Alternative gels

The basics of DNA analysis described in this lesson can be applied to “modern” DNA genetic analysis that is becoming more common-place: DNA sequencing and high throughput DNA analysis. In DNA sequencing, the exact nucleotide order of a segment of DNA is determined. Here, an electrophoresis gel system is used that can separate fragments that differ in length by a single nucleotide. This is done by employing three technical alterations to the electrophoresis. First, acrylamide is used rather than agarose. This creates a more dense gel matrix that has a higher resolving power to separate DNA segments. Second, a longer gel is run. This is synonymous with a longer race that provides more spread between the fastest and the slowest fragments. Finally, the DNA segments are often labeled with a fluorescent dye and allowed to run past a detector and off the gel. The detector then sends this information to a computer. This allows the geneticist to worry less about timing a single photo finish of a gel and more information can be obtained from each gel. Therefore, the gel electrophoresis methods can be modified, depending on the analysis needs of the geneticist. 

When genetic analysis needs to be applied to many regions of the chromosomes on hundreds of individuals, the time and expense of pouring gels can become a limitation. Therefore, capillary electrophoresis systems have been developed. In this system a lane in a gel is substituted with a capillary tube which is the matrix. DNA forced into the capillary tube is labeled with some detectable molecule and moves through the tube in the same manner as has been described with gel electrophoresis. The advantage of the capillary system is that electrophoresis runs can be done in less time compared to gels. The tube may also be used again and again. The capillary system can also be integrated into an automated system that uses robotics to pipette arrays of samples into the tubes. Consequently, the capillary system has some advantages over traditional slab gel electrophoresis when a high through-put of samples is required.