Using PCR To Amplify DNA, A Step-By-Step Guide

PCR Biological Method Overview

PCR, or polymerase chain reaction, is a method to amplify a segment of DNA for analysis. Because it is such a powerful technique, there are a HUGE number of situations where PCR may be used. Some common reasons for using it are:

Microbiology: You need to know if your bacteria was transformed properly with your plasmid
Oncology: You need to know if a particular gene exists in your cancerous cells
Forensics: You need to know if a certain criminal’s DNA was present at the crime scene

The basic steps of PCR include:

Designing primers to designate a target DNA sequence to amplify
Mixing together the primers with the target DNA strand, polymerase enzyme, and deoxynucleotides
Running a thermocycler multiple times in “cycles” to repeatedly:
- Separate DNA strands
- Allow primers to anneal
- Allow the polymerase to attach and synthesize a new DNA chain
Sequencing or Electrophoresis to prove that the PCR worked

In a nutshell, here is what Step 3, above, looks like:

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Ingredients in a PCR mixture – What every component does

In general, a PCR tube will contain the following items:

Water:	Solvent
dNTPs (or deoxynucleotide triphosphates):	Single bases A, T, C, and G which are used by the polymerase while replicating the DNA. As the polymerase adds base pairs onto the new DNA strand, one base pair is used at a time.
MgCl2:	An essential cofactor for the polymerase enzyme
Primers:	Short segments of single-stranded DNA used to frame the DNA region that needs to be amplified. They are complementary to the template DNA strand only at defined locations around the target sequence.
Target DNA:	The DNA “template” that you want to make copies of. This can be a full DNA chain or a part of a longer chain.
*Taq* Polymerase:	An enzyme from Thermis aquaticus that uses dNTPs and replicates DNA starting from the 3′ end of a template strand towards the 5′ end. Taq is used in PCR specifically because it is resistant to the high temperatures used for separating DNA strands during Step 3a above .

Complete Step-By-Step PCR Protocol

Materials

PCR tubes
PCR temperature Cycler
Pipettes
Reaction Buffer	10 mM Tris-HCl, 50 mM KCl, and 1.5 mM MgCl2, pH 8.3

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Methods

For each PCR tube set up the following mixture of materials up to a 50 ul total volume on ice

dNTP solution	200 uM for each dNTP
Forward Primer	0.2 uM
Reverse Primer	0.2 uM
Target DNA	Less than 1000 ng
Taq Polymerase	1.25 units per tube
Nuclease Free Water	Q.s up to 50 ul
Mineral Oil	Add a little bit on top of each tube if you don’t have a heated lid on the temperature cycler

Pipette each tube up and down several times, gently, so as not to add bubbles
Centrifuge each tube down for 1-2 seconds at 100 rcf to bring all contents to the bottom
Heat up the temperature cycler to 95^oC
Quickly transfer tubes from ice to the temperature cycler and begin thermocycling

Typical thermocycle procedure:

Step Name	Temperature	Time
Denaturation	95 oC	30 seconds
Cycle Denaturation	95 oC	30 seconds
Cycle Priming	50-60 oC	60 seconds
Cycle Extension	72 oC	1 minute per kilobase of target DNA
Final Extension	72 oC	5 minutes
Hold Temperature	4 oC	Infinite

Repeat the above “cycle” steps 35-45 times.
Make sure to keep the samples on ice while you are not using them. The infinite hold sequence allows you the flexibility of leaving your samples in the temperature cycler while you are busy with other lab work.

Notes on this PCR Methodology

Note 1. It is important to design your PCR primers to be specific to only the regions flanking the target sequence. Typically, specific primers are ~30-40 bases in length.
Note 2. The Tm (melting temperature) of the primers affect the temperature in Step 3b and the “Cycle priming” step.
Note 3. For greater accuracy/fidelity while copying DNA, a Pfu polymerase (from Pyrococcus Furiosus) may also be used.
Note 4. With 35 cycles, the target DNA is amplified 2³⁶ times its initial concentration. For times when you have very little target DNA, you can amplify 45 times or more.
Note 5. For Primer design, you can use tools such as Primer 3. Tools are also available for calculating the Tm of your primers such as this Tm calculator.
Note 6. G-C rich sequences will need longer denaturation times (typically up to 5 minutes) because of the additional hydrogen bonding. Any template with more than 60% G-C bases is considered G-C rich.

Applications of PCR found on SciGine

References

Karthik Raman, PhD

I am a PhD Bioengineer specialized in utilizing heparan sulfate and heparin for drug delivery to brain tumors. My expertise lies in the interface between polymer chemistry, protein biochemistry, and cellular biology.