What is the effect of viscosity on the movement of DNA fragments in strawberry jelly?
Gel electrophoresis is a procedure widely used in the separation of biological molecules (such as DNA, RNA and proteins) according to their size and charge. The technique involves running an electrical current through the gel (acting as a sieve) which then pulls the molecules of interest through it, as they hold a charge. The phosphate molecules in DNA give it its negative charge and hence the DNA molecules will be pulled through the matrix to the anode. All DNA molecules have the same amount of charge per mass and so the electrophoresis of such fragments means that they are separated by size only. They travel through the gel at different speeds (larger molecules move more slowly); the fragments have differing sizes due to polymorphism (a difference in the nucleotide sequence).
A common substance used as a gel in this process is agarose. Agarose, a polysaccharide obtained from red seaweed, is extracted from agar and used because of the large pore size in its structure. Whilst reading, The Language of the Genes by Steve Jones, I found it interesting to learn about the possible alternatives to agarose as a matrix. Jones recalls the fact that “gels were once made of potato starch” and that he himself found that strawberry jelly “works quite well”. Starch gels were introduced by Smithies and are prepared from hydrolysed potato starch. However, more recently, the use of starch gels has declined due to the “low reproducibility and the impractical handling”. It invokes my curiosity as to the suitability of starch gels, compared to the now traditional agarose ones, as well as the use of strawberry jelly, and if they could possibly impede the separation of the fragments. Furthermore, if it does in some way alter the results in the migration, it will be interesting to see how much they differ from each other and whether or not, if used in forensic investigations, would suggest different perpetrators.