How the concentration of the agarose influences the study of the DNA?
Agarose gel is a polysaccharide which acts a sieve to “catch” the molecules as they are transported through the matrix by the electrical current applied. The pore size of the agarose gel impacts the size of the DNA that can be sieved because only molecules of a certain size will be able to fit through certain pores. Smaller molecules will be able to pass through more easily than larger molecules which will have to contest with the meshwork of the gel made up of long chains of interlinked sugars. Thus, molecules of DNA are separated according to size as smaller molecules will be able to travel further.
Different concentrations of agarose gel can be used to accommodate the size of the DNA fragments being studied. Neves and Reis theorised that the more concentrated an agarose gel, the smaller the pore size the gel will be comprised of (i.e. porosity increases with lesser gel concentration). However, due to its high porosity, agarose is extremely expensive.
Alternative mediums aside from agarose have been proposed and developed, and Smithies introduced the use of starch gels in electrophoresis. With the aid of Otto Hiller, Smithies used gelatinised potato starch to reveal differences between normal human plasma proteins. However, this method has since been phased out.
Jones commented on the use of potato starch as a gel for electrophoresis and also recognised that strawberry jelly “works quite well” as an effective matrix in gel electrophoresis.
Developing this further, Castro, Teixeira, Salengke, Sastry and Vicente highlighted that the electrical conductivity of strawberry jelly increased with temperature showing that it has the potential to be a viable matrix for gel electrophoresis.
Following the information described, I hypothesise that increasing the viscosity of strawberry jelly will impede the movement of biological molecules in gel electrophoresis, similar to agarose gel given a reduction in pore size. Therefore, I have chosen to test the viability of the strawberry jelly as a possible, cheaper, alternative to the traditional agarose gel.