Molecular Diagnostics : simulation of Gel electrophoresis

On April 14, on 3d Gymnasium Of Salamina (Greece) (https://blogs.sch.gr/3gymsala) , an activity entitled “Molecular Diagnostics at school: simulation of Gel electrophoresis”  was implemented in the science laboratory by Panagiotis Kotsikis (Chemist, MSc) .

Gel electrophoresis is a simple technique, which was introduced in the early 1970s, and revolutionized the whole field of molecular biology, especially the study of DNA and RNA.

The principle of its method is based on the different speed at which charged molecules such as DNA (or RNA) or proteins can move through a porous material by applying an electric voltage . Thus the molecules with the smaller size and the larger charge will move more in the solid substrate compared to the larger and less charged ones. This will eventually lead to separation of the molecules as is the case with chromatography.

Activity 1

Age (14-15)

Duration (20 min)

Students in small groups set up simulations of “electrophoretic” devices.

Each “electrophoretic” device was made in a plastic lid , in which the agar yen was created. The agar will create the small porous material in which the molecules will move.

Five 9V batteries were used for the voltage . For the ingredients to be separated, pastry colours dissolved in glycerol were used.

Separation Duration (40 min)

Students with this activity will be able to see that the molecules would move at different distances and therefore  they have different sizes, which determines their movement through the pores of the gel.

Activity 2

Duration (25 min)

Until the separation proceeded, there was time for the second activity related to the identification of an alleged culprit. 

Principle of method

This activity was based on the fact that the applications of molecular biology in criminology focus heavily on the analysis of DNA recovered from the scene to identify the culprit. The human genome is more or less the same in all humans but contains many polymorphisms. That is, sites where the nucleotide sequence is not the same for every member of the population. For DNA fingerprinting, DNA fragments that show polymorphisms, are digested by restriction endonucleases. This results , DNA fragments of different lengths. Separating these fragments by electrophoresis will result in a unique combination of bands, which can be used to identify an individual.

The case

The case involved locating the “perpetrator” who broke the lab window. A basketball with a blood stain was found at the scene. Α small play was played in the laboratory with the 4 suspects being interrogated by the student who acted as the “detective” of the case. 

So with this clue ,the student would be able to identify the culprit among four suspects who didn’t have a class gap at that time . DNA Sequences  on paper were distributed to the groups of students. These sequences corresponded to the 4 suspected suspects. 

Students would seek to find the DNA fragments that would result from the action of specific enzymes in each sequence. The size of the fragments should be drawn on a sheet of paper that corresponded to the electrophoresis that would be done. The design was done with a special invisible pen.

Experiment Analysis

When the groups of students  finished, they had to go to the special device (with the light from the back of the invisible pen), where the results of the electrophoresis would be visualized. The suspect who would have the same bands on the electrophoresis as those from the sample isolated from the ball would also be guilty .This stage of visualization and comparison really seemed to be of great interest to the students.

The results

The set of activities seemed to arouse the interest of the students but also the recognition of the great contribution of the sciences in everyday life as well as the cooperation of the sciences  (STEM).

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