Summer Research Program for Science Teachers



Nancy Lee

Briarcliff High School


August 2005



Gel Electrophoresis Simulation




Course:  Living Environment (New York State Regents Curriculum)/Biology


Grade Level:  9th and 10th grades


Unit:  Genetics, Scientific Method, or Ecology (if done in conjunction with NYS Lab #1: Relationships and Biodiversity as a pre-lab activity)


Objectives:  Students will be able to…


Introduction:  Given the impact of biotechnology on today’s society, it is imperative that students be familiar with molecular biology techniques such as gel electrophoresis, which is used in DNA profiling.  For those teachers who lack access to equipment needed to create such relevant lab experiences for their students, this simulation provides a hands-on learning experience that exposes them to the basic principles of biotechnology.  Prior to doing the simulation, students must have a firm understanding of DNA structure and function. 


(This lesson was adapted from The American Biology Teacher, Volume 63, No. 6, August 2001.)




Time Required:  Two 40-minute periods (Steps 1-11 for the 1st period, Step 12 for the 2nd)



1)      At the beginning of class, tell the students that a wallet was stolen from a locker near the classroom.  A small drop of blood was found on the locker, assumed to be left by the guilty party.  Tell the class that someone in the room is suspected of taking the wallet, and that the police gave you a sample of the blood to run a DNA fingerprint on, using gel electrophoresis. 

2)      Explain to them what restriction enzymes are, where they are normally found, and how they are used by scientists in biotechnology today.  Also explain how restriction enzymes only cut at a specific base sequence or restriction site.

(For Steps 3-5, demonstrate each of the steps for the whole class by completing your own Gel Electrophoresis Worksheet in front of the class, step by step.  You will use the resulting fragments from these steps later in Step 10.)

3)      Give each student a copy of the Gel Electrophoresis Worksheet.  Tell the students to imagine that their DNA is only 20 base pairs long, and that they all have the restriction site AATT at least once somewhere along their DNA.  In the grid provided on the worksheet, have students fill in a row of 20 base pairs and include the AATT restriction site as many times as they wish.

4)      Tell students to use a pencil to lightly shade in the AATT restriction site on the template strand wherever it occurs in their DNA sequence.  Have them count the number of times the restriction site occurs in their sequence and write in the number on their worksheet.  The, for each restriction site, have them draw a thick line between the two A’s.  Explain that this indicates where the restriction enzyme will cut the DNA. 

5)      Give each student a pair of scissors, and have them cut out their entire DNA sequence from the middle of the worksheet so that it is one long rectangle.  Then, following the lines they drew in for each restriction site, have them cut their DNA into the fragments created by the restriction enzyme.  After the students record the total number of fragments created by the restriction enzyme on the worksheet, tell them to write their name on the back of each fragment, along with the total number of base pairs it has.

6)      Using a computer hooked up to an LCD projector (preferably with a SMART Board, but not necessary), bring up an image of the Simulated Gel saved as a Word file for the whole class to see on the board.  On the left hand side of the Simulated Gel, draw a negative (-) sign at the top of the gel, connected to a power source and then down to a positive (+) sign at the bottom of the gel.  Have the students guess what the numbers on the sides correspond to, and predict what the next steps are.

7)      Have a student volunteer come up to the board and write his or her name on the top of the first well (the rectangle on the top of each column).  Help the student demonstrate how to tape his or her fragments in the lane, being sure to put each fragment in the appropriate space according to its size.  (Two or more fragments of the same size should be taped on top of one another in the same grid space.)  Alternatively, you could just have them shade in the area where each fragment would go instead of taping it to the board.  Regardless of which method you choose, explain to students how this (taping or shading) creates a banding pattern specific to that student.

8)      Have eight other students come up to the board and choose their own lane (column) to tape their fragments in the appropriate spaces.  You can have students come up one at a time, in pairs, or all at once, depending on time constraints.  In addition, if you would like to include more students in this part of the simulation, you can expand the Simulated Gel by adding more columns. 

9)      After the students have created their banding patterns, have them analyze them by comparing them with one another.  Explain to students how in real life, because human DNA consists of 3 billion base pairs, the chances of two people (other than identical twins) having the same exact banding pattern is very slim. 

10)  Then show students what the banding pattern of the DNA recovered at the crime scene looks in the very last lane of the Simulated Gel up front.  Do this by taping up the fragments you created earlier as part of your demonstration one fragment at a time in the appropriate positions in the lane.  Ask the students to determine if anyone’s banding pattern matches this final lane. 

11)  Tell students to imagine that this is an actual set of DNA fingerprints, and pose the following questions:

a.      Is the perpetrator of the crime scene present in the classroom?  How do you know? 

b.      Ignoring the crime scene lane, are there any two banding patterns that are exactly alike?

c.      If no two banding patterns are alike, how would you explain this?

d.      If there are banding patterns that are alike, how would you explain this?

e.      Why was the Simulated Gel numbered in descending order starting from the top?

f.        What do the positive (+) and negative (-) signs represent, and why was the positive placed at the bottom of the gel?

12)  Go to the Genetic Science Learning Center website, found at, and project this web page up front for the class to see (preferably on a SMART Board, but a whiteboard/screen will also do).  This website has an online, interactive simulation that explains each of the steps involved in gel electrophoresis.  Walk through each of the pages with the students, explaining how this outlines each of the steps done in a real gel electrophoresis experiment.  Make comparisons between what is shown on the webpage versus what was done previously with the paper-and-scissors simulation.  If you have a SMART Board, you can call individual students up to the board to use their fingers to carry out the various steps of the online simulation. 

13)  Close the lesson by having the students summarize the main steps of gel electrophoresis.  In addition, ask the students to explain the impact of gel electrophoresis on today’s society, and their thoughts on how it affects their own lives. 



New York State Math, Science, and Technology Learning Standards met by this lesson:


National Science Learning Standards met by this lesson: