|This article needs additional citations for verification. (February 2009) (Learn how and when to remove this template message)|
For example, processivity is the average number of nucleotides added by a polymerase enzyme, such as DNA polymerase, per association event with the template strand. DNA polymerases associated with DNA replication tend to be highly processive, while those associated with DNA repair tend to have low processivity. Because the binding of the polymerase to the template is the rate-limiting step in DNA synthesis, the overall rate of DNA replication during S phase of the cell cycle is dependent on the processivity of the DNA polymerases performing the replication. DNA clamp proteins are integral components of the DNA replication machinery and serve to increase the processivity of their associated polymerases. Some polymerases add over 50,000 nucleotides to a growing DNA strand before dissociating from the template strand, giving a replication rate of up to 1,000 nucleotides per second.
DNA binding interactions
Polymerases interact with the phosphate backbone and the minor groove of the DNA, so their interactions do not depend on the specific nucleotide sequence. The binding is largely mediated by electrostatic interactions between the DNA and the "thumb" and "palm" domains of the metaphorically hand-shaped DNA polymerase molecule. When the polymerase advances along the DNA sequence after adding a nucleotide, the interactions with the minor groove dissociate but those with the phosphate backbone remain more stable, allowing rapid re-binding to the minor groove at the next nucleotide.
Interactions with the DNA are also facilitated by DNA clamp proteins, which are multimeric proteins that completely encircle the DNA, with which they associate at replication forks. Their central pore is sufficiently large to admit the DNA strands and some surrounding water molecules, which allows the clamp to slide along the DNA without dissociating from it and without loosening the protein-protein interactions that maintain the toroid shape. When associated with a DNA clamp, DNA polymerase is dramatically more processive; without the clamp most polymerases have a processivity of only about 100 nucleotides. The interactions between the polymerase and the clamp are more persistent than those between the polymerase and the DNA. Thus, when the polymerase dissociates from the DNA, it is still bound to the clamp and can rapidly reassociate with the DNA. An example of such a DNA clamp is PCNA (proliferating cell nuclear antigen) found in S. cervesiae.
Multiple DNA polymerases have specialized roles in the DNA replication process. In E. coli, which replicates its entire genome from a single replication fork, the polymerase DNA Pol III is the enzyme primarily responsible for DNA replication and forms a replication complex with extremely high processivity. The related DNA Pol I has exonuclease activity and serves to degrade the RNA primers used to initiate DNA synthesis. Pol I then synthesizes the short DNA fragments that were formerly hybridized to the RNA fragment. Thus Pol I is much less processive than Pol III because its primary function in DNA replication is to create many short DNA regions rather than a few very long regions.
In eukaryotes, which have a much higher diversity of DNA polymerases, the low-processivity initiating enzyme is called Pol α, and the high-processivity extension enzymes are Pol δ and Pol ε. Both prokaryotes and eukaryotes must "trade" bound polymerases to make the transition from initiation to elongation. This process is called polymerase switching.
- Stryer, L.; Berg, J. M.; Tymoczko, J. L. (2002), Biochemistry (5th ed.), New York: W. H. Freeman, ISBN 0716746840. 27.4.4
- Wyman, Claire; Botchan, Michael (April 1995). "DNA Replication: A familiar ring to DNA polymerase processivity". Current Biology 5 (4): 334–337. doi:10.1016/S0960-9822(95)00065-0. PMID 7627541. Retrieved 23 November 2014.
- Morales, Juan C; Kool, Eric T (1999). "Minor Groove Interactions between Polymerase and DNA: More Essential to Replication than Watson-Crick Hydrogen Bonds?". J Am Chem Soc 121 (10): 2323–2324. doi:10.1021/ja983502+. PMID 20852718. Retrieved 23 November 2014.
- Tsurimoto, Toshiki; Stillman, Bruce (1991). "Replication Factors Required for SV40 DNA Replication in Vitro". J Biol Chem 266 (3): 1961–1968. PMID 1671046. Retrieved 23 November 2014.
- Maga, Giovanni; Stucki, Manuel; Spadari, Silvio; Hübscher, Ulrich (January 2000). "DNA polymerase switching: I. Replication factor C displaces DNA polymerase α prior to PCNA loading". Journal of Molecular Biology 295 (4): 791–801. doi:10.1006/jmbi.1999.3394. PMID 10656791. Retrieved 23 November 2014.
- Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). Molecular Biology of the Gene 5th ed. Benjamin Cummings: Cold Spring Harbor Laboratory Press.
- http://opbs.okstate.edu/~melcher/MG/MGW4/MG424.html[dead link]
- Bedford, E; Tabor, S; Richardson, C. C. (1997). "The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I". Proceedings of the National Academy of Sciences of the United States of America 94 (2): 479–484. doi:10.1073/pnas.94.2.479. PMC 19538. PMID 9012809.
- Tabor, S; Richardson, C. C. (1987). "DNA sequence analysis with a modified bacteriophage T7 DNA polymerase". Proceedings of the National Academy of Sciences of the United States of America 84 (14): 4767–4771. doi:10.1073/pnas.84.14.4767. PMC 305186. PMID 3474623.