Bibliography

Books

Brown T.A. 2002. Genomes, 2nd edition. John Wiley. New York, and BIOS Scientific Publishers Ltd., Oxford. United Kingdom.

DePamphilis ML, 199b. DNA replication in eukaryotic cells. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Romberg A. and Baker T.A. 1992. DNA Replication.

2nd edition. W H. Freeman, New York. Chemistry of DNA Synthesis

Blautigaro C.A. and Steitz T.A. 1998. Structural and functional insights provided by crystal structures of DNA polymerases, Ctur. Opin. Sfmef. Biol. 8; 54-63.

Jäger J. and Pata J.D. 1999. Getting a grip: Polymerases and their substrate complexes. Curr. Opin. Struct. Biol. 9: 21 -28.

The Mechanism of DNA Polymerase

Doublie S. and Ellenberger T. 199«. The mechanism of action of T7 DNA polymerase, Curr, Opin. Struct. Biol. 8: 704-712.

Steitz T.A. 1998. A mechanism for all polymerases. Nature 381:231-232.

Sutten M.D. and VVaiker G.C 2001. Managing DNA polymerases: Coordinating DNA replication, DNA repair, and DNA recombination. Proc. Natl Acad, Sei. 98: 8342-8349.

The Replication Fork

Baker T.A. and Bell S.P 1998. Polymerases and the repli-some: Machines within machines. Cell 92: 295—305.

Benkovic S.f. Valentine A.M. and Salinas F. 2001. Kepli&otne-mediated DNA replication. Ajina. Rev. Biochem. 70; 181-20«;

O'Donnell M., Jeruzalmi D,, and Kuriyan J. 2001. Ciamp loader structure predicts the architecture of DNA polymerase III holoenzyme and RFC. Curt- Biol. 11: K935-R946.

Wang f.C. 2002. Cellular' roles of DNA Lopoisomerases. Nat. Rev. Mol. Cell Biol. 3: 430-440.

The Specialization of DNA Polymerases Kunkel T.A. and Bebenek K. 2000. DNA replication fidelity. Anna. Rev. Biochem. 69: 497-529.

Patel P. H., Suzuki M., Adman E., Shinkai A., and l^oeb L.A. 2001. Prokaryotk: DNA polymerase I: Evolution, Structure, and "base flipping" mechanism for nucleotide selection. /. Mol. Biol. 308: 823-837-

Initiation of DNA Replication

Gilbert D.M. 2001. Making sense of eukaryotic replication origins. Science 294: 96-100.

Jacob F., Brenner S., and Cuzin F. 1963. On the regulation of DNA replication in bacteria. Cold Spring Harbor Synip. Quant. Bivl. 28: 329-348.

Tye B.K. 1999. MCM proteins in DNA replication. Aimu, Rev. Biochem. 68: 649-R86.

Finishing Replication

GreiderC.W. 1996. Telomere length regulation. Annu. Rev Biochem. 65: 337-365.

9 The Mutability and Repair of DN A

ho perpetuation of the genetic material from generation to gen eration depends on maintaining rates of mutation al low levels.

High rates of mutation in the germ line would destroy the species, and high rates of mutation in the soma would destroy ihe individual. Living cells require the correct functioning of thousands of genes, each of which could be damaged by a mutation at many sites in its protein-coding sequence or in flanking sequences that govern its expression or the processing of its messenger RNA.

if progeny are to have a good chance at survival, DMA sequences must be passed on largely unchanged in the germ-line. Likewise, the specialized cells of the adult organism could not carry out their mission if mutation rates in the soma were high. Cancer, for example, arises from cells that have lost the capacity to grow and divide in a controlled manner as a consequence of damage to genes that govern the cell cycle. If rates of mutation in the soma were high, the incidence of cancer would be catastrophic and unsustainable.

At the same time, if the genetic material were perpetuated with perfect fidelity, the genetic variation needed to drive evolution would be lacking, and new species, including humans, would not have arisen Thus, life and biodiversity depend on a happy balance between mutation and its repair. In this chapter, we consider the causes of mutation and the systems that are responsible tor reversing or correcting, and thereby minimizing, damage to the genetic material.

Two important sources of mutation are inaccuracy in DNA replication and chemical damage to the genetic; material- Replication errors arise from tautomerization, which, as we have seen in Chapter 8, imposes an upper limit on the accuracy of base-pairing during DNA replication. The enzymatic machinery for replicating DNA attempts to cope with the mis-incorporation of incorrect nucleotides through a proofreading mechanism, but some errors escape detection. Also, DNA is a complex and fragile organic molecule of finite chemical stability. Not only does it suffer spontaneous damage such as the loss of bases, but it is also assaulted by natural and unnatural chemicals and radiation that break its backbone and chemically alter its bases. Simply put, errors in replication and damage to the genetic material from the environment are unavoidable. A third important source of mutation is the class of insertions generated by DNA elements known as transposons. Transposition is a major topic in its own right, which we shall consider in detail in Chapter 11.

Errors in replication and damage to DNA have two consequences. One is, of course, permanent changes to the DNA (mutations), which can alter the coding sequence of a gene or its regulatory sequences. The second consequence is that some chemical alterations to the DNA prevent its use as a template for replication and transcription. The effect of mutations generally become manifest only in the progeny of

Replication Errors and Theii Repair (p. 236)

Repair of DNA Damage (p. I1

the cell in which the sequence alteration has occurred, hut lesions that impede replication or transcription can have immediate effects on cell function and survival.

The challenge for the cell is twofold. First, it must scan the genome to detect errors in synthesis and damage to the DNA, Second, it must mend the lesions and do so in a way that, if possible, restores the original DNA sequence. Here we will discuss errors thai are generated during replication, lesions that arise from spontaneous damage to DNA, and damage that is wrought by chemical agents and radiation. Tn each case we shall consider how the alteration to the genetic material is detected and how it is properly repaired. Among the questions we shall address are the following: how is the DNA mended rapidly enough to prevent errors from becoming set in the genetic material as mutations? How does the cell distinguish the parental strand from the daughter strand in repairing replication errors? How does the cell restore the proper DNA sequence when, due to a break, or severe lesion, the original sequence can no longer be read? How does the cell cope with lesions that block replication? The answers to Uiese questions depend on the kind of error or lesion that needs to be repaired.

We begin by considering errors that occur during replication and how they are repaired. We then consider various kinds of lesions that arise spontaneously or from environmental assaults before turning to the multiple repair mechanisms that allow the eel! to mend this damage. We will see that multiple overlapping systems enable the cell to cope with a wide range of insults to DNA, underscoring the investment that living organisms make in the preservation of the genetic material.

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