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Spooling the Stuff of Life |
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by Shawn Carlson |
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At work Michelle employs the latest techniques in biochemistry to unravel the secrets of photosynthesis. By manipulating the smallest units of inheritance, the individual base pairs on a single strand of DNA, she can change one by one the amino acids that make up a key protein and then study how well this altered molecule can do its job. Hearing about Michelle's research so often at the dinner table recently prompted me to try my hand at molecular biology. Although the many cutting-edge techniques she uses are probably beyond the range of amateur dabbling, recent advances have opened up intriguing avenues for informal explorations into biotechnology. To help clear the way, this column explains how anyone can do what biotechnologists do routinely: extract and purify DNA. DNA is the largest molecule known. A single, unbroken strand of it can contain many millions of atoms. When released from a cell, DNA typically breaks up into countless fragments. In solution, these strands have a slight negative electric charge, a fact that makes for some fascinating chemistry. For example, salt ions are attracted to the negative charges on DNA, effectively neutralizing them, and this phenomenon prevents the many separate fragments of DNA from adhering to one another. So by controlling the salt concentration, biologists can make DNA fragments either disperse or glom together. And therein lies the secret of separating DNA from cells. The procedure is first to break open the cells and let their molecular guts spill into a buffer, a solution in which DNA will dissolve. At this point, the buffer contains DNA plus an assortment of cellular debris: RNA, proteins, carbohydrates, and a few other bits and pieces. By binding up the proteins with detergent and reducing the salt concentration, one can separate the DNA, thus obtaining a nearly pristine sample of the molecules of inheritance. My profound thanks go to Jack Chirikjian and Karen Graf of Edvotek, an educational biotech company in West Bethesda, Md., for showing me how anyone can purify DNA from plant cells right in the kitchen. You'll first need to prepare a buffer. Pour 120 milliliters (about four ounces) of water into a clean glass container along with 1.5 grams (1/4 teaspoon) of table salt, five grams (one teaspoon) of baking soda and five milliliters (one teaspoon) of shampoo or liquid laundry detergent. These cleaners work well because they have fewer additives than hand soaps--although do feel free to try other products as well. The detergent actually does double duty. It breaks down cell walls and helps to fracture large proteins so they don't come out with the DNA. The people at Edvotek recommend using pure table salt and distilled water, but I have used iodized salt and bottled water successfully, and once I even forgot to add the baking soda and still got good results. In any case, try to avoid using tap water. To slow the rate at which the DNA degrades, it's best to chill the buffer in a bath of crushed ice and water before proceeding. For a source of DNA, try the pantry. I got great results with an onion, and the folks at Edvotek also recommend garlic, bananas and tomatoes. But it's your experiment: choose your favorite fruit or vegetable. Dice it and put the material into a blender, then add a little water and mix things well by pulsing the blades in 10-second bursts. Or, even simpler, just pass the pieces through a garlic press. These treatments will break apart some of the cells right away and expose many cell walls to attack by the detergent. Place five milliliters of the minced vegetable mush into a clean container and mix in 10 milliliters of your chilled buffer. Stir vigorously for at least two minutes. Next you'll want to separate the visible plant matter from the molecule-laden soup. Use a centrifuge if possible. (To learn how to build a centrifuge, see the January Amateur Scientist column.) Spin the contents at low speed for five minutes and then delicately pour off at least five milliliters of the excess liquid into a narrow vessel, such as a clean shot glass, clear plastic vial or test tube. If you do not have a centrifuge, strain the material through an ordinary coffee filter to remove most of the plant refuse. With luck, any stuff that leaks through should either sink or float on top, so it will be a simple matter to pour off any solids into the sink and then pour the clear liquid into a clean vessel. The solution now contains DNA fragments as well as a host of other molecular gunk. To extract the DNA, you will need to chill some isopropyl alcohol in your freezer until it is ice-cold. Most drugstores sell concentrations between 70 and 99 percent. Get the highest concentration (without colorings or fragrances) you can find. Using a drinking straw, carefully deposit 10 milliliters of the chilled alcohol on top of the DNA solution. To avoid getting alcohol in your mouth, just dip the straw into the bottle of alcohol and pinch off the top. Allow the alcohol to stream slowly down along the inside of the vessel by tilting it slightly. The alcohol, being less dense than the buffer, will float on top. Gently insert a narrow rod through the layer of alcohol. (Edvotek recommends using a wooden coffee stirrer or a glass swizzle stick.) Gingerly twirl back and forth with the tip of the stick suspended just below the boundary between the alcohol and the buffer solution. Longer pieces of DNA will then spool onto the stick, leaving smaller molecules behind. After a minute of twirling, pull the stirrer up through the alcohol, which will make the DNA adhere to the end of the stick and appear as a transparent viscous sludge clinging to the tip. Although these results are impressive, this simple and inexpensive procedure does not yield a pure product. Professionals add enzymes that tear apart the RNA molecules to make sure they do not get mixed up with the coveted DNA. Even after the most thorough extraction, some residual DNA typically lingers in the vessel, forming an invisible cobweb within the liquid. But with a little more effort, you can see that material, too. Some dyes, like methylene blue, will bind to charged DNA fragments. A tiny amount added to the remaining solution will thus stain tendrils of uncollected DNA. I don't know whether any household dyes, like food coloring or clothing or hair dyes, will also work, so I invite you to find out. Add only a drop: you want all the dye molecules to bind to the DNA, with none left over to stain the water. Exciting as it may be, extracting an organism's DNA is only the first step in most biological experiments. You'll probably want to learn what further investigations you can do--for example, sorting the various DNA fragments according to their lengths. This department hasn't described suitable methods for separating large organic molecules in decades. (See the Amateur Scientist columns for August 1955, July 1961 and June 1962.) But I'll be revisiting some of these techniques in coming months to help you bring your kitchen lab into the modern age of biotechnology. The Society for Amateur Scientists and Edvotek have joined forces to create a kit containing cell samples, lab ware, enzymes, buffers and detergents that can help you create higher-quality preparations. To order, send $35 to the Society for Amateur Scientists at 5600, Post Road, #114-341, East Greenwich, RI 02818. For more information about this and other amateur science projects, visit the forum hosted by the Society for Amateur Scientists on the World Wide Web. You may also write the society at the above address or call 1-401-823-7800. Image: Rick Jones Suppliers and Organizations The Society for Amateur Scientists (SAS) is a nonprofit research and educational organization dedicated to helping people enrich their lives by following their passion to take part in scientific adventures of all kinds. The Society for
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