Parabon NanoLabs to use power of grid computing to design novel macromolecules based on synthetic DNA

9 April 2009

Extreme computing specialist Parabon Computation has announced the spin-off of Parabon NanoLabs, a subsidiary dedicated to developing breakthrough nano-scale products based on designer DNA technology.

The company will initially focus on developing nano-scale sensors for therapeutics, diagnostics and other molecular detection systems. The nanotechnology and resultant nanostructures have potentially limitless applications, ranging from nanomedicine to detergent additives and next-generation electronics.

In a radical departure from carbon-based (C60) nanotechnologies, such as buckyballs and carbon nanotubes, which gained media attention early in the millennium, the key to Parabon NanoLab’s approach is synthetic DNA.

Although DNA is best known as a carrier of genetic information, individual strands of DNA can be synthesized to have any sequence of bases (commonly represented by the letters A, C, G and T).

Because certain sequences of DNA are mutually attractive, strands can be 'programmed' with sequences that cause them to 'swim to the right spot', with respect to one another, and then bind to form nanostructures of virtually any shape.

By attaching DNA strands to other types of molecular subcomponents (eg therapeutics, nanoparticles or enzymes), nanostructures can be richly functionalized to form novel macromolecules with uses across countless application domains.

The ability of DNA structures to self-assemble in this manner allows designer macromolecules to be deliberately and precisely engineered and then mass-produced — feats not achievable with any other nanotechnologies.

“The challenge to orchestrating successful self-assembly of a given design,” according to Dr Steven Armentrout, Parabon Founder and CEO, “is determining, from the countless possibilities, the rare few sets of DNA sequences that satisfy all of the design constraints. For that, we depend on inSēquio.”

Developed by Parabon over the past four years, the inSēquio Sequence Design Studio is a one-of-a-kind computer-aided design (CAD) application that optimizes DNA sequences for nano-engineering using grid-scale computing capacity.

A single DNA strand of just 135 bases has more possible sequence arrangements than the estimated number of atoms in the universe and some nanostructures have more than 15,000 bases. Since evaluation of each candidate sequence set requires compute-intensive molecular dynamics calculations, the computational workload to discover effective sequences is vast.

Co-Founder and Chief Scientist of Parabon NanoLabs, Dr Michael Norton, who is also a professor at Marshall University, believes this is why others have not tackled the sequence optimization problem. “Without the grid-scale capacity Parabon provides, solving a problem of this magnitude doesn’t seem possible,” he says, “so people shied away from it.”

By simultaneously employing the power of thousands of computers on the Frontier Grid Platform, the inSēquio optimizer discovers ideal sequences for nano-assembly. Utilizing this revolutionary technology, scientists within Parabon NanoLabs are creating a catalog of proprietary nano-products for licensing in several domain areas including cancer therapeutics, biometrics and bio-weapons defense.

In addition, Parabon NanoLabs provides custom design and fabrication services for companies and researchers seeking to nano-enable their products.

Dr Chris Dwyer, co-founder of Parabon NanoLabs, and a professor at Duke University, said, “Beginning with the microfabrication of transistors in the 1960s, control of matter at the micro-scale enabled the era of electronic miniaturization that ultimately led to the Information Revolution. An even greater opportunity exists with the Nanotechnology Revolution and we’ve attracted the right combination of talent and technology to realize it.”

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