WELCOME TO THE WORLD OF MOLECULAR BIOLOGY
There are two types of experiments that are particularly easy to do, and I recommend that even the most adventurous experimenters start with one of these: discovering how much DNA can be extracted from different organisms under different circumstances, and exploring the conditions that cause DNA to degrade.
Measuring the amount of DNA you’ve extracted from a sample couldn’t be simpler. First, measure the inner diameter of your straight-walled container holding the DNA. Once you know that number, just measure the thickness of the sludge. With that information, it’s easy to calculate the volume of DNA you’ve produced: the equation is V = D² T/4, where D is the inner diameter of the vessel and T is the thickness of the layer of DNA sludge. Next, divide the volume of extracted DNA by either the volume or the mass of the material it came from. The simplest way to do that is to accurately measure how much mush you put into your buffer, and then process all of the buffer to extract every scrap of the DNA that leached into it. If you have an accurate scale, weigh your sample before processing it. If not, just measure the volume of the material before you blend it.
Example: Suppose you processed 5g of onion into 10ml of buffer and extracted 1ml of DNA. How much DNA did you get from each gram of onion? Easy! Just divide what you got by what you started with: 1ml DNA / 5g onion = 0.2ml/g.
You can also run experiments with the DNA itself. Usually, the first step is to remove the DNA sludge. It takes a little practice, but you can do it using a clean glass and a swizzle stick. Gently insert the stick through the layer of alcohol and swirl it very slowly in the same direction, with the tip suspended just below the top of the buffer solution. Longer pieces of DNA will spool into the glass, leaving smaller molecules behind.
After a minute of swirling, slowly pull the stirrer up through the alcohol. This will make the DNA adhere to the end of the stick, where it will appear as a transparent, viscous, “snotlike” clump clinging to the tip.
batch of buffer, you can expose them to chemicals, sunlight, temperatures, or anything else that might break up the DNA. Make a new batch exactly as before and chill it, but don’t bother adding the detergent. Submerge the swizzle stick and gently agitate for several minutes as the DNA dissolves into the buffer. Then divide the buffer equally into 2 clean glass containers. Expose one — your test sample — to whatever agent you wish to test. Leave the other — your control— alone. Then process both as quickly as possible and compare the amount of DNA you can extract from each buffer. The difference between the volumes from your test and control is a measure of how much damage your agent does to DNA.
If this sounds too easy, keep in mind that DNA is fragile stuff and it can be affected by lots of subtle things that might escape your notice. Getting consistent results takes practice, so make sure you vary the exposure and that your plotted data shows a regular behavior before drawing any conclusions.
COLD STORAGE
It’s actually easy to store your DNA for later use. Just place the “snot bulb,” swizzle stick and all, in a container filled with ice-cold isopropyl alcohol and put it in the freezer. Your DNA will keep almost forever.
DR. SHAWN’S DNA EXTRACTION KIT
As a special service to MAKE readers, Dr. Shawn has assembled a kit that contains everything you need to perform at least 20 DNA experiments, including laboratory-grade SDS detergent and chemicals, a fast-flow filter, a generous amount of nontoxic DNA stain, a protein-busting enzyme, a shatterproof graduated test tube, a laboratory-style glass DNA extraction rod, and complete instructions. The cost is $27 + $4 shipping (U.S. only). You may send a check to: 5600 Post Rd. Suite 114-341, East Greenwich, RI 02818, or call (401) 398-7001, or order online at scifair.org.
Dr. Shawn (Shawn Carlson, Ph.D.) is a MacArthur Fellow and the founder and executive director of the Society for Amateur Scientists. To learn more about the society, visit sas.org.
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