Paper Clip PCR PURPOSE The purpose of this activity is to reinforce basic DNA concepts and to introduce students to the technique of PCR and its many uses. Part one of the activity uses a virtual PCR animation that takes students through the steps involved in PCR. Part two of this activity allow students to perform PCR using paper clips to represent individual nucleotides. MATERIALS Note that this activity assumes students have some prior knowledge of DNA, its basic structure, and function. For a tutorial of DNA basics, see box at right. For this activity you will need: Access to the internet and a projector Small colored paper clips (blue, red, green, yellow and white) Each group will need about 25 paper clips of each color in a separate bag/ cup, and about 6 white paper clips Label cups/bags with A, T, G, or C according to color key in activity Copies of the Paper Clip PCR activity for each student Go Online! For: A tutorial of DNA basics Visit: http:// learn.genetics.utah.edu/ content/begin/tour/ LESSON PLAN Engagement (30 minutes) Begin by asking students what they know about DNA. As students answer, write their information on the board. Be sure that your discussion includes the following questions/points: 1. What role does DNA perform in a living organism? 2. What is the basic shape or structure of DNA? 3. What are the four nucleotide bases or letters that make up DNA? How do they pair together? 4. What is a gene? What do genes code for? Paper Clip PCR v.1 1
Next, introduce students to the technique of PCR (Polymerase Chain Reaction). PCR is a method used in the lab to make many copies of a specific piece of DNA that we want to study. This process uses repeated cycles of heating and cooling to separate DNA strands and make new copies of the desired DNA segment. Project for students the Virtual PCR lab found on the University of Utah Website: http://learn.genetics.utah.edu/content/labs/pcr/ Slowly click through the virtual PCR lab, being sure to note the various components or ingredients used to perform PCR and why they are used: Extracted DNA - the Template Primers (two different primers are used in a PCR reaction) Nucleotides (A, T, G, and C for building new DNA strands) Polymerase enzyme (to catalyze the building of new DNA strands) Fact Files The FBI and PCR PCR is the method of choice used by the FBI to perform DNA profiling in order to identify individuals. For more on how this works, visit www.dnai.org and click on Applications and Profiling. Finish clicking through the virtual PCR lab, noting to students how the target DNA sequence, usually a gene or a piece of a gene, is copied many times in the thermal cycler. Address any questions as they arise, reinforcing that the goal of PCR is to produce many copies of a desired segment of DNA. Exploration (30 minutes) Arrange students in groups of three. Pass out to each group a set of colored paper clips. Tell the students that they are now going to perform two rounds of PCR using paper clips as their DNA. Each color paper clip represents one of the four nucleotides in the DNA code. Students should follow their Paper Clip PCR activity, with all members of the group sharing the various steps. At the end of the activity, students should have a copy of the desired DNA segment. Paper Clip Tip Make sure that students keep track of the orientation of their paper clip DNA strands. Keeping the paper clips strands flat and straight on their desk will help. Explanation and Assessment (5 minutes) After each group has completed the Paper Clip PCR activity, go around the room to check each group s final PCR product. In class or for homework (if permitted) have each student pick one topic area below and ask each student to research and do a brief write-up of how PCR is useful in the following areas: Go Online! For: Great DNA resources Visit: http://www.dnai.org DNA profiling Detecting Genetically Modified Organisms Disease diagnosis Phylogeny Paper Clip PCR v.1 2
Paper Clip PCR Name: In this activity you will be performing PCR (polymerase chain reaction) using paper clips to represent DNA. Each colored paper clip represents a particular nucleotide in the DNA code: Blue - Adenine (A) Red - Thymine (T) Green - Guanine (G) Yellow - Cytosine (C) White - hydrogen bonds to connect DNA strands 1. Start by creating your template or starting DNA strand out of paper clips. Connect the proper colors of paper clips to represent the following DNA sequence: A-G-A-T-C-G-C-A-A-A-G-C-A-T-T Keep all strands flat on your desk! 2. Using your first strand as a guide, create the complementary (matching) strand out of the proper colors of paper clips. Hint: A pairs with T and G pairs with C. Use two white paper clips to connect the ends of your two DNA strands together. Your template strand should be on top. 3. Create your Primers out of the following sequences: Primer 1: T-A-G Primer 2: G-C-A 4. Repeat step three to make a second pair of primers. Now you are ready to perform PCR.. OVER. Paper Clip PCR v.1 3
Blue (A) Red (T) Green (G) Yellow (C) 5. Begin by denaturing or separating your two DNA strands (remove white paper clips). 6. Attach (or anneal) Primer 1 to the template (top) strand in its proper place using a white paper clip. Remember base pairing: A with T and G with C. Keep all strands in order and flat on the desk. 7. Attach (or anneal) Primer 2 to the bottom strand in its proper place using a white paper clip. Primer 1 T - A - G G - C - A Primer 2 8. Now, using each DNA strand as a guide, finish building (extending) new top and bottom DNA strands using the primers as the starting pieces. T - A - G G - C - A 9. Denature (separate) your new DNA strands by removing the white paper clips. 10. Next, anneal (attach) your second set of primers to the new DNA strands. This time, primer 2 will attach to the top strand, and primer 1 will attach to the bottom strand. (Other primers would also attach to the original strands again, but for now, we will leave those out). Primer 2 G - C - A T - A - G Primer 1 Paper Clip PCR v.1 4
Blue (A) Red (T) Green (G) Yellow (C) 11. Finally, extend your two primers to create a second set of new DNA strands. These strands represent our desired PCR product, the sequence we wish to make many copies of. The sequences of the top and bottom PCR products should match (complement) each other. How many nucleotides is our desired?. What are the DNA sequences of our? (hint: The top and bottom sequences should pair with each other.) top strand : bottom strand: Congratulations. You have just performed PCR. Remember, each round of PCR doubles the number of DNA strands in the sample. A typical PCR will go through about 30 cycles of replication to make millions of copies of our desired PCR product. How long did it take you to replicate your paper clip DNA? Although it may have taken you a few minutes to do this, your cells replicate DNA very quickly, at a rate of about 50 base pairs per second! How many mistakes did you make when replicating your DNA? Your cells make mistakes only once for every 1,000 to 100,000 base pairs during replication. Not bad! Paper Clip PCR v.1 5
Blue (A) Red (T) Green (G) Yellow (C) ANSWER KEY 11. Finally, extend your two primers to create a second set of new DNA strands. These strands represent our desired PCR product, the sequence we wish to make many copies of. The sequences of the top and bottom PCR products should match (complement) each other. A T C G C A A A G C A T A G C G T T T C G T A A A G A T C G C A A A G C A T T T C T A G C G T T T C G T A A A G A T C G C A A A G C A T A G C G T T T C G T How many nucleotides long is our desired? 11. What are the DNA sequences of our? Top : ATCGCAAAGCA Bottom : TAGCGTTTCGT Paper Clip PCR v.1 6