Biochemistry and Molecular Biology 
Genetics 
Introductory Biology Author(s): Danica C. Levesque 1 , Athena L. Wallis 1 , Jenna Daypuk 1 , Jesse Petahtegoose 1 , Mitchell Slobodian 1 , Allie K. Sutherland-Hutchings 1 , Ian Black 1 , Jessica M. Vélez 2 , Abdullah Abood 3 , Marah H. Wahbeh 4 , Romina B. Cejas 5 , Angel F. Cisneros 6 , Laerie McNeil 1 , Kento Konno 1 , Lissa McGregor 1 , Birha Farooqi 1 , Carla Bautista 6 , Subhash Rajpurohit 7 , Divita Garg 7 , Jiechun Zhu 1 , Guangdong Yang 1 , Solomon Arthur 1 , Thomas J. S. Merritt* 8
1. Laurentian University 2. Genetics Society of America 3. University of Virginia 4. Johns Hopkins University School of Medicine 5. University of Buffalo 6. Université Laval 7. Ahmedabad University 8. Laurentian Univeristy
Editor: Te-Wen Lo
Published online: 22 Sep 2023
Courses: Biochemistry and Molecular Biology Genetics Introductory Biology
Keywords: genetics DNA biochemical structure and function
2046 total view(s), 197 download(s)
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Article MenuUsing commonly available materials, this tool allows students to extract DNA, exploring DNA chemistry and the principles of experimental design and execution. We take a “Choose Your Own Adventure” approach encouraging students to explore the protocol and vary individual steps. Students learn the science behind each step of extraction, how that science can allow us to identify and understand certain aspects of the structure of DNA, and how modifying experimental steps can change the observed results. The lesson is intended for an undergraduate setting, but we include adaptations to allow delivery of this lesson to a variety of ages from preschool through adult science events. The manuscript is in English, but we have included supporting materials in Anishinaabemowin, French, Spanish, Urdu, Arabic, Japanese, Mandarin, Hindi, Twi, and English, so that more learners can access these materials in their first language. We have included a supplemental figure showing the simplified structure of DNA using a color scheme that is effective with those with typical sight and colorblindness. We have also linked a video demonstration of the extraction that is available in both French and English and with closed captioning. Inclusion of materials in multiple languages and formats makes the material more user-friendly, allowing its direct inclusion in non-English speaking classrooms, and allows learners to understand that science is not limited to the “universal” scientific language and can be conducted in any language of choice.
Primary Image: This image highlights the basic steps of the extraction process, showing the experimental setup, the DNA precipitation, the product and variation observed amongst different group members.
Levesque DC, Wallis AL, Daypuk J, Petahtegoose J, Slobodian M, Sutherland-Hutchings AK, Black I, Vélez JM, Abood A, Wahbeh MH, Cejas RB, Cisneros AF, McNeil L, Konno K, McGregor L, Farooqi B, Bautista C, Rajpurohit S, Garg D, Zhu J, Yang G, Arthur S, Merritt TJS. 2023. An Interactive Protocol for In-Classroom DNA Extraction. CourseSource 10. https://doi.org/10.24918/cs.2023.37
The central, and almost universal, role of deoxyribonucleic acid, DNA, as the informational molecule of life makes its extraction a great engagement tool in the classroom (and the community). Most students will know what DNA is, but many will have never seen the molecule for themselves. The tool described here is a standardized method for teachers to use to extract DNA and explore the properties of the molecule by modifying the protocol. We include suggestions for alterations in the protocol to allow students to use a “choose your own adventure” model to explore DNA properties and experimental design.
Our understanding of DNA essentially begins in 1869 with Swiss physician, Friedrich Miescher’s study of the chemical composition of cells (1). Miescher discovered a new molecule unlike anything previously recorded that differed from proteins and lipids. He gave this mysterious molecule the name nuclein since it was located within the nucleus of the cell. Interestingly this linguistic naming root is conserved in the current appellation of deoxyribonucleic acid. Miescher’s first successful crude extraction of DNA was performed with leucocytes (white blood cells) which he collected from bandages (2). At the time, the scientific community did not fully appreciate this amazing discovery. Many protocols have stemmed from this original one, evolving through time to incorporate modern innovations including centrifuges and quantification methods. Simple extraction methods, such as the one outlined in this experiment, include simply salting out the DNA and other methods of DNA precipitation (3).
The double helix of the DNA molecule is an icon of science and perhaps the most widely used and recognized symbol of modern biology and genetics. Two anti-parallel sugar-phosphate chains linked by phosphodiester covalent bonds make up the backbone of the helix. Each negatively charged phosphate group is attached to a deoxyribose sugar ring that also has a single nitrogenous base covalently linked to it. DNA contains a four-letter alphabet of these nitrogen bases: adenine (A), thymine (T), guanine (G), cytosine (C), and the information in DNA is encoded in a specific sequence of these bases. The two strands of the DNA molecule are held together by hydrogen bonds between nitrogen bases. This bonding, called “pairing,” between bases is specific: Gs pair only with Cs, and Ts pair only with As. This specificity allows either strand to serve as a template for DNA replication. The information contained in DNA is the basis of biological similarities and differences, coding for proteins, and regulating proper cell function including cell division and replication.
