AUG 14, 2016 9:01 PM PDT

PCR Primer Design Pointers

WRITTEN BY: Carmen Leitch

In this video from Thermo Fisher Scientific, a few tips for better PCR primer design are presented. PCR, Polymerase Chain Reaction, is a common and vital part of genetic studies, biomedical research and medicine in general.

Considerations important to the creation of good primers, such as primer length and melting temperature of the primers are highlighted in the video.

In PCR, the reaction mixture cycles through a series of temperatures. One of those, the annealing temperature, is also related to specificity and can be varied if needed for troubleshooting. For example, a PCR reaction that produces non-specific amplification products can likely tolerate a higher, more stringent annealing temperature. If no product is observed following the PCR reaction, the annealing temperature could be lowered as one way of trying to generate a successful reaction product.

Some pitfalls of PCR primers are shown too, such as hairpins that can form in primers that have sequences amenable to bending such that ends of the primer anneal to each other. Another thing to avoid are long sequences of the same base, or primers that have ends with a lot of cytosine (C) or guanine (G) bases.
About the Author
  • Experienced research scientist and technical expert with authorships on 28 peer-reviewed publications, traveler to over 60 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
DEC 15, 2019
Space & Astronomy
DEC 15, 2019
MAVEN Mission Connects Mars' Wind Patterns to Surface Features
NASA’s MAVEN mission, launched on November 18th, 2013, has been orbiting Mars and investigating the planet’s features for more than half a deca...
DEC 17, 2019
Plants & Animals
DEC 17, 2019
Watch Seals Band Together to Scare a Great White Shark Away
Great white sharks are rather renowned for being massive and merciless predators of the ocean, and among their favorite prey are fur seals, which are rich...
DEC 31, 2019
Space & Astronomy
DEC 31, 2019
Why Does This Star Dim Unpredictably?
KIC 8462852, also known as Tabby’s Star or the infamous ‘alien megastructure star,’ is peculiar because the star’s light seems to d...
JAN 08, 2020
Chemistry & Physics
JAN 08, 2020
Florence Nightingale: Nursing Pioneer, and Data Scientist?
Florence Nightingale, the pioneer in modern nursing care, served as a nurse manager in the Crimean War in the 1850s. Due to her wholeheartedly devotion to...
JAN 16, 2020
Health & Medicine
JAN 16, 2020
Babies in Africa Receive World's First Malaria Vaccine
Would you accept a vaccine that was only 40% effective? For those at risk of malaria, the answer is likely a resounding, "yes!" According to the...
JAN 20, 2020
Plants & Animals
JAN 20, 2020
Horned Lizards Do Anything to Protect Their Eggs From Predators
When a female horned lizard lays her eggs, she finds herself up against several predators that want to devour them. Fortunately, the female horned lizard d...
Loading Comments...