UC Berkeley bioengineers develop ultra-fast method to copy DNA using light

PCR---Kevin-Cheung
Kevin Cheung/Staff

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UC Berkeley bioengineers have developed a technology that can make millions of copies of a single gene in less than five minutes using a plastic chip, gold film and an LED light.

The technology upgrades the traditional method of DNA amplification — known as the polymerase chain reaction method, or PCR — which relies on being able to alternatively heat and cool a sample of DNA over a large temperature range.

The traditional PCR method takes hours to amplify a sample of DNA because of the slow heating and cooling process, according to Luke Lee, a UC Berkeley bioengineering professor and senior author of the study.

The team’s method — termed photonic PCR — works by shooting light at an ultra-thin film of gold, which energizes the electrons floating at the surface of the film. The excited electrons start oscillating and emitting heat, but as soon as the light turns off, they relax again, and the heating stops.

In PCR, DNA needs to be heated to separate its two strands and then cooled so that small bits of DNA can be added to each strand to start the rebuilding process. Heating the sample again allows enzymes to continue rebuilding each strand. This whole process is repeated until enough DNA is made from the original sample.

PCR is a very important step in DNA diagnostics because the DNA collected from the environment is often present in extremely small quantities. For instance, a smudge of blood left at a crime scene would not contain enough DNA for scientists to work with.

When scientists have to determine the unique composition of a genetic sample through a process known as sequencing, they must first amplify the gene, Lee said.

“One copy to make thousands of copies,” he said. “And what is the best way? PCR.”

Lee and his team are in Berkeley’s Bioinspired Photonics-Optofluidics-Electronics Technology and Science, or BioPOETS, group. They hope that photonic PCR will make gene diagnostics more accessible in that scientists will no longer have to bring a genetic sample all the way to the laboratory or hospital to prepare it for analysis.

Lead author Jun Ho Son, a postdoctoral researcher in Lee’s lab, said they chose the LED light for its low power consumption: It requires only two or three watts, compared with the several hundred watts required by a conventional PCR machine.

Moreover, the team wants to focus on using existing “off-the-shelf” LED, Lee said. The team hopes to develop a PCR device the size of a cellphone.

“By just using LED, we can amplify any nucleic acid at the point of care,” Son said.

Son is currently working on designing the chip that will be the center of this device. The DNA sample will be placed in tiny gold-coated wells in the plastic chip, and an LED light shining from below can then be turned on and off to rapidly heat and cool the sample up to 30 times in a row for a full PCR amplification.

Because the process amplifies any sort of nucleic acid, such as genetic material, Lee said photonic PCR can expedite the investigation of not only human genes but also those of microbes, animals and plants.

Son is also working on a PCR chip that would take in a sample of blood and filter the DNA-containing blood plasma into gold-coated wells, where the DNA would be amplified immediately with LED light.

“You don’t have to go to the hospital to do sample prep,” said Son. “Everything is on this chip.”

Contact Rachel Lew at [email protected] and follow her on Twitter at @Rlew12C.

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