PAPER PCR
STUDENT MANUAL
Background Information
The term PCR is an acronym that stands for the phrase polymerase chain reaction.
PCR is a scientific technique used to amplify, or create millions of identical copies of, a
particular DNA sequence, all within a tiny reaction tube. You can think of this procedure as
similar to the DNA replication that occurs in your body cells every time they divide.
However, PCR is different in two major ways. First, PCR only copies a specific region of
DNA (rather than your entire genome). And second, it makes millions of copies of DNA
(rather than just one).
PCR is an incredibly powerful tool that scientists use to analyze DNA. We refer to
these kinds of reactions as DNA amplification reactions, although most people just call them
PCR reactions. You may be most familiar with the use of PCR reactions in constructing
human DNA profiles or “fingerprints” that can be used for forensics, paternity testing, and
genetic disease diagnosis.
So, what things do you need to put into a tiny reaction tube to do a PCR-based DNA
amplification reaction? Let’s deal with each of the key components separately so you can
understand the role that each one plays in the reaction.
DNA Template – This is double-stranded genomic DNA isolated from the cells of
the organism being studied. It can be human DNA, plant DNA, mouse DNA,
bacterial DNA, whatever DNA you would like to have copied! The point is that if
you would like to copy something, then you must have a master template from which
to start.
Taq DNA Polymerase – This enzyme can add complementary nucleotides to a DNA
strand during DNA synthesis. It is similar to the human DNA polymerase responsible
for copying your genome every time one of your body cells divides.
Oligonucleotide Primers – These are short pieces of single-stranded DNA that
match up to DNA sequences flanking (to either side of) the region of genomic DNA
that you would like to copy. One is a forward primer and one is a reverse primer.
When they have bound to the complementary sequences on the genomic DNA
template strand, they show the Taq where to start DNA synthesis. The “oligos” or
“primers” are responsible for making sure that only the region of interest is copied.
Nucleotides – Free floating single nucleotides must be present in the reaction because
they are what the Taq puts in place during DNA synthesis. We can’t copy DNA if we
don’t have something to make the copies with! So we must have As, Ts, Cs, and Gs
in our reaction tube.
Unfortunately, we can’t just micropipette all of these components into a tube and expect new
DNA strands to magically synthesize. There is another critical part to PCR and this is the
thermal cycling.
Paper PCR
Specific changes in temperature, or thermal cycling, are what make the PCR DNA
amplification reaction work. There are three different temperatures involved and a specific
thing happens to the reaction components at each of those temperatures. Let’s look at each
one separately.
STEP 1 – DENATURING
The reaction mixture is heated up to 96°C so that the double-stranded DNA template
denatures and becomes single-stranded. (This high temperature breaks the hydrogen
bonds between the complementary bases in double-stranded DNA.)
STEP 2 – ANNEALING
The reaction mixture is cooled down to 50°C so that the oligonucleotide primers can
base pair with, or anneal to, the DNA template. (This cooler temperature allows
hydrogen bonds to form between complementary bases.)
STEP 3 – EXTENSION
The reaction mixture is warmed up to 60°C, so Taq DNA polymerase can perform
DNA synthesis. Taq can recognize an oligonucleotide primer as a starting point for
DNA synthesis. It is able to put free-floating nucleotides into the correct places along
the DNA template so that a new complementary strand of DNA is extended from the
primer.
So, how do we get our tiny reaction tube to go through this series of temperatures?
The tube is placed in a PCR machine, or thermal cycler, which is able to make rapid
transitions between the different temperatures. Each time the reaction mixture is heated for
denaturing, cooled for annealing, and warmed for extending, more DNA fragments are
created. The reaction mixture in a single tiny tube can generate millions of copies of the
region of interest. How is this possible? In the first round of PCR, only the initial genomic
DNA serves as a template. However, in the second and all subsequent rounds of PCR, the
newly synthesized copies can also be used as templates. This concept will become clear as
you and your partner complete the Paper PCR modeling activity that follows.
Activity Overview
In this activity, you and a partner will play the part of Taq DNA polymerase as you
amplify, or make several copies of, a particular DNA sequence of interest. Your whole class
will represent several DNA amplification reactions occurring simultaneously in a single
reaction tube. Your teacher will play the part of the PCR machine, directing the timed
changes in temperatures during three cycles of PCR.