In this experiment, we are isolating the genome, essentially all the DNA in an organism. Many students will understand the concept of a gene and that most genes are made of DNA. This experiment isolates total DNA in the sample and a review of DNA and genome content may be helpful. Remember that most of the DNA in a genome is not actually gene coding sequence. In part because of all the non-coding DNA, genome size varies tremendously across eukaryotes. Genome size also varies because of differences in the sets of chromosomes. Many eukaryotes are diploid, having pairs of homologous chromosomes. Other eukaryotes, polyploids, have multiple chromosome-sets which can lead to very large genome sizes (some diploid also have very large genomes). Domesticated plants are often polyploid as a result of hybridization and the large number of chromosomes seems to be related to faster growth and larger fruit size (4). Wild strawberries, for example, are diploid, but some commercial varieties, often used in DNA extractions like the one described here, are octoploid (5). This impressive ploidy may play a role in the commercial characteristics of fruits, such as size, fertility, flowering periods, taste, and certainly has a great impact on the total genome size (6, 7). The large genome size, and resulting large amount of DNA in the fruit, means that commercial strawberries are a particularly effective biological sample for the DNA extractions described here. This soft fleshy fruit is easy to pulverize and carries the natural enzymes pectinase and cellulase that help break down cell walls. Similarly, commercial bananas, another common choice for these DNA extractions, is triploid and has a relatively large genome (8).
Experimental design is a crucial element in scientific investigation. Generating your own ideas and using them to frame questions that can be answered is the foundation of any experiment and a skill that can be taught and practiced. Allowing students to design and execute an experiment with variables of their choosing is a great method to use as this stimulates creativity and develops useful skills for the workplace like communication and organization. In this lesson, the “Choose Your Own Adventure” format permits students to exercise these abilities by asking questions around the effects on extraction yield, and even the purity, of modifications to the reagents used or the steps followed. To aid students in organizing their experiment, we created a flowchart (Supporting File S1) detailing the experimental steps and areas to mark down the modifications made to the original protocol. The flowchart and an experimental protocol have been translated into ten different languages to allow more students to practice science in the language they are most comfortable speaking.
Prior to the experiment day, students should have discussed and selected the variables of interests, enabling them to design their experiment. Multiple modifications can be made to the original protocol. Instructors can give students free reign or oversee to ensure things like controls and replication. The experiment can also be set up so that students work in groups or individually. The instructor should encourage students to formulate a hypothesis on the expected result from the altered protocol. We created a table of some common modifications and scientific explanations for the possible outcome to aid the instructor in assessing student’s comprehension of the topics discussed (Supporting File S4). In addition, we have created video demonstrations (in French and English, with captions) of the experiment that detail the procedure, it may be useful for students to watch the video prior to get an understanding of DNA chemistry and the steps to be performed.
The experiment is easily performed step by step. If the group goes through each step together, the instructor can give a running commentary to students on the role of each reagent in the extraction and how this role reflects the structure and function of DNA.
The instructor can choose to prepare stations with allocated materials prior or allow students to gather the materials needed. In our experience, the latter helps students remember the experimental steps.
Students place approximately 30 g of sample in a plastic bag, expelling the air, and crush their sample until there are no discernable chunks of sample left. This mechanical disruption breaks up the solid structure of the cell walls of the sample and is the first step in releasing the DNA from the nucleus. This is one of the lengthiest steps and serves as a good time to engage students in experimental theory and DNA biology. Once the sample is thoroughly mashed, students add an equal mass of tap water about 30 mL, and a pinch of salt (1 g), and gently mix.
Next, the students slowly pour the mixture on top of the filter and allow the homogenization liquid, containing the cells and DNA, to filter through the paper and into the collection cup (Figure 1A). Through experience, cheap, thin filters work best, allowing faster, but still effective, filtration—we are just removing large solids in this step. Depending on the age group with which this experiment is performed, students may speed the filtration by squeezing the liquid through the filter. To do so, cautiously remove the rubber band and gather the filter edges to create a pouch, then gently squeeze the filter into the cup to speed up this process. While this added step does speed the process and improve homogenate recovery, there is a chance the filter bursts. If a filter does burst and solids fall into the collection cup, the instructor can provide the student with an additional filter to repeat this step. This step is often omitted because of the risk of bursting a filter, but we have found that the risk adds a little excitement to the experiment.
Figure 1. A series of photographs showing experimental filtration process and results. (A) The filter is set up using a coffee filter, rubber band, and clear plastic cup. (B) The interface between the alcohol and water layer, showing the precipitated DNA. (C) Sixteen extractions, four from each of four participants with the participants grouped in columns. Precipitated DNA is clearly visible in each cup, although less DNA appears to be present in the cups in the second column. This difference likely reflects variation in experimental technique between individuals, the phenomena we refer to as The Slobodian Effect. The first two cups in the first column appear to have more precipitated DNA, the ethanol was poured vigorously for these samples. (D) The last step in the extraction, strands of DNA wrapped around the end of a stir stick!
