17Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
Step 3. Breaking open the cells with soap
Now we need to break the cells open, a process scientists called lysing. This process will release the DNA from
being contained in the cell.
Add 1/4 teaspoon of shampoo/soap with EDTA, also called Lysis Buffer into the fruit slurry and mix for 3
minutes. If Step 2 was not completed successfully and cells were left in clumps, lots of cells inside the clumps
would be protected from coming into contact with the cutting power of the shampoo, resulting in less freed
DNA. When the DNA has been released into the saltwater environment, it remains dissolved.
EDTA & Surfactants Going Deeper 1-3
EDTA or Ethylenediaminetetraacetic acid (also called Ethylenediaminetetraacetate) is a small molecule
made of carbon, nitrogen, oxygen, and hydrogen that is really good at binding to positively charged metal
ions like calcium (Ca
), magnesium (Mg
) and even iron (Fe
). It does this by sandwiching
the metal ion between its four “arms” very tightly. Have a look at the periodic table at the end of the book
During regular cell operation, DNA is bound to cellular molecules called proteins, with the help of metal ions.
The proteins are essential for cell operation as they read and copy the DNA. Our goal in this experiment is
to get pure DNA. Therefore, we have to remove the proteins bound to the DNA.
The proteins cannot easily bind to the DNA on their own - they have help from positively charged metal
like magnesium (Mg
) and calcium (Ca
). The Mg
and Ca
act as a glue which binds to the proteins and
Shampoo / EDTA
Shampoo / EDTA
Figure 1-4 Step 3. Breaking open the cells using surfactants and EDTA.
Figure 1-5. EDTA molecule before (left) and after (right) it binds up a metal ion (orange sphere). Dashed lines indicate the
bonding between the metal ion and EDTA. By binding most metal ions, proteins no longer bind to DNA. The small red and
white V-shaped molecule on the right that is also bound to the metal ion is a water molecule.
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18 Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
the negatively charged DNA (Figure 1-6). If we can
remove the metal ions, then we remove the proteins!
EDTA is a great way to do this because it binds so tightly
to the metal ions. This is also why EDTA is added to
shampoo and soaps, it helps to clean you by removing
metal ions that bind other molecules to your body. See
Figure 4-14 in Chapter 4 to see a similar phenomenon
when Ca
causes DNA to interact with the surface of
cells during genetic engineering.
In addition to EDTA, shampoos and hand soaps have
surfactants inside. Surfactants are the molecules that
cause bubbles to form. A common surfactant is called
sodium laureth sulfate (SLS). Surfactant molecules can
bind to many different molecules and sequester them.
They have a hydrophobic end (“water-avoiding”) that
can bind to hydrophobic molecules such as fats and oils,
and a hydrophilic (“water-loving”) end that can bind to
other hydrophilic molecules such as water, proteins and
sugars. A general rule to consider when thinking about how molecules interact is “like binds to like”. In other
words, molecules that are water-avoiding will generally ‘like’ to interact with other water-avoiding molecules.
When a surfactant is added to the cells, the surfactant “attacks” and cuts into the membrane of the cells
(Figure 1-7; Step 1). As the cell breaks into pieces, different cell parts will interact with the surfactants as
they form micelles and get parceled away in the micelles (Figure 1-7; Step 2). The same thing happens when
you wash your hair! Dirt, grease, and metal ions are gobbled up into the micelles, but your hair is strong
enough to hold up against the cutting power of the surfactant.
Surfactants (SLS)
Head Group
Tail Group
Figure 1-6. The surfactant “SLS” has a charged head that can interact with watery environments and a non-charged tail which
doesn’t like to interact with watery environments and other charged heads but like to interact with other non-changed mole-
cules. This results in the surfactant molecule heads interacting with one another and the normal watery cell environment, and
the tails interact with each other. Ultimately they form a micelle, a spherical ball with the inside being the surfactant tails and
the surface being the charged head group.
ProteinsMetal ionsDNA
Figure 1-6. Metal ions are like a ‘glue’ holding the
(-) charge DNA and the proteins together.
Surfactants (SLS)
Cell Membrane
Figure 1-7. (1) The soap molecules called surfactants, attack and cut into the cell membranes of the fruit cells; (2) The surfac-
tants then form spherical jumbles called micelles which contain surfactants and cell debris.
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19Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
Step 4. Filtering the cell debris
You now want to separate the DNA that is still dissolved in the salt water from the rest of the cell “debris” and
micelles that you are not interested in for this exercise. This debris includes the carbohydrates and lipids from
Set a 
next step, the precipitation may not work as well - the next section will explain why.
You will notice that the DNA liquid looks like red water. How do you know that DNA is actually in there? Lets
make it visible using a chemistry technique called a precipitation!
Step 5. Precipitating the DNA
In this last step, you are going to use chemistry to cause the DNA to “fall” out of the solution so that it can be
seen with the naked eye. This “precipitation” is one of the most commonly used techniques in chemistry. Get
Surfactants Pro-tip
There are many different kinds of surfactants used when doing genetic engineering experiments. In this
exercise, you used SLS—a common surfactant in body soaps. In laboratories, a very common surfactant
is called sodium dodecyl sulfate, or, SDS. Another popular surfactant which you will use in later chapters
experiment. In many cases you can use many surfactants for a particular experiment. For example, we
could have used Triton X-100 for this exercise. We did not because Triton X-100 is much more expensive
and harder to get then body soap, which provides the same result in the fruit DNA extraction.