Paper PCR
Materials
1 DNA Template (blue)
7 Forward Primers (green)
7 Reverse Primers (green)
1 Nucleotide Grab Bag (envelope) containing the following:
36 As
36 Ts
36 Cs
36 Gs
1 roll of transparent tape
Procedure
1. Locate all of the materials listed above. Lay out your double-stranded DNA
Template in front of you and your partner. Wait for your teacher (the PCR machine)
to start the first cycle of PCR.
2. Your teacher will indicate that the PCR machine has reached a temperature of 96°C.
You may now denature your DNA Template, or separate it into two single strands of
DNA. Slide one strand in front of you and slide the complementary strand in front of
your partner.
3. Your teacher will indicate that the PCR machine has dropped to a temperature of
50°C. You and your partner may now anneal Oligonucleotide Primers to the
complementary bases at each end of your single-stranded DNA Templates. One of
you will be using a Forward Primer one of you will be using a Reverse Primer,
depending upon which single-stranded DNA Template you have in front of you. (The
Forward Primer will match up at the left end of one DNA Template and the Reverse
Primer will match up on the right end of the other DNA Template.) Lay your Primer
down so that the correct bases match up to those on your DNA Template.
4. Your teacher will indicate that the PCR machine has heated up to a temperature of
60°C. You will now act as Taq DNA Polymerase, extending a complementary strand
of DNA out from your Oligonucleotide Primer, one base at a time. To do this, you
and your partner will each blindly choose a nucleotide from the Nucleotide Grab Bag.
a. If your selected nucleotide does NOT correctly match up to the corresponding
base on the DNA Template, then you must put it back in the Nucleotide Grab
Bag and select again.
b. If your selected nucleotide correctly matches up to the corresponding base on
the DNA Template then you may lay it down and tape it to the end of the
Primer.
5. Keep selecting nucleotides and putting them in place, taping each one to the previous
one, until you have completed the whole double-stranded DNA fragment. Notice that
PAPER PCR
STUDENT MANUAL
Background Information
The term PCR is an acronym that stands for the phrase polymerase chain reaction.
PCR is a scientific technique used to amplify, or create millions of identical copies of, a
particular DNA sequence, all within a tiny reaction tube. You can think of this procedure as
similar to the DNA replication that occurs in your body cells every time they divide.
However, PCR is different in two major ways. First, PCR only copies a specific region of
DNA (rather than your entire genome). And second, it makes millions of copies of DNA
(rather than just one).
PCR is an incredibly powerful tool that scientists use to analyze DNA. We refer to
these kinds of reactions as DNA amplification reactions, although most people just call them
PCR reactions. You may be most familiar with the use of PCR reactions in constructing
human DNA profiles or “fingerprints” that can be used for forensics, paternity testing, and
genetic disease diagnosis.
So, what things do you need to put into a tiny reaction tube to do a PCR-based DNA
amplification reaction? Let’s deal with each of the key components separately so you can
understand the role that each one plays in the reaction.
DNA Template – This is double-stranded genomic DNA isolated from the cells of
the organism being studied. It can be human DNA, plant DNA, mouse DNA,
bacterial DNA, whatever DNA you would like to have copied! The point is that if
you would like to copy something, then you must have a master template from which
to start.
Taq DNA Polymerase – This enzyme can add complementary nucleotides to a DNA
strand during DNA synthesis. It is similar to the human DNA polymerase responsible
for copying your genome every time one of your body cells divides.
Oligonucleotide Primers – These are short pieces of single-stranded DNA that
match up to DNA sequences flanking (to either side of) the region of genomic DNA
that you would like to copy. One is a forward primer and one is a reverse primer.
When they have bound to the complementary sequences on the genomic DNA
template strand, they show the Taq where to start DNA synthesis. The “oligos” or
“primers” are responsible for making sure that only the region of interest is copied.
Nucleotides – Free floating single nucleotides must be present in the reaction because
they are what the Taq puts in place during DNA synthesis. We can’t copy DNA if we
don’t have something to make the copies with! So we must have As, Ts, Cs, and Gs
in our reaction tube.
