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The Oncologist, Vol. 10, No. 5, 361-362, May 2005; doi:10.1634/theoncologist.10-5-361
© 2005 AlphaMed Press

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 The Molecular Perspective: Double-Stranded DNA Breaks
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Fundamentals of Cancer Medicine

The Molecular Perspective: Double-Stranded DNA Breaks

David S. Goodsell

Correspondence: David S. Goodsell, Ph.D., Associate Professor, The Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. Telephone: 858-784-2839; Fax: 858-784-2860; e-mail: goodsell{at}scripps.edu Website: http://www.scripps.edu/pub/goodsell


   LEARNING OBJECTIVES
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 Learning Objectives
Additional Reading
 
After completing this course, the reader will be able to:

  1. Discuss double-stranded DNA breaks and their role in cancer.

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Our long, delicate DNA strands are easily broken. Ionizing radiation, such as x-rays and gamma rays, as well as drugs like bleomycin (Blenoxane®; Bristol-Myers Squibb, Princeton, NJ, http://www.bms.com) create reactive forms of oxygen, which in turn attack DNA and cause breakage. Double-stranded DNA breaks can occur when DNA polymerase runs into an unrepaired nick in the DNA. Topoisomerase inhibitors can also cause breaks: topoisomerase breaks and rejoins DNA in the course of its function, and inhibitors can block the rejoining step. Cells also break their DNA on purpose for special functions, most notably during the gene shuffling that occurs as lymphocytes mature, which generates diversity in antibodies, T-cell receptors, and other highly variable immune system proteins.

These breaks can cause serious problems. A single break in a key gene can kill a cell, or cause it to kill itself by apoptosis. So cells have powerful methods to repair this damage as soon as it happens. In your lifetime, each of your cells will have repaired, more or less successfully, several thousand double-stranded DNA breaks. Radiation therapy overwhelms this natural repair system, using high doses of radiation to fragment the DNA in cancer cells.

Cells use two major methods to repair double-stranded DNA breaks. The first method—homologous recombination—uses the fact that we carry a duplicate set of DNA in our cells. The break is repaired using the duplicate set as a template. As you might imagine, this can be very precise, since the cell can use the undamaged DNA strand to ensure that the repair is correct. The second method—nonhomologous end joining—repairs the break directly, without any outside information. It is less accurate, and may result in the addition or removal of a few nucleotides at the repair site.

Nonhomologous end joining requires the concerted action of a series of proteins. The process is thought to start with the Ku protein (Fig. 1Go), a dimer composed of two similar proteins. It is prevalent in the cell nucleus and binds readily to DNA ends. Ku then binds to DNA-dependent protein kinase and begins the process of synapsis that holds the two broken ends in close proximity. Other proteins, such as Artemis, and perhaps polymerases, then bind to the break, trimming the two ends and filling in gaps, making them ready for rejoining. Finally, the two ends are rejoined by DNA ligase IV with the help of XRCC4 (Fig. 2Go).



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  		Figure 1. Ku protein. The structure of the Ku protein dimer (blue) reveals one of the mysteries of its action: how can a protein bind tightly to damaged DNA (pink and orange) but still allow access by other repair proteins? The protein wraps two thin arms around the DNA, gripping the DNA but still leaving most of the surface available. Coordinates were taken from entry 1jey at the Protein Data Bank (http://www.pdb.org).

 


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  		Figure 2. DNA ligase and XRCC4. Human DNA ligases (purple) use ATP to rejoin breaks in DNA strands (the DNA is shown end-on in pink and orange). Ligases wrap entirely around the DNA when they perform their joining reaction. DNA ligase IV, used in nonhomologous end joining, is assisted by the factor XRCC4 (green). Coordinates were taken from entries 1ik9, 1x9n and 1in1 at the Protein Data Bank.

 
Because of the trimming that occurs at each end, and because synapsis may occur between any two broken DNA ends, this process is imprecise. In the case of the antibody genes, this is a good thing, since it is the way that our immune system builds a large repertoire of slightly different antibodies. But for repair of accidental damage, these small (and large) errors can be dangerous, in some cases leading to cancer. For instance, if two breaks occur at once, and the ends get mixed up when the repair is made, genes may be translocated from one place to another. In the case of Burkett’s lymphoma, this process moves a normally inactive c-myc gene into a very active area, causing overexpression of the gene and leading to uncontrolled growth in the cell. In other forms of leukemia, the arms of two different chromosomes are switched, forming the "Philadelphia chromosome" with a fused Bcr-Abl protein at the join site. The fused protein is overactive and leads to transformation of the cell.


   ADDITIONAL READING
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Received February 25, 2005; accepted for publication February 25, 2005.





This Article
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 The Molecular Perspective: Double-Stranded DNA Breaks
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