My goal for this year is to pop the hood on my teaching pedagogy and write about how to practically teach molecular biology. Over the next few months, I am going to be posting information about teaching common biological activities but in a more intuitive that makes the procedure less cookbook and more of an exploration. The first entry is about the very common practice of purifying DNA from fruit using simply household chemicals, a great starting point for the practice of molecular bio. Many students have done this but there are many different adaptions and add-ons one can do to the procedure in order to add elements of experimentation and mystery all while exploring the chemical properties of the DNA molecule.
Students tend to vary greatly in their overall knowledge of DNA and so it is important to ensure students understand what it is and provide a number of fast facts that will hook the student’s attention.
Talking Points to Build Interest Around DNA Prior to Purifying It
- Each one of your cells has about 6 feet of DNA packaged inside. DNA is coiled around a complex of proteins called histones which tightly bond to the DNA and keep it condensed. Since this is an abstract concept to envision, envision a long of yarn wrapped into a tight ball. Unwrapped, it would stretch on for a hundred foot but when wrapped, it is easy to handle and takes up a lot less space
- If one were to remove the DNA in each of their cells and line up the strands from end to end, it would stretch to somewhere between Jupiter and Saturn! Imagine spending months upon months in a space ship viewing the same person’s DNA the whole time. Wow!
- Most of the attention DNA gets is from genes, the blueprints for proteins that students and scientists alike spend lots of time studying but that only accounts for a small percentage of the overall genome! The other sequences, called introns, have a fascinating story to tell as well.
- Transposons are remnants of viruses that have implanted themselves in our DNA and are present in our evolutionary ancestors. During times of extreme cellular stress, some have the availability to catalyze their own removal and move to different places in the genome.
- There are also psuedogenes, inactive copies of nearby genes that collect mutations at a higher rate than their functioning neighbors.
- There are sequences that allow for intramolecular bonding that can be sometimes be millions of bases apart but loop together to find each other to allow for tighter packing. After all, 6 feet of DNA have to fit into a space far smaller than the head of a pin
Quart freezer bags
Fruit (strawberry works best but bananas and blueberries also work)
Plastic cups or beakers
wood or glass stir rod
Cold 99% Isopropyl Alcohol or Ethanol
Note: The most important piece of pre-experimental planning is to place the alcohol required for the last step of the process in a freezer. The DNA solubilizes in alcohol and chilling the alcohol enables the DNA to clump together faster as well as rise to the top.
Below is a common procedure for purifying DNA from fruit. Connections to other areas or experimental variations are in bold below the steps.
- Remove the stem and place the strawberry in the bag and seal, ensuring that all the air has been removed from the bag
- Mathematics connection: Have the students weigh the strawberry and hypothesize what percentage of the total weight of it is represented by DNA.
2. Gently mush the strawberry ensuring that all chunks are broken into small pieces. No single piece of strawberry is larger than a couple of millimeters
- Math/Physics connection: Why is it important to get the pieces as small as possible? Take a rough volume of the pieces and consider the importance of surface area in allowing reagents to reach their target.
3. Place 1 squirt of soap/shampoo along with 1/2 tsp salt or meat tenderizer into the bag and 25-50 mL of water into the bag and gently slosh around the slurry allowing the surfactants and
- Experimental design challenge: What effect would changing the amounts of reagents have on the amount of DNA recovery? Students can change one variable at a time and see how that changes the overall DNA yield
- Chemistry connection: Soap is required to break down the cell membrane, which is largely composed of lipids. Why is soap such a powerful degreasing agent? And why don’t our cells pop open when we use soap?
- Biochemistry connection: Why is meat tenderizer used? Read the ingredient label and hypothesize which components of the tenderizer make the most different. 4. Allow the bag to rest for 10-15 minutes to allow the chemical reactions to proceed
5. Pour the contents of the bag into a coffee filter place on top of a beaker and allow the liquid containing the DNA to filter down into the beaker below.
6. With the DNA solution in the beaker below, about 2-3 volumes of COLD alcohol can be poured in. The results work best if the students are stirring their solutions as the alcohol is poured.
The DNA should be stuck to the stir rod and the students can squeeze out as much of the water and alcohol as possible. If the students weighed the strawberry in the first step, they can weigh the DNA, on the stir rod and calculate what percentage of the total weight of the strawberry is taken up by the genetic material.
This process can be repeated with different fruits though their DNA is not as sticky as strawberries. This can make quantitative comparisons of fruit DNA more difficult but a qualitative observation is still possible.
History Connections to DNA in general
- The discovery of DNA as the genetic material of the cell and its structure was filled with colorful scientists and characters. The research of Griffith, Avery, McCleod, Watson, Crick, and Franklin helped to prove the properties and structure of DNA. Their research and lives also demonstrated what science in the 1940’s and 1950’s ws like. The discovery of the double helix was a race between competing labs and while Watson and Crick published first, there were others. What were some of the other researchers studying DNA and what contributions to science did they provide?
- While Watson and Crick get most of the credit for the discovery of the DNA double helix, Franklin’s work on elucidating its X-ray structure was paramount. For decades, her work was marginalized. What were the social circumstances around the role of women in science during that era and how has it changed?