BioTech

PCR process, the DNA sequencing

PCR process (Polymerase Chain Reaction)
- PCR or polymerase chain reaction is a technology indispensable to genetic and molecular
biology. Many of its applications are widely used worldwide, including DNA sequencing, DNA
fingerprinting, forensics, detection of microorganisms, and diagnosis of hereditary diseases.
PCR allows rapid and inexpensive amplification of DNA fragments. Because it is able to
generate large quantities of DNA from a small amount of nucleic acid, PCR is also referred to as
molecular photocopying. PCR depends on a series of 20 to 40 repeated cycles of DNA
replication by a DNA polymerase enzyme. After each process, the number of DNA strands is
doubled, at the end of a 40-cycle reaction, more than 1 trillion copies are generated from a
single copy of the DNA.

Thermal Cycler:
- it carries out the temperature cycles.

YOU NEED:
- DNA samples
- DNA primers
- DNA Nucleotides
- DNA polymerase / Taq Polymerase (heat-resistant polymerase)
- Stable Solution
THE PCR PROCESS
1. Denaturation - separates the two complementary strands of DNA
2. Annealing- specifies the region of DNA that will be copied
3. Extension - copies the DNA

1. Denaturation
- the first step is called DENATURATION, it involves separating the two strands of a starting
DNA sample apart. This starting DNA sample is referred to as our template DNA. To do this, we
heat the DNA up to about 95° Celsius, almost reaching the boiling point of water. In just a few
seconds, the high temperature causes hydrogen bonds between the two strands of DNA to
break. After an initial longer denaturation to start off the PCR, each cycle requires a shorter
denaturation, which can be as little as ten seconds but is often between 30 seconds and one
minute.

2. Annealing
- In this second step of PCR, we specify the region of DNA to be amplified. We do this using
short pieces of DNA called primers. Each reaction will have two types of primers, forward and
reverse. The forward primer will match a sequence on one strand of DNA at the beginning of
region we want to amplify. The reverse primer will match the end of the region on the other
strand. Primers are typically around 20 bases long. When we cool our reaction down, the
primers will anneal (or stick) to their complementary regions on the template DNA. Lowering the
temperature allows hydrogen bonds to form between the primers and the template at areas
where the sequence is complementary. We add lots of extra primers to increase the chances
that they stick to the DNA rather than the DNA strands annealing back to each other. Annealing
temperatures are typically between 50 - 65C, but the exact temperature you use in your reaction
depends on the specific length and sequence of the primers themselves. We usually let our
reactions anneal for five to thirty seconds. Our reaction may be allowed to anneal for as short as
5 seconds or as long as 30 seconds. Next, we heat the reaction back up again to extend, or
copy, these new double-stranded areas where primer and template DNA have annealed. For
this, we use an enzyme called DNA polymerase. The polymerase will find the ends of the short,
double-stranded regions of DNA where the primers have bound. It then moves along the DNA
by bases into a 5’ (prime) to 3’ (prime) direction and adds the correct complementary DNA
nucleotides as it goes. If it finds a C on the template strand, it adds a G. if it finds an A, it adds a
T, and so on, creating a complementary strand of DNA.

3. Extension
Our Extension Step can Vary in Time:
- When our target is long, we can extend this step to a few minutes long to give the polymerase
time to copy the entire region. If we are copying very short regions, it may only need a few
seconds. An extension typically happens around 72°C, the optimal working temperature of the
polymerase. Of course, 72C is hot--our own body temperature is around 37C, so if we used a
human or typical bacterial polymerase, it would likely denature and stop working at these high
temperatures. Instead, we use a special polymerase known as Taq Polymerase. This enzyme
was originally found in thermophilic bacteria living in the hot springs of Yellowstone National
Park and remains stable in our reaction through multiple rounds of heating and cooling.

Cycle repeats:
- After one cycle of these three steps (denature, anneal, and extend) we have turned our
original one piece of target DNA into two. But of course, we don’t want to stop there! We repeat
this cycle over and over again, now turning our two into 4, then 4 into 8, 8 into 16, and so on.
The process creates new identical copies of DNA. We are exponentially amplifying our DNA.
This “chain” of copying explains why it’s called “Polymerase Chain Reaction.” Most PCRs will
run for around 30 cycles, which should give us about 1 billion copies of our original target
sequence for every copy we started with.

Sanger sequencing: The chain termination method

Regions of DNA up to about 900 base pairs in length are routinely sequenced using a method
called Sanger sequencing or the chain termination method. Sanger sequencing was
developed by the British biochemist Fred Sanger and his colleagues in 1977.

In the Human Genome Project, Sanger sequencing was used to determine the sequences of
many relatively small fragments of human DNA. (These fragments weren't necessarily 900 bp or
less, but researchers were able to "walk" along each fragment using multiple rounds of Sanger
sequencing.) The fragments were aligned based on overlapping portions to assemble the
sequences of larger regions of DNA and, eventually, entire chromosomes.

