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A common cleanser is cheaper and faster way to separate DNA for genetic analysis

By identifying a 30-year-old mistaken assumption, Johns Hopkins Kimmel Cancer Center scientists have found that substituting a simple bleach solution for more complex tools makes a DNA separation technique called electrophoresis five times faster and less costly.

Reported in the February issue of BioTechniques, the scientists say that using the compound sodium boric acid in DNA electrophoresis may speed genetic discoveries. The scientists searched old literature and dozens of compounds to find one that could replace antiquated solutions used to conduct the electric current necessary to separate negatively charged DNA molecules, the building blocks of genetic code. In electrophoresis, DNA is fed through porous, jellylike slabs of sugar (also known as a 'DNA gel') to reveal the outlines of the code, with small DNA molecules crawling up the gel faster than less mobile larger particles as the current passes through.

Like the two poles on a battery, the difference in the positive and negative charges represents a voltage. "DNA just needs to know it's in a voltage and it will move," says Scott Kern, M.D., professor of oncology and pathology at the Johns Hopkins Kimmel Cancer Center. "So, the most important feature of a solution in electrophoresis is its ability to carry a voltage."

Solutions historically used for DNA electrophoresis are called Tris-acetic acid-disodium EDTA (TAE) and Tris-boric acid-disodium EDTA (TBE). For 30 years, scientists have mistakenly assumed these solutions were good conductors and 'buffers.' Buffers serve to reduce acidity or pH and were used for protein electrophoresis in the 1950s. They are still used today and work well in protein electrophoresis because pH balance is important for separating proteins, which in their natural state carry an unpredictable charge.

However, Kern and postdoctoral fellow Jonathan Brody conducted experiments demonstrating that TBE and TAE provide only some buffering --
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Contact: Vanessa Wasta
wastava@jhmi.edu
410-955-1287
Johns Hopkins Medical Institutions
9-Feb-2004


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