FEATURE GENOMICS
a matching primer. With each heating-cooling cycle, the amount of the DNA sample is doubled. In order to speed up the process, Professor Lee and his colleagues took advantage of plasmonics, or the interaction between light and free electrons on a metal’s surface. When exposed to light, the free electrons get excited and begin to oscillate, generating heat. Once the light is off, the oscillations and the heating stop. They used LEDs to heat electrons at the interface of thin films of gold and a DNA solution. They clocked the speed of heating the solution at around 55°F per second. The rate of cooling was equally impressive, coming in at about 43.9° per second.
For their experiments, the researchers used thin films of gold that were 120nm thick, or about the width of a rabies virus. The gold was deposited onto a plastic chip with microfluidic wells to hold the PCR mixture with the DNA sample. The light source was an array of off-the-shelf LEDs positioned beneath the PCR wells. The peak wavelength of the blue LED light was 450nm, tuned to get the most efficient light-to-heat conversion. The researchers were able to cycle from 131°F to 203°F 30 times in less than five minutes. They tested the ability of the photonic PCR system to amplify a sample of DNA, and found that the results compared well with conventional PCR tests.
Schulze. ‘Optical technology is ideal for high- throughput and high accuracy and we believe laser-based systems will remain dominant as the industry moves to third-generation sequencing.’ But Schulze admitted that the industry needs
to be prepared as optical technologies face an increasing amount of competition from non- optical technologies. ‘Costs have already come down substantially so, at the moment, high- throughput and not cost is the issue,’ he said. ‘But the optical community needs to be ready to face competition from non-optical technologies, when the technology concepts for sequencing continue to diversify to optimise tools in cost, packaging and performance for each application subsegment.’ The authors of the Nature paper admit that while the MinION is definitely portable, one piece of their kit was bulky – the thermocyclers that carried out the reverse transcriptase polymerase chain reaction (RT–PCR), an essential step in order to isolate sufficient DNA for sequencing. Researchers in the US have come up with an optical solution not only to bring down the size of
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PCR equipment, but also to speed up the process. ‘PCR is powerful, and it is widely used in
many fields, but existing PCR systems are relatively slow,’ said study senior author Luke Lee, a professor of bioengineering at UC Berkeley in the US. ‘It is usually done in a lab because the conventional heater used for this test requires a lot of power and is expensive. Because it can take an hour or longer to complete each test, it is not practical for use for point-of-care diagnostics.’
‘This photonic PCR system is fast, sensitive and low-cost,’ said Professor Lee. ‘It can be integrated into an ultrafast genomic diagnostic chip, which we are developing for practical use in the field. Because this technology yields point-of-care results, we can use this in a wide range of settings, from rural Africa to a hospital ER.’
A portable
device that can reliably and quickly sequence DNA in the field has been a dream for researchers for many years
Conventional PCR is slow because of the time it takes to heat and cool the DNA solution. The PCR test requires repeated temperature changes – an average of 30 thermal cycles at three different temperatures – to amplify the genetic sequence, a process that involves breaking up the double- stranded DNA and binding the single strand with
Professor Lee is now looking to mass manufacture his PCR technology and is currently in discussions with several companies. The genomic diagnostic chip that his group is developing also relies on optical technology. ‘Optical technologies for DNA analysis and sequencing have a well- established infrastructure, and electrical measurement is not
as accurate as optical,’ said Professor Lee. ‘I think sequencing with optical technologies may be possible in the future, but it will require a huge team effort involving engineers, biologists and computer scientist working together.’ Professor Lee’s genomic diagnostic chip is one of many similar lab-on-a-chip technologies
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