Unfortunately, we can’t just micropipette all of these components into a tube and expect new
DNA strands to magically synthesize. There is another critical part to PCR and this is the
thermal cycling.
Paper PCR
Specific changes in temperature, or thermal cycling, are what make the PCR DNA
amplification reaction work. There are three different temperatures involved and a specific
thing happens to the reaction components at each of those temperatures. Let’s look at each
one separately.
STEP 1 – DENATURING
The reaction mixture is heated up to 96°C so that the double-stranded DNA template
denatures and becomes single-stranded. (This high temperature breaks the hydrogen
bonds between the complementary bases in double-stranded DNA.)
STEP 2 – ANNEALING
The reaction mixture is cooled down to 50°C so that the oligonucleotide primers can
base pair with, or anneal to, the DNA template. (This cooler temperature allows
hydrogen bonds to form between complementary bases.)
STEP 3 – EXTENSION
The reaction mixture is warmed up to 60°C, so Taq DNA polymerase can perform
DNA synthesis. Taq can recognize an oligonucleotide primer as a starting point for
DNA synthesis. It is able to put free-floating nucleotides into the correct places along
the DNA template so that a new complementary strand of DNA is extended from the
primer.
So, how do we get our tiny reaction tube to go through this series of temperatures?
The tube is placed in a PCR machine, or thermal cycler, which is able to make rapid
transitions between the different temperatures. Each time the reaction mixture is heated for
denaturing, cooled for annealing, and warmed for extending, more DNA fragments are
created. The reaction mixture in a single tiny tube can generate millions of copies of the
region of interest. How is this possible? In the first round of PCR, only the initial genomic
DNA serves as a template. However, in the second and all subsequent rounds of PCR, the
newly synthesized copies can also be used as templates. This concept will become clear as
you and your partner complete the Paper PCR modeling activity that follows.
Activity Overview
In this activity, you and a partner will play the part of Taq DNA polymerase as you
amplify, or make several copies of, a particular DNA sequence of interest. Your whole class
will represent several DNA amplification reactions occurring simultaneously in a single
reaction tube. Your teacher will play the part of the PCR machine, directing the timed
changes in temperatures during three cycles of PCR.
Paper PCR
Materials
1 DNA Template (blue)
7 Forward Primers (green)
7 Reverse Primers (green)
1 Nucleotide Grab Bag (envelope) containing the following:
36 As
36 Ts
36 Cs
36 Gs
1 roll of transparent tape
Procedure
1. Locate all of the materials listed above. Lay out your double-stranded DNA
Template in front of you and your partner. Wait for your teacher (the PCR machine)
to start the first cycle of PCR.
2. Your teacher will indicate that the PCR machine has reached a temperature of 96°C.
You may now denature your DNA Template, or separate it into two single strands of
DNA. Slide one strand in front of you and slide the complementary strand in front of
your partner.
3. Your teacher will indicate that the PCR machine has dropped to a temperature of
50°C. You and your partner may now anneal Oligonucleotide Primers to the
complementary bases at each end of your single-stranded DNA Templates. One of
you will be using a Forward Primer one of you will be using a Reverse Primer,
depending upon which single-stranded DNA Template you have in front of you. (The
Forward Primer will match up at the left end of one DNA Template and the Reverse
Primer will match up on the right end of the other DNA Template.) Lay your Primer
down so that the correct bases match up to those on your DNA Template.
4. Your teacher will indicate that the PCR machine has heated up to a temperature of
60°C. You will now act as Taq DNA Polymerase, extending a complementary strand
of DNA out from your Oligonucleotide Primer, one base at a time. To do this, you
and your partner will each blindly choose a nucleotide from the Nucleotide Grab Bag.
a. If your selected nucleotide does NOT correctly match up to the corresponding
base on the DNA Template, then you must put it back in the Nucleotide Grab
Bag and select again.
b. If your selected nucleotide correctly matches up to the corresponding base on
the DNA Template then you may lay it down and tape it to the end of the
Primer.
5. Keep selecting nucleotides and putting them in place, taping each one to the previous
one, until you have completed the whole double-stranded DNA fragment. Notice that
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