Rapid Analysis of DNA Damage Now Possible

New DNA analysis technology offers a new way to test potential cancer drugs and to determine the effects of environmental toxins.

DNA in living organisms is under constant siege from a variety of damaging agents. Damage to DNA and the ability of cells to repair that damage has wide health implications, from aging and heritable diseases to cancer. Unfortunately, the tools used to study DNA damage are quite limited, but researchers have developed a new tool for rapid DNA damage analysis that has the potential to make an impact on human health.

The researchers, led by Dr. Bevin Engelward, Massachusetts Institute of Technology (MIT; Cambridge, MA, USA) associate professor of biological engineering, and Dr. Sangeeta Bhatia, professor in the Harvard-MIT Division of Health Sciences and Technology and MIT's department of electrical engineering and computer science, have produced a completely revamped version of a 30-year-old lab test known as the comet assay. This new technique combines the versatility and sensitivity of the comet assay for DNA damage analysis with a robust high-capacity platform, which could make DNA damage analysis routine across a variety of applications, ranging from epidemiology to drug screening.

Dr. Engelward, Dr. Bhatia, postdoctoral fellow David Wood and graduate student David Weingeist described the technique in an article that was published in the journal Proceedings of the [U.S.] National Academy of Sciences (PNAS) the week of May 3, 2010. The technology could offer a new approach for epidemiologists to detect deadly environmental exposures long before they cause cancer, for clinicians to provide better cancer treatment, and for researchers in the pharmaceutical industry to identify new drugs and screen out hazardous drugs.

The comet assay is based on the idea that during gel electrophoresis, a typically used lab test in which an electric field is applied to DNA placed on a polymer gel, damaged DNA moves farther across the gel than undamaged DNA. The result is a "comet” made of DNA, which looks extraordinarily like its astronomic namesake. The assay is both sensitive and versatile, but it is also time-consuming and tedious. It requires at least one microscope slide for every experimental condition, which means that researchers need to handle dozens of slides just to do a few experimental conditions. Moreover, the readout is manual, meaning researchers have to spend hours staring into a microscope and selecting cells for analysis. The investigator's goal was to harness the strengths of the comet assay while overcoming its limitations in throughput and labor.

Using a micropatterning technique developed by the MIT scientists, the research team imprinted a grid of tiny wells the size of a single cell on a DNA electrophoresis gel. Cells in the array can be individually "addressed,” which allows fully automated readout and replaces the time-consuming manual analysis. They also put their microscopic cell array into a 96-well plate so that many cell types, drugs, or other conditions can be assayed simultaneously. This setup allows dozens of experimental conditions to be tested on just one slide, and it enables slides to be automatically analyzed using custom-designed imaging software.

The team is using knockout cell lines to determine which genetic deficiencies are detectable with their platform and to determine better the molecular mechanisms of DNA repair. They are also optimizing their system for human samples in order to study the DNA damaging effects of the environment. Ultimately, they hope that the CometChip will be commercialized and made available worldwide. This technology was designed not only to enable high throughput screening, but also to be compatible with basic laboratory equipment so that virtually any laboratory can use it.

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