12 Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
Chapter 1
Isolating DNA, the Blueprints of Life
Zero to Genetic Engineering Hero is unique in many ways.
So before we jump into the topic of Chapter 1, let’s
learn how the chapters in this book are structured.
You will notice that this book is packed with hands-on
exercises. Each chapter starts with the hands-on
activities so that you can “pull up your sleeves” imme-
diately and start building genetic engineering skills.
“Going Deeper” and “Breakout” sections that will
provide more information about what is going on in
the hands-on exercise. You can read them or skip
them - you decide how much you want to learn. At
some points, you may feel like you need more back-
ground information, but trust us and continue with
the exercise to completion as there is a wealth of
information later on.
Each chapter has a Fundamentals section which covers
These fundamentals are deliberately placed after the
hands-on exercises so that you can use real-world
skills and context to anchor the concepts in the Funda-
mentals. If, during the hands-on, you would prefer
more context, you can always start with the Funda-
mentals and circle back to complete the exercises.
In Chapter 1, you start your Genetic Engineering jour-
ney with a simple, engaging hands-on exercise:
extracting DNA (deoxyribonucleic acid) from fruit.
You’ve likely heard of DNA before in classic movies
like Jurassic Park, forensic television shows, or in the
news. But very few individuals have ever seen DNA in
real life or know how to extract it from a living or dead
organism. As you learn how to extract (separate) DNA
from their cells and see it with the naked eye, you will
also be learning the general principles of breaking
cells open & extracting DNA. You’ll likely be surprised
at how much DNA you consume when you eat fruit!
This exercise will help you to more richly understand
the knowledge gained in the Fundamentals section,
which focuses primarily on DNA, its structure, and its
function. Further, by completing the hands-on exer-
cise, you will begin laying the foundation for
understanding and doing genetic engineering in the
chapters to follow.
For this chapter, you do not need any special equip-
ment, and you can do the exercise in your kitchen or
at your desk. Chapter 2 will cover setting up the neces-
sary equipment and space for the exercises in later
chapters.
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13Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
Getting Started
Equipment and Materials
You do not need any special equipment for this exercise. The materials can be obtained either by purchasing
a DNA Extraction Kit online at www.amino.bio or by purchasing the components listed below at a local grocery
store or pharmacy. The last three items (in bold) are not included in the DNA Extraction Kit.
If you are eager to complete all of the exercises in this book, you can purchase all the hands-on kits in packs.
These Zero to Genetic Engineering Hero Kit Packs are separated into a beginner pack: (Ch. 1-4) and advanced
pack (Ch. 5-7) and are available for both home and the classroom. Find them at www.amino.bio
Shopping List
Water (distilled, or bottled water) - 1 tablespoon
White salt - 1/4 teaspoon
Translucent (non-creamy) shampoo, hand or dish soap with EDTA (ethylenediaminetetraacetic acid)
- 1/4 teaspoon
1 very narrow glass, such as a shot glass
1 small sandwich resealable bag
91 to 99% isopropyl alcohol (rubbing alcohol) - 2 tablespoon (70% isopropyl alcohol will also work
1 small drinking cup
Instructional Overview
1. Make a salt water solution in a resealable bag
2. Mash up fruit in salt water to separate the fruit into individual cells
3. Add soap to lyse (cut open) the cells to release the DNA
4. Filter the lysed cell debris to isolate dissolved DNA
Precipitate (separate) the DNA in alcohol so it becomes visible
Chapter Timeline Overview
Timeline to complete the hands-on exercise is:
Day 1
Timeline to read Fundamentals is typically 3 hours.
Keep in mind!
When doing genetic engineering or any life science project, the activities boil down to chemistry. As you go through
this and future exercises, pay attention to the Going Deeper sections and to how you are using chemistry to manipulate
the biological systems. The more you understand the rules of chemistry, the better you will be able to engineer biology.
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14 Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
What is DNA? Breakout Exercise
While you wait for your DNA Extraction Kit or supplies, you can prepare with some contextual exercises
on DNA and get going now!
