mtDNA Amplification and Comparison

Overview & Concepts

This series of lessons is designed to introduce students to PCR - its  function and the process. Students will have hands-on experience extracting their own DNA, working with an online computer program to create primers for their targeted region of mtDNA, running a PCR reaction, and comparing their own mtDNA with ancient and modern human mtDNA to understand the mutation rate of DNA, the concept of molecular clocks, and the relationships among various human groups and between human groups and animal groups.

Grade Level: 

Concepts Covered: 

DNA extraction, PCR, DNA sequencing, mutations, mutation rates, phylogenetics 

Prior Knowledge Required: 

DNA structure, DNA replication, Types of mutations (point, frameshift, etc) 

Activity Notes

Days to Teach: 

DNA extraction (20 min), PCR mini-lecture (15 min - can do after setting up PCR to run), Creating Primers / Primer-3 (30 min), PCR (10 min set-up and 1 hr to run), mtDNA comparisons (80 min)


  • worksheets (DNA extraction, Creating Primers, PCR Procedure, mtDNA Comparisons)
  • computers with Internet access
  • materials for DNA extraction (saline solution, plastic cups, 1.5 ml tubes, micropipettes, microcentrifuge, 10% Chelex solution, boiling water)
  • materials for PCR (micropipettes, Ready-To-Go PCR tubes, Ready-To-Go PCR Beads, DI water, forward primer, reverse primer, DNA sample, microcentrifuge, thermocycler, vortex machine (not essential))

Teaching Tips / Activity Overview: 

Day 1

  1. DNA Extraction.  Use DNA Extraction worksheet.

Day 2

  1. PCR lecture
  2. Creating Primers.  Use the Creating Primers worksheet. Do Primer3 activity before handing out PCR procedure worksheet, as the PCR worksheet contains the actual sequence for the primers used.
  3. PCR.  Use the PCR Procedure worksheet.
  4. Send samples to ColdSpring for sequencing.

Day 3 - mtDNA Comparison.  Will be ~ 1 week after PCR procedure to give time for DNA to be sent off and sequences returned.

  1. Use the mtDNA Comparisons worksheet (see attached documents)
  2. Use the website to obtain student results.  
  3. Use Dolan site for phylogenetic activity.
  4. Students will need to make sure they only enter the most reliable portion (that which does  not have a lot of discrepancy on bases) of their sequence into the BioServer when doing mtDNA comparison.

For PCR Amplification:

  1. You can use Science in Motion to borrow necessary equipment if you do not have it readily available in your school.
  2. You can order materials for the procedure (Carolina and WARDs each sell kits/materials) or you can make your own.


Discussions, quizzes and exams, progress of and final work on the lesson/assignment.



These teacher notes and resources were produced, modified, and collected by Rachel Hanner. Some of the procedures were taken/modified from those used during Franklin and Marshall's Bioinformatics Seminar for High School Teachers. 

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