References on DNA replication

BIOC/MCB 568 -- Fall 2010
John W. Little--University of Arizona

BIOC/MCB568 Home Page

 References

 

Note: Most of the links given here are to PubMed pages; from University computers, there should be a link near the top of the page to the article itself. If there is no link, you can usually get there from the Science Library Biochem Journals link. Some links here are to the articles themselves; these can be accessed from University computers, or from your home computer if you have VPN installed on it.

Movie:

An animated movie showing the architecture and dynamics of the replisome is at a link in the middle of the page at http://www.hhmi.org/research/investigators/odonnell.html. Repeated viewing helps you visualize the operation of the various parts of the replisome. Note how the clamp loader holds the complex together, in addition to loading a new clamp onto the RNA primer. Note also how the lagging strand polymerase switches from one clamp to another. Finally, observe how the lagging strand loops out as the Okazaki fragment is being made--the so-called "trombone model".

Reviews:

DNA structure

Kool, E.T. Annu. Rev. Biophys. Biomol. Struct. 30, 1–22 (2001). "Hydrogen bonding, base stacking, and steric effects in DNA replication." Reviews the forces that stabilize double-stranded DNA, concluding that hydrogen-bonding and base-stacking contribute roughly equally to stability.

DNA replication

Kool, E.T. Annu. Rev. Biochem. 71, 191-219 (2002). "Active site tightness and substrate fit in DNA replication". Discusses contribution of a tight DNA polymerase active site to fidelity of DNA replication.

O'Donnell, M. JBC 281, 10653-10656 (2006). "Replisome architecture and dynamics in Escherichia coli." A current overview of the components of the replication fork. Relatively short and accessible.

Indiani, C. and O'Donnell, M. Nat. Rev. Mol. Cell Biol. 7, 751-761 (2006). "The replication clamp-loading machine at work in the three domains of life". A more detailed discussion of clamp loaders in bacteria, archaea and eukaryotes.

Lovett, S.T. Mol. Cell 27, 523-526 (2007). "Polymerase switching in DNA replication". Brief overview of recent evidence that the replisome might contain not two but three DNA polymerases, with the "spare" being bound to the clamp loader. Article also briefly describes the "toolbelt" model for the sliding clamp.

Blow, J.J. and Dutta, A. Nat. Rev. Mol. Cell Biol. 6, 476-486 (2005). "Preventing re-replication of chromosomal DNA". A detailed discussion of "licensing" of replication forks in eukaryotes.

A web page on the class web site gives an overview of licensing.

Papers:

Meselson, M. and Stahl, F. PNAS 44, 671-682 (1958). "The replication of DNA in Escherichia coli."

Okazaki, R., Okazaki, T., Sakabe, K., Sugimoto, K. and Sugino, A. PNAS 59, 598-605 (1968). "Mechanism of DNA chain growth, I. Possible discontinuity and unusual secondary structure of newly-synthesized chains. "

Amado, L. and Kuzminov, A. JBC 281, 22635-22646 (2006). "The replication intermediates in Escherichia coli are not the products of DNA processing or uracil excision". A recent version of the Okazaki paper, leading to the same conclusion that leading-strand synthesis in vivo is discontinuous.

Indiani, C., McInerney, P., Georgescu, R., Goodman, M.F. and O'Donnell, M. Mol. Cell 19, 805-815 (2005). "A sliding-clamp toolbelt binds high- and low-fidelity DNA polymerases simultaneously." Some of the evidence for the "toolbelt" model.

Pomerantz, R.T. and O'Donnell, M. Nature 456, 762-767 (2008). "The replisome uses mRNA as a primer after colliding with RNA polymerase". Another mechanism (aside from DNA damage blocks to replication) for making the leading strand discontinuous.

Yao, N.Y., Georgescu, R.E., Finkelstein, J. and O'Donnell, M.E. PNAS 106, 13236-13241 (2009). "Single-molecule analysis reveals that the lagging strand increases replisome processivity but slows replication fork progression". Cool single-molecule experiments; the following reference has clear diagrams that illustrate the experimental set-up much more clearly.

Georgescu, R.E., Yao, N.Y. and O'Donnell, M. FEBS Letters 584, 2596-2605 (2010). "Single-molecule analysis of the Escherichia coli replisome and use of clamps to bypass replication barriers." Partly a review of the previous paper. Single-molecule methods are used to demonstrate that the pol III core that copies the lagging strand does not dissociate from the replisome between Okazaki fragments.