DNA & Principles of
Gel Electrophoresis Field Trip

Background Information

DeoxyriboNucleic Acid (DNA) is many things.

It is the genetic determinant of heredity. It is the “Blueprint/Code/Software of Life”. It is “the double helix”. It is a biopolymer. DNA can hold a prominent place for a student of science in understanding molecular concepts that connect the building blocks of matter, atoms, to cells which are the building blocks of life.

In the DNA and Principles of Electrophoresis Biotechnology Field Trip, students will explore DNA molecules. By creating models, they will learn how atoms connect together to give a molecule of DNA its shape and its function. Students will learn that the molecular composition of DNA gives it a negative charge and will use this characteristic to separate DNA pieces of different size from one another using the technique of agarose gel electrophoresis.

Gel electrophoresis is a laboratory technique used the to separate charged molecules. DNA is negatively charged and moves, under the force of an electric current, through the matrix of an agarose gel. Molecules separate by size, with the smaller ones moving more rapidly through the gel than the large ones.

Purified agarose is a powder that is insoluble in water (or buffer) at room temperature but dissolves in boiling water (or buffer). As it cools, agarose undergoes polymerization. The sugar monomers crosslink with each other and cause the solution to "gel", much like JELLO. Higher concentrations of agarose give firmer gels. If you were inside a gel, it would resemble a very dense spider web. If you were a small fragment of DNA, then you could easily crawl through the spaces between the webs (they are too tough for you to just pull out of the way) but as you increase in length, it gets harder and harder for you to fit through the spaces. We use a 0.8% agarose gel in 1x sodium borate buffer for this experiment. The agarose is kept molten at 55° C until the gels are poured. Gels are prepared by pouring the molten agarose into casting trays around a six-well comb and allowing them to solidify. The comb is removed from the solidified gel and the DNA is loaded into the wells left by the comb.

The gel box is prepared by pouring 1x sodium borate buffer into the chambers and placing the gel in the box. The digested DNA and some DNA markers will be mixed with a safe-stain called FOTO/Vision ^TM. FOTO/Vision^TM serves as a loading and tracking dye during electrophoresis, and is used for visualization of DNA bands in the resulting gel. The samples are loaded into the agarose gel wells and then electrophoresed by connecting the gel box to a power supply.

After running the gel, the DNA is visualized using medium wavelength ultraviolet (UV) light (we always wear safety glasses while using a UV light source). A component of FOTO/Vision^TM binds to the DNA during electrophoresis. When the gel is exposed to UV light, the DNA bands fluoresce in a distinctive pattern of DNA fragments, one band for each different size fragment. We take a photograph of the gel so that it is easier to study the banding pattern.

If you have any questions or would like more information before you bring your students to the BTC Institute for this field trip, please give us a call. Alternatively, bring your questions along and we can discuss them during the lab. We look forward to seeing you and your group on your scheduled field trip day. Thank you for your interest in the BTC Institute's Biotechnology Field Trips program!