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Protein chip helps study of bacterial DNA
Issue date: 3/6/08
Hopkins researchers have devised a new way of identifying the proteins that are active in a cell. By using a specially designed chip, scientists from the biology department were able to identify which enzymes are most commonly used by the bacterium E. coli when there is an error in its genetic code.
DNA, which holds the core information of the cell, is prone to many errors. The four nitrogen bases that form the double-stranded molecule are often disfigured or mismatched.
The cell has a natural repair mechanism, in which proteins recognize mistakes in the DNA code, and fix the errors. Knowing what proteins are involved in this process could potentially aid in developing a cure for genetic diseases.
The prospect of identifying the repair proteins may seem easy, but the methods for procuring such information are very difficult. A eukaryotic cell, such as an animal cell, makes millions of proteins that assist the cell in its functions. Singling out the DNA repair enzymes is an almost impossible task.
This task is daunting even in a much simpler prokaryotic cell. E. coli, for instance, manufactures 4,288 proteins. The Hopkins team has become closer to identifying most of E. coli's proteins, but it would take too long to isolate each protein and observe its function.
Scientists have characterized 99.3 percent of the cell's proteome, or the complete set of proteins made in the cell. The Hopkins group used these proteins to make a chip that can easily search for their presence in cells.
The proteins are extracted from the cell and purified, and then embedded onto a glass slide, called a proteome chip. The chips contain trace amounts of all the proteins that an E. coli cell makes.
In order to see which proteins are involved in DNA repair, the researchers had to first create strands of DNA with errors. In this study, seven short strands of DNA were used: one without errors that served as the control, two with mismatched bases, and six with one abasic or misshapen site each.
DNA, which holds the core information of the cell, is prone to many errors. The four nitrogen bases that form the double-stranded molecule are often disfigured or mismatched.
The cell has a natural repair mechanism, in which proteins recognize mistakes in the DNA code, and fix the errors. Knowing what proteins are involved in this process could potentially aid in developing a cure for genetic diseases.
The prospect of identifying the repair proteins may seem easy, but the methods for procuring such information are very difficult. A eukaryotic cell, such as an animal cell, makes millions of proteins that assist the cell in its functions. Singling out the DNA repair enzymes is an almost impossible task.
This task is daunting even in a much simpler prokaryotic cell. E. coli, for instance, manufactures 4,288 proteins. The Hopkins team has become closer to identifying most of E. coli's proteins, but it would take too long to isolate each protein and observe its function.
Scientists have characterized 99.3 percent of the cell's proteome, or the complete set of proteins made in the cell. The Hopkins group used these proteins to make a chip that can easily search for their presence in cells.
The proteins are extracted from the cell and purified, and then embedded onto a glass slide, called a proteome chip. The chips contain trace amounts of all the proteins that an E. coli cell makes.
In order to see which proteins are involved in DNA repair, the researchers had to first create strands of DNA with errors. In this study, seven short strands of DNA were used: one without errors that served as the control, two with mismatched bases, and six with one abasic or misshapen site each.
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