Vol. 23, Issue 1: Fall 2015

Photoionic PCR

Chelsea Muennichow

Imagine the endless possibilities that could result from faster DNA diagnostics, especially in a world where DNA sequencing is becoming increasingly relevant in all aspects of science and medicine; for example, in molecular biology, genetic recombination and transgenic animals have become increasingly important tools. An important aspect of these and many other diagnostic tests is the polymerase chain reaction (PCR), a tool used by molecular biologists to amplify DNA and generate millions of copies of a specific DNA sequence. Researchers at UC Berkeley in the lab of Dr. Luke Lee, the co-director of the Berkeley Sensor and Actuator Center and a professor of bioengineering, have engineered a novel approach to high-speed DNA concentration recording. This technique allows for direct optical DNA sequence detection.

In traditional PCR, approximately thirty cycles of repeated heating and cooling separate double-stranded DNA, allowing the strands to be bound to a matching primer, and allow for DNA replication by a high temperature-stable DNA polymerase enzyme. The PCR amplifies one copy of DNA to produce millions of copies. It is absolutely essential in various aspects of genomics, including forensic analyses, cloning research, and even paternity tests. Nonetheless, it can take over an hour to complete these thirty thermal cycles in order to successfully amplify the DNA. According to Dr. Lee, “PCR is powerful…[but] it takes a lot of power and is expensive.” Therefore, traditional PCR assays are simply impractical for rapid point-of-care diagnostics, especially when one considers the high cost, impracticality, and power requirements for the heaters and coolers of these thermal cyclers.

UC Berkeley bioengineers have recently developed an advanced cycling system which is expected to vastly expand all aspects of polymerase chain reaction tests, from clinical performance to research applications. This exciting new technology uses photonics, an extremely cheap, fast, and accurate system that can yield results in as little as five minutes. The photonic system involves alternating cycles of heating and cooling that are powered by energy from photons of light from light-emitting diodes, or LEDs. Researchers foresee the implementation of this technology in a wide range of settings beyond research in molecular biology. For example, point-of care-diagnostics is medical diagnostic testing performed outside of a clinical laboratory, but still in close proximity to the patient’s place of care. The cheap, fast system of photonics for polymerase chain reactions will allow for such testing to be used for critical, on-the-spot decision making in these and other fields. This method promises to transform point-of-care diagnostics in everything from medicine to evolutionary biology, food security, ancient DNA sample analysis, diagnosis of infectious and hereditary diseases, and many more academic disciplines and healthcare fields.

The photonic PCR system is grounded in plasmonics. Plasmonics involves the interaction of light with free electrons on a metallic surface, usually to produce heat. The researchers’ design involves thin gold films that are approximately 120 nm thick, which they deposited onto a plastic chip with several microfluidic wells filled with DNA in solution. Gold is usually used in photonic heating because of its high efficiency in absorbing light, as well as its lack of activity in biological systems, making it perfect for this interaction with DNA. Then, using a 3.5 Watt LED array with a wavelength of 450 nm emitting light from beneath the film, the electrons in the gold strip are excited. The resulting heat generated from this processes is used to warm the DNA in solution, accelerating the thermal denaturation step that is required to separate the double-stranded DNA strand into usable single-stranded DNA templates. To complete the cooling cycle, the LED array shuts off, cutting off heat flow to the electrons, causing rapid cooling of the system.

Not only was the accuracy of this method identical to traditional polymerase chain reaction methods, but the researchers at Berkeley found that thirty thermal cycles could be completed in less than five minutes, over ten times faster than traditional PCR. In fact, the researches clocked the solution’s heating speed at approximately 55 degrees Fahrenheit per second, with the cooling rate coming in at about 43.9 degrees Fahrenheit.

The possibilities and ramifications of this discovery are seemingly endless. One of the professors working on the project at UC Berkeley says the photonic system would be perfectly suitable for “ultrafast point-of-care, on-chip genomic diagnostics” that could be used everywhere from emergency rooms to rural areas. This is a truly revolutionary technology that will allow for the direct optical detection of DNA-protein interactions, protein-protein interactions, RNA-protein interactions, and many other biological systems.

About the Author

Chelsea Muennichow is senior molecular cell biology major concentrating in neurobiology and minoring in nutrition. She has been vegan for four years, and loves vegan cooking and baking and animals. She is a certified yoga teacher and loves all things related to reading, writing, health, and wellness. Her future career goals include medical school and/or healthcare administration/consulting, and she can’t wait to travel the world after graduation.