Expt004 : Effect of time on separation

The aim of this experiment is to observe the migration of a mixture of fragments with time.

Method

Load Expt004. It contains eight samples of DNA.

• Load sample 1 into a reaction tube and run it on a gel.

On the left side of the Agarose Gel Electrophoresis module, there are some radio-buttons and spin edit boxes that control the properties of the gel. In this experiment, we are going to concentrate on the run time control.

run time is the length of time the electric voltage is applied to the gel, i.e. the length of time the gel runs! In BioLab, the gel seems to run in no time, but in a real lab, a quick gel normally takes about an hour to run. The numbers shown in the run time control represent the number of minutes that the gel would take to run in a real lab.

To change the run time :

• Click on the up or down arrows at the right of the run time control, or type the time you want the gel to run in the edit box.
• As soon as you change this value the gel changes

Start with small values of time (0, 10, 20 minutes) and gradually increase to 100 minutes and more.

Results and discussion

This animation shows several bands running in a track. At the beginning of the migration, all the DNA is close to the well where it has been loaded. As the electrophoresis goes on, the small fragments are separated from the bigger ones. When the gel is run for a short time, the bands are close to the top of the gel, and grouped together. It is almost impossible to see separate bands. When the gel is run for longer, we observe how the small fragments move faster than the bigger ones, and how the bands separate. If the gel is run for a very long time, some bands run off the end of the gel and are lost. NB: When any bands run off the end of the gel this is indicated by the well going red.

In the illustration below, the run time has been set to a very short time (5 minutes).

In the next diagram, the run time is longer and some DNA has run out of the gel.

Your turn

There are seven more samples in the sample rack. Load them all onto the gel, next to sample 1 and observe the gel at the default run time of 100 min. Now change the run time to 200 min. What do you observe in the fourth track in both cases? What is your conclusion?