Although genomes are now typically sequenced using other methods that are faster and less
expensive, Sanger sequencing is still in wide use for the sequencing of individual pieces of
DNA, such as fragments used in DNA cloning or generated through polymerase chain reaction
(PCR).

Ingredients for Sanger sequencing

Sanger sequencing involves making many copies of a target DNA region. Its ingredients are
similar to those needed for DNA replication in an organism, or for polymerase chain reaction
(PCR), which copies DNA in vitro. They include:

● A DNA polymerase enzyme

● A primer, which is a short piece of single-stranded DNA that binds to the template DNA
and acts as a "starter" for the polymerase
● The four DNA nucleotides (dATP, dTTP, dCTP, dGTP)
● The template DNA to be sequenced

However, a Sanger sequencing reaction also contains a unique ingredient:

● Dideoxy, or chain-terminating, versions of all four nucleotides (ddATP, ddTTP, ddCTP,

ddGTP), each labeled with a different color of dye
Dideoxy nucleotides are similar to regular, or deoxy, nucleotides, but with one key difference:
they lack a hydroxyl group on the 3’ carbon of the sugar ring. In a regular nucleotide, the 3’
hydroxyl group acts as a “hook," allowing a new nucleotide to be added to an existing chain.

Once a dideoxy nucleotide has been added to the chain, there is no hydroxyl available and no
further nucleotides can be added. The chain ends with the dideoxy nucleotide, which is marked
with a particular color of dye depending on the base (A, T, C or G) that it carries.

Method of Sanger sequencing

The DNA sample to be sequenced is combined in a tube with primer, DNA polymerase, and
DNA nucleotides (dATP, dTTP, dGTP, and dCTP). The four dye-labeled, chain-terminating
dideoxy nucleotides are added as well, but in much smaller amounts than the ordinary
nucleotides.

The mixture is first heated to denature the template DNA (separate the strands), then cooled so
that the primer can bind to the single-stranded template. Once the primer has bound, the
temperature is raised again, allowing DNA polymerase to synthesize new DNA starting from the
primer. DNA polymerase will continue adding nucleotides to the chain until it happens to add a
dideoxy nucleotide instead of a normal one. At that point, no further nucleotides can be added,
so the strand will end with the dideoxy nucleotide.

This process is repeated in a number of cycles. By the time the cycling is complete, it’s virtually
guaranteed that a dideoxy nucleotide will have been incorporated at every single position of the
target DNA in at least one reaction. That is, the tube will contain fragments of different lengths,
ending at each of the nucleotide positions in the original DNA (see figure below). The ends of
the fragments will be labeled with dyes that indicate their final nucleotide.
After the reaction is done, the fragments are run through a long, thin tube containing a gel
matrix in a process called capillary gel electrophoresis. Short fragments move quickly through
the pores of the gel, while long fragments move more slowly. As each fragment crosses the
“finish line” at the end of the tube, it’s illuminated by a laser, allowing the attached dye to be
detected.

The smallest fragment (ending just one nucleotide after the primer) crosses the finish line first,
followed by the next-smallest fragment (ending two nucleotides after the primer), and so forth.
Thus, from the colors of dyes registered one after another on the detector, the sequence of the
original piece of DNA can be built up one nucleotide at a time. The data recorded by the
detector consist of a series of peaks in fluorescence intensity, as shown in the chromatogram
above. The DNA sequence is read from the peaks in the chromatogram.

Uses and limitations

Sanger sequencing gives high-quality sequences for relatively long stretches of DNA (up to
about 900 base pairs). It's typically used to sequence individual pieces of DNA, such as
bacterial plasmids or DNA copied in PCR.

However, Sanger sequencing is expensive and inefficient for large-scale projects, such as the
sequencing of an entire genome or metagenome (the “collective genome” of a microbial
community). For tasks such as these, new, large-scale sequencing techniques are faster and
less expensive.

Next-generation sequencing

The name may sound like Star Trek, but that’s really what it’s called! The most recent set of
DNA sequencing technologies is collectively referred to as next-generation sequencing.

There are a variety of next-generation sequencing techniques that use different technologies.
However, most share a common set of features that distinguish them from Sanger sequencing:

● Highly parallel: many sequencing reactions take place at the same time
 ● Microscale: reactions are tiny and many can be done at once on a chip
● Fast: because reactions are done in parallel, results are ready much faster
● Low-cost: sequencing a genome is cheaper than with Sanger sequencing
● Shorter length: reads typically range from 50-700 nucleotides in length

Conceptually, next-generation sequencing is kind of like running a very large number of tiny
Sanger sequencing reactions in parallel. Thanks to this parallelization and small scale, large
quantities of DNA can be sequenced much more quickly and cheaply with next-generation
methods than with Sanger sequencing.