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Sandia Researchers Invent Wheel-based Thermal Cycler

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NEW YORK (GenomeWeb) – Thermal cyclers usually come in two varieties — either a sample rests on a heating element that changes temperature, or a sample shuttles between fixed heating blocks.

Researchers at Sandia National Laboratories in Livermore, Calif. have now developed a third way, distinct from temporal and spatial designs, in which a wheel-shaped heat block with faces of different temperatures rotates to contact a stationary sample. Called the rotary zone thermal cycler, or RZTC, it will be used in a modular, automated microfluidics hub.

A description of the device was published last week in PLoS One. To prove that RZTC is truly novel, the report also included an extensive review of all extant thermal cycler technology.

In fact, in addition to disseminating the research, publishing a comprehensive resource on thermal cyclers in an open-access format was one of the goals of publication. "We're doing work primarily with taxpayer dollars, so we try to return some value to the taxpayers," Michael Bartsch, a developer at Sandia and first author on the publication, told GenomeWeb in an interview.

A short video in the supporting information section of the online article shows a prototype of the device in action, its diameter approximating a Sharpie nearby on the bench top. The motors rotating the wheel require little power, so wattage consumption is due almost entirely to powering the heaters, Bartsch said.

The RZTC system was initially developed for portable forensic genotyping applications as part of a collaboration with the US Army Criminal Investigation Laboratory, he explained.

Development was also targeted to meet the needs of a separate project that required high analytical capability for biosurveillance in low-resource settings.

"In addition to being interested in low power and small size, we really needed something that was going to offer the capability to have a high level of automation, because you're not always going to have laboratory technicians who can perform analyses for you — if you need a sample-in, answer-out assay, you really need the workflow to be fully automated and user-friendly," said Bartsch.

The forensics project is no longer ongoing, he said, adding, "We would be more than happy to pursue that with other sponsors if there was interest."

Standard thermal cyclers usually require a lot of electricity and are large. "The vast majority of commercial systems are based on thermoelectric heating and cooling, and that is a pretty power-intensive process because you're ramping the thermal block up and down in temperature," Bartsch noted.

So, the group initially experimented with a spatial method instead, transitioning sample between heat blocks. "We were a little bit green and we hadn't fully appreciated that when a very small volume is transiting a lot of tubing … you end up losing your polymerase along the way," Bartsch said.

He and co-author Ken Patel then began brainstorming new ways that could retain the low-power, fixed-temperature block design and overcome the difficulties of too much tubing.

"We were scratching our heads over this surface chemistry problem, and started kicking around ideas [like], can we move the blocks in and out, and then, if you are going to move them in and out you might as well do it with a wheel … but then you've got to worry about how do you wrap the tubing around the wheel [and] do you need a clutch mechanism to bring it in and out of contact," Bartsch said.

The final design "kind of came up organically from that sort of iterative brainstorming process," he said. "After that we started digging through the literature and looking at what was available in the commercial space to understand whether or not this was really a novel concept."

And, it is. A somewhat similar method in which thermal cycling was accomplished via tubing wound around fixed temperature blocks was recently described, and the PLoS One report describes the few other devices that come close, but Bartsch believes the RZTC wheel is indeed a first.

It is ultimately meant to be integrated with a plug-and-play digital microfluidics hub called the Automated Microbiology system, which includes automated library prep for next generation sequencing, as previously reported by GenomeWeb. That device manipulates droplets between one and five microliters, so the thermocycler node needed to be compatible.

The digital microfluidic hub also uses recently described "just-in-time" droplet replenishment, which is required because it is water-based, as opposed to oil-based, emulsion PCR. Aqueous PCR will allow the RZTC module to be easily interfaced with the overall system, Bartsch said.

The development went "from napkin to hardware" in less than a month, he noted, but troubleshooting it took a while, as did the deep dive into the literature to establish the device's originality.

It has so far been tested with STR multiplex PCR and second strand synthesis experiments. These led the group to compensate for PCR inhibitory effects of higher surface areas by increasing polymerase concentrations and adding bovine serum albumin. "Once we did that, the system was in a state where we could pretty much plug and play, and do sample after sample … to generate lots of data, show reproducibility, and test the rigor of our cleaning protocols," Bartsch said.

"At a personal level, I would certainly love to see somebody who finds value in this design or this approach to thermal cycling pick it up and run with it," said Bartsch. The patent on the wheel design has been filed, so this could be through licensing or a corporate research and development agreement with Sandia, he said.

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