Grab your laptop or go to your desktop computer and visit www.amino.bio/vbioengineer to access the
What is DNA? virtual simulator. Note that the virtual simulators are not compatible with mobile devices.
What is DNA? is a simple exercise that will provide you with basic context and historical facts about DNA
in relation to the genome. You can do the exercise as many times as you like or need, and at any point
during this book. We’ve found that a few tries at the drag-and-drop exercise really helps grasp what
genomic DNA is.
During this chapter’s hands-on activity, you will be getting a piece of fruit like a single strawberry and
mashing it up so that the cells that make up the fruit become separated. You will then break open these
cells to release the inside components into the outer environment. This includes releasing the cell’s DNA!
visible to the naked eye.
In other words, you will be extracting the genome from the strawberry cells, so knowing what a genome
is will clarify what is happening in your experiment!
Find out about genomes now with What is DNA? This will also prepare you to grasp the more in-depth
information found in the Fundamentals section.
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15Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
Learning Hands-On:
Breaking Cells Open & Extracting DNA
Step 1. Create salt water inside the resealable bag
In a small resealable bag, mix together 1 tablespoon of distilled or bottled water with
salt. The distilled/bottled water will help you in creating a liquid slurry of mashed up fruit, ultimately enabling
you to create a suspension of separated fruit cells. It is important to use distilled or bottled water because tap
water contains lots of salts and other impurities that could ruin the experiment.
Why these ingredients? Going Deeper 1-1
Why distilled or bottled water? Lots of calcite (CaCO
3
) and dolomite (CaMg(CO
3
)
2
) are often found in tap
water and as you’ll see in coming chapters, calcium (Ca
2+
) and magnesium (Mg
2+
) ions play an essential role
in how DNA is regulated, driving molecular interactions, and even controlling many biochemical reactions
bacteria and other organisms. While your DNA extraction may still work using tap water, it will work better
with distilled or bottled water which has reduced ions (ions are charged atoms like Ca
2+
).
Why add salt? Salt is added to help the DNA stay separate from the cellular machinery and macromole-
cules that make up the fruit slurry. When you break open the cells in the next steps, there will be thousands
table salt, which is mostly sodium chloride (NaCl), the salt binds to and create “buffers” or shields around
many of the molecules, including the DNA. Just like the bumper on a bumper car that causes you to bounce
off another car during a collision salt ions become the bumpers around DNA. In other words, the salt helps
keep the DNA free from binding with (sticking to) other molecules. This enables you to get a larger quantity
of ‘pure’ DNA at the end of the exercise.
Distilled Water
Electrolyte (salt)
Figure 1-1. Step 1. Create salt water using distilled or bottled water.
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16 Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
Step 2. Mashing the strawberry into individual cells
You will now add one strawberry
massaging it in the resealable bag until it is a smooth fruit slurry with no pieces or lumps. (You can keep or
remove the leaves, it is your choice.) At the end of this step, the fruit cells will have been separated from each
other (Figure 1-2).
These individual cells are now “suspended” in the slurry. Most of the cells will still be intact and functioning, but
some will have been torn open by the mixing.
The strawberry is made of millions of individual cells that are tightly packed together, each containing genomic
DNA. By separating the cells as much as you can, it will be easier for the soapy chemicals used in Step 3 to come
into contact with each cell and cut them open (Figure 1-3).
Extracting DNA from other organisms Going Deeper 1-2
If you want to extract DNA from other organisms, similar principles are applied. You collect a sample such
as a leaf, some other fruit, suspend it in a salt solution, break the cells apart, and continue the following
steps in this exercise. You can even collect your cells from your mouth by gently scraping them with a uten-
sil and depositing them into a cup or small resealable bag and follow the same procedure.
Some cells have solid outer membranes/cell walls (like yeast) and could require further chemistry or heat
to be broken open. You are likely familiar with the COVID-19 virus; in this case, the genome is made of RNA
(Ch. 4). Similarly, this virus can be broken open using surfactants. The RNA is then accessible for testing!
Figure 1-2 Step 2. Mash the strawberry to separate the cells that make up the strawberry.
Figure 1-3
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