to cover the chunks. Then break up (or lyse, as
biologists say) the cells by pulsing the blades in
short bursts until you’ve blended the material into
a slushy mass. This will rip open some of the cells
directly and expose many more cell walls and nuclei
to the detergent’s attack.
Finally, you need to leach out the organic molecules. Place 5ml ( 1 tsp) of the minced mush into a
clean container. Mix in 10ml ( 2 tsp) of your chilled
buffer. Swirl gently for 2 minutes, and the guts of
the shattered cells will separate into the buffer
intact. If you stir too vigorously, you’ll break up
some of the DNA.
Step Three: Dump the Gunk
Next, you’ll want to separate the solid gunk from
the molecule-laden soup. This is best done with
a centrifuge. If you don’t have access to one, you
can always build one yourself from an old kitchen
blender. (To learn how, check out “A Kitchen
Centrifuge” on my Tail-Kicking Downloads page
scifair.org). If you choose this route, spin at low
speed for 2 minutes.
If you don’t have a centrifuge lying about and
don’t want to build one, there are simpler options,
such as the toe of an old nylon stocking. Just cut
6 inches off the foot, drop the toe into a clean
drinking glass or jar, stretch the fabric across the
opening, and pour your molecular broth through.
The stretch fabric will cling to the glass and the fine
mesh makes a wonderful filter.
Step Four: Extract the DNA
When you’ve extracted the liquid from the gunk,
carefully pour at least 5ml ( 1 tsp) of the fluid into
a narrow vessel, such as a clean shot glass, clear
plastic vial, or test tube. (If you’re using a vessel
larger than a test tube, you’ll need more fluid. Use
enough to fill the container at least one-quarter
full.) You are now ready to coax the DNA molecules
to stick together and fall out of the solution.
Remember, the DNA is only suspended in the
buffer because salt ions prevent these giant negatively charged molecules from sticking together.
Now, you’re ready to reduce the salt concentration
enough to let the DNA molecules clump together
and fall out of solution.
Remove your chilled alcohol from the freezer.
Along the inside of the container, you’ll need to
carefully pour about the same amount of alcohol as
you have buffer, so that the alcohol gently settles
on top of your DNA-laden buffer. To do this, dip a
narrow drinking straw into the alcohol bottle and
then block off the top of the straw with your finger
to capture some alcohol. Remove the straw, tilt the
glass, and touch the tip to the inside of the glass.
Then, simply let the alcohol flow down along the
side. Because the alcohol is less dense than the
buffer, it will float on top. If you have a very steady
hand, you can also do this step by gently decanting
the alcohol into the container by pouring the solution down along a pencil into the container.
Where the 2 liquids meet, a gelatinous sludge will
suddenly appear. That sludge is DNA!
At this point, you should see 3 distinct layers: the
alcohol on the top, the DNA sludge directly below
that, and the buffer on the bottom. The DNA should
appear as stringy filaments that stick together. If,
instead, it appears as chunky pieces of floating debris,
something happened to break up the molecules. You’ll
still be able to measure its volume, but you may not
be able to remove it for study.
Buffer Banter
In the lab, scientists often use the
detergent sodium dodecyl sulfate, or
SDS, to extract DNA from cells. SDS is
also common in shampoos and household detergents, where it goes by the
name sodium lauryl sulfate.
Scientists also use table salt — pure
sodium chloride — without additives.
Morton (“When it rains, it pours”)
adds calcium silicate to its brand
of salt to prevent caking in high
humidity. But too many calcium (or
magnesium) ions can react to lace
your buffer with a white “soap scum,”
especially if you use a soap rather
than a detergent. You can use a liquid
soap, but you’ll need a salt with no
calcium or magnesium compound
added (read the label). Water softener
salts (both sodium chloride and potassium chloride) work well. Otherwise,
use detergent and table salt.
Scientists also use distilled water
but bottled water will work just fine.
Just don’t use tap water because it’s
loaded with undesirable ions and
(often) worse, chlorine, which destroys
DNA on contact.
