SAN FRANCISCO (GenomeWeb) – Armonica Technologies, a startup that has spun out of the University of New Mexico, is looking to develop nanopore sequencing technology that relies on stretching DNA through nanochannels that have a porous roof.
In August, the firm received $1.5 million in seed investment from New Mexico’s Catalyst Fund.
The nanopore technology will be based on work from several UNM researchers: Steven Brueck, a professor of electrical and computer engineering at UNM’s Center for High Technology Materials with an expertise in nanofabrication; Yuliya Kuznetsova, a research assistant professor whose expertise is in microscopy imaging techniques; Alexander Neumann, a postdoctoral fellow in the department of electrical and computer engineering; and Jeremy Edwards, a professor in the department of chemistry and chemical biology who focuses on sequencing technologies. Scott Goldman is president and CEO.
Brueck said that the goal is to commercialize the sequencing technology in around two years.
The design of the instrument will be based on porous nanochannels, which Brueck described in a 2008 study published in Nano Letters. The nanochannels, which have a porous roof that is made out of silica beads, enable DNA to be manipulated while it is captured inside. The enzyme lambda exonuclease is introduced through the roof of the nanochannel and converts double-stranded to single-stranded DNA, Brueck said. The channel also includes a barrier at one end, and after creating ssDNA, a voltage is applied to force the DNA through the porous roof.
Brueck described the process as a piece of yarn threading its way through a stack of oranges. This “extended and convoluted” transport is actually an advantage, Brueck said, because it slows the DNA down.
A metal film and an insulator are built on top of the nanochannels with gaps that align with the nanochannel holes. Ultimately, Brueck said, some of the holes will have to be sealed, to keep the DNA molecules far enough apart from each other so that each is detected and read independently.
The insulator atop of the nanochannel will be just 1 nanometer thick, Brueck said, to give spatial resolution. To detect individual bases, the firm plans to use surface-enhanced coherent anti-Stokes Raman scattering (SECARS), a vibrational imaging technique that takes advantage of the fact that each nucleotide has a unique vibrational frequency. Cameras then capture the DNA moving through the pores.
The detection piece is the biggest remaining challenge, Brueck said. Surface enhancement of the insulator improves the sensitivity of detection, he said, but “whether we can get down to single-molecule detection remains to be proven.”
In the Nano Letters study, Brueck’s team demonstrated that the nanochannel constructs could be built and that DNA would go through them. In that study, they tested lambda phage DNA that had been fluorescently stained. The DNA was 48.5 kilobase pairs long, which is the read length the firm is targeting initially.
In addition, In 2013, Brueck’s team published a study in IEEE, to show that Terahertz microscopy could detect absorption signatures of DNA in the nanochannel chips, which helped lay the initial groundwork for detection, but “terahertz microscopy cannot resolve individual bases,” he said. The researchers are now working on developing the SECARS-based detection technique, but have so far not yet demonstrated it on the single-molecule level or coupled it with the nanochannel constructs.
The initial platform will be a large laboratory instrument that uses lasers and a microscope for detection, Brueck said, but the ultimate goal is to shrink that down to a handheld device.
Brueck said that the next step is to refine the process of moving the DNA through the nanochannels and up through the porous roof and metal insulator — to quantify the translocation and figure out the exact configuration of the pores. After that, he said, the company will tackle the detection process.
Armonica has discussed both developing a device on which it would offer services as well as commercializing a platform. Which model it ends up pursuing will “depend on how robust we can make the device,” Brueck said.
One advantage of the technology is that sample prep will be minimal — all that will be required is an initial DNA purification step, as well as some fragmentation to generate the long DNA fragments. Brueck said that although 50 kilobases is the starting point for read lengths, the team does not yet know whether that’s the limit.
In terms of applications, Brueck said that the company is targeting a sequencing instrument that reads individual bases, but if it identifies intermediate applications with commercial potential, it would pursue those.