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Nanotech Meets Genomics

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  • Title: Assistant Professor, Department of Electrical Engineering, University of Washington
  • Education: PhD, University of Michigan, 2001
  • Recommended by: Deirdre Meldrum

Babak Parviz believes it's high time to get serious about applying readily available nanotechnology to genomics. “We have a lot of very interesting tools and capabilities that people have developed over the years [in the semiconductor industry],” says Parviz. “I think it would be wonderful to take advantage of these unique capabilities to make tools for biology to enable medicine.”

Just head down to your local Best Buy, Parviz says, and you can find any number of cheaply made electronic products containing high-speed components smaller than an average virus. “We can now build microprocessors that have tens of millions of transistors, and chips that have billions of transistors,” he says. “I think it's historic because we've never been able to make such complicated things work, and [now] they're available to us for just a few hundred dollars.”

Parviz is currently leading an effort to develop a portable DNA sequencer using the same kind of commercially available semiconductor technology. The device functions on a quantum mechanics principle known as tunneling current, which can be measured when electrons move through a thin barrier that they normally shouldn't be able to penetrate. The sequencer works by placing a single strand of DNA on either a gold or graphite substrate that is then scanned with a platinum iridium tip. The tunneling current measurement provides an electronic signature that is then deciphered to determine the bases.

“This is quite different from more conventional sequencing methods that involved quite a few steps of biochemistry,” Parviz says. “There's no amplification; all the complexity has been shifted from biochemistry to electronics.” His sequencer holds serious potential for both biological field research as well as personalized medicine.

But even with the most bleeding-edge nanotechnology and powerful microprocessors, Parviz still needs software. At some point, he would like to see the same kind of design simulation programs engineers have for logic circuit design made available for biochemistry. “I don't have any programs right now where I can ask, 'I want this molecule; tell me how to synthesize it,'” says Parviz.

Looking ahead

Parviz says there are still quite a few kinks to work out. “Electron transport through DNA, that's something people have worked on quite a bit, but we need to do more,” he says. “We really need to understand this and be able to model it and use those models to figure out how to get our sequencing systems to work properly.”

The top two priorities are figuring out how to properly develop parallel scanning probe microscopy — and how to do it cheaply. Although that has yet to be done with microfabrication, he says, it is possible. Parviz is equally confident that his portable sequencer will soon become a reality, cost being the only real stumbling block. “I'm actually quite confident that it will happen, but it remains to be seen if we can make it cheap enough, reliable enough, and profitable for people to use it out in the field,” he says.

Publications of note

Parviz and his colleagues recently published a paper in PNAS called “Self-assembled single-crystal silicon circuits on plastic” in which they describe their approach to building complex microsystems for biological research. The researchers are using this same technology to develop thousands of individually controlled fluorescent microscopes at the microscale through self assembly.

And the Nobel goes to…

Babak Parviz would be quite pleased to accept his award for developing a way to electronically interface with millions of live cells and monitor and alter their action.

The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.