations in the gene encoding pol I (the polA gene) do not prevent cells from growing. o Such mutations do interfere with DNA repair. o A second DNA polymerase called pol II is also not essential for cell division, and is probably also involved in repair. o DNA pol III is the main replication DNA polymerase in E. coli, although pol I activity is important for rapid and efficient completion of the lagging strand (see below) o pol III functions as part of a large complex.
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* E. coli genomic DNA is replicated by DNA polymerase III at two diverging replication forks. o Autoradiographic experiments produce "theta structures" that indicate that DNA replication is bidirectional. o The site at which the replication is proceeding in one direction away from the origin of replication is called a replication fork. o The unreplicated parental DNA ahead of the polymerase represents the "handle" of the fork and the newly synthesized daughter strands are the tines of the fork. o Because duplex DNA strands are antiparallel, and because synthesis only occurs in the 5'->3' direction, the strategy for synthesis of the two daughters is different.
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* At the replication fork, one strand is synthesized quickly (the leading strand), and the other more slowly (the lagging strand). o The leading strand is synthesized continuously in the 5'->3' direction as the parental duplex is opened up. o The lagging strand must be synthesized in the 5'->3' direction away from the fork. o In order to keep up with the fork, DNA synthesis must be re-initiated many times on the lagging strand, whereas it need only be initiated once on the leading strand.
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