In this experiment I extract DNA from the cells of strawberries using a home made extraction kit. The experiment is perfect for any young scientist and introduces the concept of DNA extraction with in-depth explanation of the hands-on scientific procedure. All materials and equipment are inexpensive, easy to find and safe to use at home.
Introduction to DNA
In 1953, using x-ray diffraction data collected by Rosalind Franklin, James D. Watson and Francis Crick proposed the double helix structure of deoxyribonucleic acid (DNA). Their paper, “Molecular Structure of Nucleic Acids: A Structure of Deoxyribonucleic Acid”, proposed a simple and elegant solution to the then mystery of the chemical structure of DNA. It also provided an insight into how genetic instructions are stored inside organisms and passed from one generation to the next.
The human genome contains just over 2.85 billion DNA base pairs, containing 20,000-25,000 protein-coding genes, which are coded through the arrangement of the nucleotide bases. Believe it or not you share some of these genes with Chimpanzees (98%), Round Worms (21%) Fruit flys (36%) and with every other living organism. By extracting the DNA from animals, bacteria, humans, etc, scientists can study the sequences and learn more about how DNA encodes the instructions for all lifes processes. DNA extraction can also be used to create DNA fingerprints to help diagnose genetic diseases, solve criminal cases, identify victims of disaster and war, and establish paternity or maternity. Scientists can also genetically engineer changes in DNA to create robust, disease-resistant genetically modified plants and animals.
The DNA consist of three components, a heterocyclic base, a pentose sugar and a phosphate residue. The heterocyclic bases that make up the code in DNA can be categorised into two different groups The bicyclic purines, guanine (G) and adenine (A); and the monocylic pyrimidines, cytidine (C), thymidine (T). Purines form hydrogen bonds to pyrimidines (Watson-Crick base pairs), with adenine binding to thymidine or uracil in RNA, while cytidine binds with guanine. G:C base pairs contain three H-bonds whereas A:T contains two, the result being that polymer chains rich in G:C pairs are more thermally stable. This stability can be measured by finding the temperature required to disrupt the H-bonded base pairs in a sequence. This temperature (Tm) is defined as the mid-point temperature at which there is an equilibrium between the bound and unbound states of the DNA strands. The sugars are joined together by phosphodiester bonds, catalysed by DNA polymerase between the third and fifth carbon atoms on an adjacent sugar ring. This asymmetric bond means a strand of DNA has a direction. In a double helix, the direction of the nucleotides in one strand is opposite to their direction in the other (antiparallel).
DNA Strawberry Extraction
DNA is located inside the cells of all species. However, different organisms are made up of different types of cells. Members of the Animal, Plant, Protist and Fungi kingdoms are comprised of eukaryotic cells. Their DNA is located within a membrane bound organelle named the nucleus. The entire cell is bound by a cell membrane made of two layers of phospholipids that protects and separates the cell from its surroundings. Therefore, in order to extract DNA from the strawberries cells, the phospholipid cell walls and nuclear membranes must first be broken (cell lysis). This can be accomplished by using a a detergent-based extraction buffer and by mashing, crushing, etc. Just like dishwashing detergent dissolves fats (lipids) to clean plates, the nuclear membrane extraction buffer will dissolve the phospholipids holding the cell together. With the cell wall being disrupted the contents of the cell is allowed to flow into solution. This is called the lysate or cell extract. The detergent-based extraction buffer also contains salt (NaCl). The salt causes some of the cellular debris in the lysate to precipitate out of solution whilst the DNA remains in solution. The precipitate can then be removed via filtration. The DNA is soluble in the aqueous cellular environment, but is insoluble in alcohol (such as isopropanol and ethanol). Applying a layer of alcohol on top of the filtrate causes the DNA to precipitate out of solution at the point where the alcohol and the filtrate meet. Strawberries are an excellent source of DNA as they are multicellular and octoploid. This means that they have eight copies of their seven chromosomes in each cell. Strawberries also produce pectinase and cellulase enzymes that contribute to the breakdown of cell walls, making DNA extraction relatively easy to accomplish at home
Materials and Equipement
- Iso-propanol (rubbing alcohol) or ethanol (NOT! vodka or beer)
- Table salt (NaCl)
- Dishwashing detergent
- Paper towel
- Plastic sandwich bag
- Small glass
- Chill the alcohol in the freezer, refrigerator, or on ice until use.
- In a small glass add 100 ml of water with 0.2 g of table salt, 2 drops of dishwasher detergent and mix. This is your extraction fluid.
- Place a strawberry in the sandwich bag and remove most of the air before sealing. Then mash the strawberry in the bag in your hand.
- Add 20 ml of your extraction fluid into the sandwich bag containing the mashed strawberry. Push out all the air and reseal the bag and continue to mash the mixture.
- Make a funnel using the paper towel (as shown in video) and place on top of an empty glass.
- Pour the strawberry/extraction fluid mixture into the funnel. Gently squeeze, filtering the pulp until there is no liquid left in the funnel.
- Remove the filter and tilt the glass to the side and very slowly add the chilled alcohol down the side of the glass. The alcohol layer should sit on top of the strawberry extract layer. Leave for 5 minutes and DO NOT MIX!
- Watch closely as translucent strands of DNA begin to clump together where the alcohol layer meets the strawberry extract layer.
- Using the chopstick, slowly and carefully poke the clumps of DNA in the alcohol layer and rotate. Remove the chopstick, and the DNA should be attached.