Harvard University

For fun, I decided to commit to learning one new thing per month. Something that is completely out of my knowledge domain. This month, I decided to learn to perform a simulated experiment of a process known as gel electrophoresis. Basically this process is used in clinical chemistry to separate proteins by charge or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge.

We used dyes for this experiment. The samples are then transferred to the gel electrophoresis box, segregated by internal wells within the box so that they do not mix. These dyes differ in size, with the yellow dye being the smallest, the blue dye being larger and the purple dye being the largest. 

Always remember to balance the test tubes within the micro centrifuge before activating the spin. 

An electric field is applied to transport molecules (such as DNA) along the agarose gel. The electric field is made up of a negative charge on one end that pushes molecules through the gel and a positive charge on the other end that pulls molecules through the gel.

The charge determines how far the dye migrates in the gel; the purple dye has a greater negative charge per mass than the blue dye. As a result, it migrated farther than the blue dye in the gel, despite being larger in size.

By choosing an agarose gel of different concentration, we can also sieve the molecules according to their lengths, the shorter molecules move faster and migrate farther than longer ones because shorter molecules migrate more easily through the pores of the gel. This phenomenon is called sieving. So, it is either sieving by electrical charges or by the length of the molecules. 

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