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Photonic PCR: When Lightening Strikes Your DNA

Before I get into today’s topic, please allow me to digress a bit and start with a few sentences that sum up the polymerase chain reaction (PCR); the grand-daddy of molecular biology.

PCR, a method that is at the heart of modern day molecular biology discoveries, is a process that amplifies genetic material through our own biological copy-machinery. The indispensible nature of PCR is far-reaching for biomedical researchers on two levels. For people who work in a basic research lab, it is one of the most essential tools to perform genetic engineering/re-engineering work. In addition, the versatility and effectiveness of PCR has ushered in a new era in molecular diagnostics in the applied science field. It is fast, precise, and can be easily performed in most laboratory settings.

Wait! “So what’s wrong with PCR right now?” Actually there is nothing wrong with it, but it is about to get a lot faster! For those of you who have done PCR before, you might feel the urge to slap on the early retirement stickers on all the current PCR systems after you learn about photonic PCR.

What the Heck is Photonic PCR

“So what is it?” Well, the conventional PCR uses “hotplates” to regulate the temperature inside a reaction tube. It proves to be simple and effective; with steps consisting of ramping up (heating) or ramping down (cooling) the temperature in each cycle. Yet, when compared to photonic PCR, the heating and cooling steps in a conventional PCR take too much time. The original article that describes photonic PCR shows an impressive rate of 13°C per second during ramp up and 6.6°C per second during ramp down1. This translates to a high performance thermo-cycler that is able to complete a 30 cycle reaction in merely 5 minutes; a feat that would take a conventional PCR system close to an hour to complete!

The idea of using photonics (light sources) to control the temperature in PCR reactions has been thought of before. A team of researchers at SRI international had successfully used laser to control the temperature in a Nano droplet of oil in a PCR reaction2. Using their self-designed apparatus, a 40-cycle PCR reaction was completed in 370 seconds. Photonic PCR also uses a light source to provide the energy, but the similarity between these two system stops here.

Photonic PCR uses a technology called “plasmonics,” a process in which the electrons on a metal surface are rapidly excited by the electromagnetic force of light particles. Therefore, when a light source is shown on a metal surface, the free electrons gets excited quickly, giving off heat as a form of energy and vice versa. Imagine a PCR machine that is capable of ramping the temperature in a reaction tube up and down in lightening speed; performed by simply switching the light source on and off.

Interestingly, the light sources used are light-emitting diodes (LEDs), which can be readily purchased. After several rounds of trial and error, the photonic PCR team has found the best combination between the wavelength of the LED and the type of metal surface for a PCR reaction. The blue light LED with a characteristic peak wavelength of 450nm works best in combination with a thin layer (120nm!) of gold embedded in a plastic chip containing microfluidic wells. It turns out that gold is the ultimate choice for a “heat medium.” First, it is very efficient at absorbing light energy. Second, its “inertness” ensures that it does not react with any components that are important in a PCR reaction; thus avoiding containment issues.

Conclusion

The idea of using plasmonics to increase the efficiency of each PCR cycle is a big step forward in PCR platform technology. The prototype shows that the time required for a typical 40 cycle PCR reaction has been cut from 1 hour to only 5 minutes. There are amazing potentials in photonic PCR. In addition, when it finally hits the shelf, its lightening speed will be a big addition to the current and future sequencing technologies such as Illumina and nanopore sequencing, respectively. This will result in tremendous leaps in scientific output, in which generation of large sets of data is essential. I can’t wait to see the bright future research! Research on!

References

  1. Son JH et. al. (2015) Ultrafast Photonic PCRLight: Science & Applications.  4(7): e280. doi:10.1038/lsa.2015.53.
  2. Kim H et. al.  (2009) Nanodroplet Real-Time PCR System with Laser Assisted HeatingOptics Express. 17(1): 218. doi:10.1364/OE.17.000218.
  3. Yang, S. (2015) Heating and Cooling with Light Leads to Ultrafast DNA DiagnosticsBerkeley News. Accessed November 22, 2015.

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