The Molecular Perspective: DNA Polymerase
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《干细胞学杂志》
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@scripps.edu Website: http://www.scripps.edu/pub/goodsell
DNA polymerase is our most accurate enzyme, for a good reason. It is the keeper of our most precious resource: our genetic information. DNA polymerase takes our DNA, gently unwinds it, and builds a complementary mate to each strand (Fig. 1). Thymine is paired with adenine, and cytosine is paired with guanine. The result is two identical copies of the genome, for use as cells divide or for passing on to our children.
Figure 1. DNA polymerase, shown here at the center in red, is part of a large molecular machine with all of the pieces needed to replicate DNA, shown in yellow. It contains helicases that separate DNA strands, primases that start to copy the strands, and the polymerase that does the major replication. The arrangement of the entire complex is still under study—an artist’s concept is shown here. Each polymerase contains a doughnut-shaped clamp that surrounds the DNA strand, holding the strand in place and allowing DNA polymerase to slide along the strand and build a long, continuous copy. In this picture, the parent DNA helix enters from bottom center and is separated by the helicase. The strand on the right feeds directly into the polymerase and is duplicated, leaving the picture at upper right. The strand on the left is facing the wrong direction, however, and is duplicated in parts, looping back into the polymerase and finally leaving the picture at lower left.
As you can imagine, this process must be as close to perfect as possible, so that the information is not corrupted. However, the hydrogen bonds between the four bases—two between adenine and thymine and three between cytosine and guanine—are only so strong. These bases can also form improper pairings, albeit with significantly weaker binding strength. If DNA polymerase relied only on the difference in pairing strength between proper matches and improper matches, it would make a mistake once in 10,000 nucleotides. This would introduce far too many mutations when our genome of six billion nucleotides is duplicated.
DNA polymerase uses several schemes to improve the accuracy of its copying. The first is a proofreading capability. DNA polymerase has a separate active site that checks each base after it is added. It wiggles the base a bit, and if it is loose, it clips it off. This improves the accuracy by one hundred times, at the cost of being wasteful, since it occasionally clips off proper bases as well. Finally, there is a separate repair enzyme that scans the DNA for errors after DNA polymerase finishes. The final error rate is about one in a billion nucleotides, so only half a dozen mutations are typically introduced with each cell division.
Our cells also use special forms of DNA polymerase for special tasks. DNA polymerase (Fig. 2) corrects common defects in the DNA. One of the most common problems is damage of DNA by ultraviolet light. It causes a chemical reaction between bases at thymine-thymine steps, forming a rigid thymine dimer. This lesion stalls our major DNA polymerase, blocking replication of the DNA. So, the cell brings in DNA polymerase . It is not as accurate, making a mistake once every hundred or thousand nucleotides, but it can copy straight past lesions in the DNA, including thymine dimers, sites where the base is missing, and sites modified by drugs such as cisplatin. People who cannot make this special polymerase suffer from the condition xeroderma pigmentosum and are highly prone to skin cancers.
Figure 2. DNA polymerase can copy DNA strands that contain molecular lesions, such as the thymine dimer shown here in purple. In this remarkable crystallographic structure, an adenine base has already been added next to one thymine in the dimer, and an ATP molecule is aligned next to the other thymine, ready to be added to the growing strand. The structure was taken from entry 1pm8 at the Protein Data Bank.
Of course, the evolution of life on the Earth would not be possible without mutations. If cells could reproduce DNA perfectly and shield it from damage, the Earth might still be covered by a thin layer of protocells, never able to change and never progressing to fill new environmental niches. Instead, the occasional mutation, when combined with natural selection, adds diversity to life, building slowly over millenia to yield the biosphere we enjoy today. However, these mutations can have a terrible cost at the individual level: they occasionally modify a key protein and lead to cancer. For instance, mutation of the ras oncogene can tell the cells to proliferate continually or mutation of the p53 gene can block the controls that normally stop this unnatural growth. Cells do their best to control mutation, keeping each of us as healthy as possible, and the occasional errors that slip through are also turned to advantage, at least on the evolutionary timescale.
ADDITIONAL READING
Waga S, Stillman B. The DNA replication fork in eukaryotic cells. Annu Rev Biochem 1998;67:721–751.
Baker TA, Bell SP. Polymerases and the replisome: machines within machines. Cell 1998;92:295–305.
