Physicists have manufactured a tiny device that can size up individual pieces of DNA about 100 times faster than standard techniques while requiring a million times less sample. The new device, described in today's issue of the Proceedings of the National Academy of Sciences, might lead to quicker identification of mutant strains of bacteria, which could guide the treatment of diseases such as tuberculosis, and might also speed up the sequencing of the human genome.
Chopping up a sample of DNA with special enzymes and measuring the sizes of the resulting fragments is a quick way to look for mutations and other sequence variations, because the enzymes recognize and cut the double helix only at specific sequences. Currently, a method known as gel electrophoresis is used to measure the fragment lengths. This technique involves timing the progress of electrically charged DNA when an electric field drags it through a gel. But it takes hours to run the DNA through the gel, and the technique fails entirely for molecules larger than about 10 micrometers.
To overcome these problems, physicist Stephen Quake and his colleagues at the California Institute of Technology (Caltech) in Pasadena developed a new DNA sizing technique based on fluorescence. The researchers spiked a solution of DNA molecules with a dye called YOYO-1, then applied the mixture to a silicon-based mold riddled with channels just a few micrometers wide. Single DNA molecules dabbed with dye were pulled by capillary action into each of the channels. The molecules were then illuminated with a laser and the dye fluoresced. The amount of escaping light revealed the size of about 3000 DNA pieces (the brighter the fluorescence, the bigger the piece) to within 5% in roughly 10 minutes. The devices are easier and cheaper to make than gels, the researchers say, and can be reused several times.
The team is now working on developing a multiplex device that can size up to eight different samples at once. Mel Simon, a molecular geneticist also at Caltech, is enthusiastic about using the new device to help map the human and mouse genomes. "Although there are a variety of methods [which measure the size of DNA], few cover the size range that this one does," says Simon.