Figure 1-8. Step 4. Filtering cell debris.
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20 Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
and tinted red thanks to some red pigment from the strawberry that remained in the salt water. You cannot see
DNA into the isopropyl alcohol tube or glass. As you pour, you will begin to see the DNA precipitate out of solu-
Molecular interactions Going Deeper 1-4
Why was the DNA dissolved in the salt water? What causes the DNA to precipitate? If you tried the What is
DNA? simulator, you would have seen that DNA is negatively charged due to the phosphates in the sugar-phos-
phate backbone. If you have forgotten, or haven’t done it yet, have another look at What is DNA? Pay special
attention to the phosphate molecules - notice how many negative charges are on each phosphate.
In chemistry, “bonding” is a phenomenon where atoms and molecules have a tendency to attract or repel
one another. A deeper overview of bonding can be found in Chapter 6. For this exercise, however, you can
a general theme whereby “like interacts with like”. Charged molecules with a positive or negative charge
do interact, uncharged molecules do interact, while charged and uncharged molecules do not interact.
Table 1-1 - Simplied rules for molecular interactions
Molecule 1 Characteristic Molecule 2 Characteristic Interaction?
Charged (+ or -) Charged (+ or -) Likely
Uncharged Charged (+ or -) Unlikely
Uncharged Uncharged Likely
Because both DNA and water are charged, they interact with one other. Before pouring the DNA into the
alcohol, the DNA is fully surrounded by, and is interacting with water molecules. The water molecules are
able to bond to and “hold onto” the DNA. When the DNA interacts with the water, the DNA is said to be
dissolved. You’ll learn about bonding later on in Chapter 6.
When you poured the dissolved DNA into the isopropyl alcohol, something different happens. Isopropyl
alcohol is an uncharged molecule, and so it does not like to interact with the DNA. As you poured the water-
DNA into the isopropyl alcohol, the water molecule shell surrounding the DNA can move away into the
isopropyl alcohol. Because water is partially charged, unlike DNA which is very charged, water can mix and
partially interact with the alcohol. This means the water does not need to stay bonded to the DNA.
Figure 1-9. 
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21Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
Further, a process called diffusion causes water to move away from the DNA throughout the tube of alcohol.
Because there are fewer and fewer water molecules dissolving the DNA, and the DNA molecule does not
like to interact with the uncharged isopropyl alcohol molecules, the DNA begins to fold upon its charged
self with help from the (+) charged salt you added, also known as sodium (Na
). The folding DNA becomes
larger and more dense to the point where it becomes visible to the naked eye and “falls out of solution.
When this happens, the DNA is said to precipitate.
people who are clapping, singing, and cheering. The singer dives off of the stage into the crowd and begins
included, is a sea of water molecules. The arms of the water people in the audience are the bonds that can
hang onto the DNA singer. As the DNA singer surfs across the crowd, you put your arms up into the air, and
the singer passes over top of you. Your arm bonds can connect to the singer and temporarily hold onto the
singer keeping them in the air. The DNA molecule singer coasts across the arena because all of the water
molecule bonds are keeping the singer held up “dissolved”. This is what is happening in the DNA/salt/water
solution; the DNA is dissolved.
What would happen to the DNA if the water bonds disappeared? What if all of a sudden the crowd of people
was replaced by thousands of cats? Lets pretend that the cats are the isopropyl alcohol molecules. Cats
have no desire to hold up people, even a world-famous singer at a concert. Of course, the cats wouldn’t be
capable of holding up the singer, even if they wanted to. The singer falls to the ground as the cats scatter
the ground in the sea of cats (isopropyl alcohol molecules).
people. But as more and more cats pour in, they start causing the people to separate. No one likes to step
on a cat, so the people accommodate the cats that are taking over the auditorium and separate from each
nervous because the water audience and the arm bonds are no longer blanketing the auditorium - there
are patches of holes forming which the singer might fall through. The DNA singer curls up into a ball to
brace for a fall. This makes the situation worse because whereas before the singer was spread out and many
arm bonds could hold them up, now they are more compact and dense and fewer arm bonds can touch
them and hold them up. With the high number of isopropyl alcohol cats and the low number of water people,
the curled up DNA singer falls to the ground - they precipitate out of solution.
This happens because:
The isopropyl alcohol cats don’t have the arm bonds to dissolve the charged DNA singer
The cats caused the water people to spread apart, lowering the arm bonds that could hold onto the singer
The DNA singer curled up into a ball and became denser
The cat analogy isn’t a perfect one, but it does drive the point across. The non-charged isopropyl alcohol
molecules are not keen on interacting with partially charged water or the charged DNA. Because DNA is
a charged molecule, and isopropyl alcohol is not charged, only weak interactions occur, and the following
occurs as you pour:
isopropyl alcohol, the water molecules surrounding the DNA
become spread out in the isopropyl alcohol leaving the DNA “naked”. The isopropyl alcohol and the DNA
do not like to interact with one another so the DNA folds up and binds to other parts of itself with the help
of sodium (white salt) and becomes denser.
The large DNA molecule will continue to fold upon itself into large compact clumps of DNA. When the
clumps become large enough, the DNA becomes visible, and it also can no longer be dissolved in the
isopropyl alcohol. It begins to precipitate out of solution.
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