Keck JL, Berger JM. DNA replication at high resolution. Chem Biol 2000;7:R63–R71.(David S. Goodsell)
DNA polymerase is our most accurate enzyme, for a good reason. It is the keeper of our most precious resource: our genetic information. DNA polymerase takes our DNA, gently unwinds it, and builds a complementary mate to each strand (Fig. 1). Thymine is paired with adenine, and cytosine is paired with guanine. The result is two identical copies of the genome, for use as cells divide or for passing on to our children.
Figure 1. DNA polymerase, shown here at the center in red, is part of a large molecular machine with all of the pieces needed to replicate DNA, shown in yellow. It contains helicases that separate DNA strands, primases that start to copy the strands, and the polymerase that does the major replication. The arrangement of the entire complex is still under study—an artist’s concept is shown here. Each polymerase contains a doughnut-shaped clamp that surrounds the DNA strand, holding the strand in place and allowing DNA polymerase to slide along the strand and build a long, continuous copy. In this picture, the parent DNA helix enters from bottom center and is separated by the helicase. The strand on the right feeds directly into the polymerase and is duplicated, leaving the picture at upper right. The strand on the left is facing the wrong direction, however, and is duplicated in parts, looping back into the polymerase and finally leaving the picture at lower left.
As you can imagine, this process must be as close to perfect as possible, so that the information is not corrupted. However, the hydrogen bonds between the four bases—two between adenine and thymine and three between cytosine and guanine—are only so strong. These bases can also form improper pairings, albeit with significantly weaker binding strength. If DNA polymerase relied only on the difference in pairing strength between proper matches and improper matches, it would make a mistake once in 10,000 nucleotides. This would introduce far too many mutations when our genome of six billion nucleotides is duplicated.
DNA polymerase uses several schemes to improve the accuracy of its copying. The first is a proofreading capability. DNA polymerase has a separate active site that checks each base after it is added. It wiggles the base a bit, and if it is loose, it clips it off. This improves the accuracy by one hundred times, at the cost of being wasteful, since it occasionally clips off proper bases as well. Finally, there is a separate repair enzyme that scans the DNA for errors after DNA polymerase finishes. The final error rate is about one in a billion nucleotides, so only half a dozen mutations are typically introduced with each cell division.
Our cells also use special forms of DNA polymerase for special tasks. DNA polymerase (Fig. 2) corrects common defects in the DNA. One of the most common problems is damage of DNA by ultraviolet light. It causes a chemical reaction between bases at thymine-thymine steps, forming a rigid thymine dimer. This lesion stalls our major DNA polymerase, blocking replication of the DNA. So, the cell brings in DNA polymerase . It is not as accurate, making a mistake once every hundred or thousand nucleotides, but it can copy straight past lesions in the DNA, including thymine dimers, sites where the base is missing, and sites modified by drugs such as cisplatin. People who cannot make this special polymerase suffer from the condition xeroderma pigmentosum and are highly prone to skin cancers.
Figure 2. DNA polymerase can copy DNA strands that contain molecular lesions, such as the thymine dimer shown here in purple. In this remarkable crystallographic structure, an adenine base has already been added next to one thymine in the dimer, and an ATP molecule is aligned next to the other thymine, ready to be added to the growing strand. The structure was taken from entry 1pm8 at the Protein Data Bank.
Of course, the evolution of life on the Earth would not be possible without mutations. If cells could reproduce DNA perfectly and shield it from damage, the Earth might still be covered by a thin layer of protocells, never able to change and never progressing to fill new environmental niches. Instead, the occasional mutation, when combined with natural selection, adds diversity to life, building slowly over millenia to yield the biosphere we enjoy today. However, these mutations can have a terrible cost at the individual level: they occasionally modify a key protein and lead to cancer. For instance, mutation of the ras oncogene can tell the cells to proliferate continually or mutation of the p53 gene can block the controls that normally stop this unnatural growth. Cells do their best to control mutation, keeping each of us as healthy as possible, and the occasional errors that slip through are also turned to advantage, at least on the evolutionary timescale.
ADDITIONAL READING
Waga S, Stillman B. The DNA replication fork in eukaryotic cells. Annu Rev Biochem 1998;67:721–751.
Baker TA, Bell SP. Polymerases and the replisome: machines within machines. Cell 1998;92:295–305.
Keck JL, Berger JM. DNA replication at high resolution. Chem Biol 2000;7:R63–R71.(David S. Goodsell)