With ultra-sensitive detection down to zeptomoles — just hundreds to thousands of molecules — Zeptosens is confident it can conquer the market for second-wave DNA chips and have an edge in the emerging protein array market. The Witterswil, Switzerland-based startup recently launched its first product, a DNA-chip system co-developed with and marketed by Qiagen.
This array — the SensiChip — is the first fruit reaped from about ten years of research into planar waveguide technology, Zeptosens’ patented detection platform, work that its founders started at Ciba-Geigy before Zeptosens was spun out in late 1998 after Ciba and Sandoz merged to form Novartis.
The secret behind Zeptosens’ high sensitivity without amplification is a “thin layer” of light, or evanescent field, created just above the chip surface. This layer excites only fluorophores that are bound to the chip, leaving those in the solution above dark. As a result, background fluorescence decreases and the signal-to-noise ratio improves, allowing users, for example, to omit washing steps to preserve delicate protein-protein interactions. To produce the evanescent field, a glass substrate is etched with parallel nanochannels and coated with a thin tantalum pentoxide layer. When illuminating the chip from below, the grating bends the light into the tantalum pentoxide waveguiding layer, where it propagates and creates the 200-300 nm thick evanescent field above the surface.
One µg of RNA is usually enough to detect even low levels of gene expression on the DNA chip, according to Martin Potgeter, Qiagen’s global product manager of microarrays. Zeptosens has also been able to measure as few as 600 protein molecules, each labeled with three fluors, in a 150 µm spot, according to CEO Markus Ehrat. “For all experiments where you have a limited amount of starting material, it’s a very interesting approach,” commented Thomas Joos of the Natural and Medical Sciences Institute in T bingen, Germany, who has used Zeptosens’ protein chip platform.
Ehrat and his colleagues have also put a lot of effort into developing a polymer-based surface chemistry that prevents non-specific binding, Ehrat said. Meanwhile the company has grown to 31 employees, and all the scientific founders are still on board. During the first financing round in early 1999, Zeptosens raised nine million Swiss Francs from Novartis Venture Fund and Qiagen, followed by an additional 14 million Swiss Francs in December 2000 from TVM, Swiss Life, and private investors.
In addition to making this equity contribution, Qiagen seemed like a good partner to co-develop DNA microarrays. “We were looking for a partner that is well-known in the market, has first-class, high-quality products and that we could add a certain puzzle stone [to] that they did not possess,” said Ehrat. Qiagen holds an exclusive license for Zeptosens’ system for nucleic acid analysis.
The recently launched SensiChip system, which includes a chip reader, a hybridization station, and imaging software, complements Qiagen’s products for gene expression analysis that include RNA preparation kits and real-time PCR. Each customized chip or bar contains six flow-through compartments with each up to 340 spots of 70-mer oligos according to the customer’s specifications. Qiagen synthesizes the oligos and provides them to Zeptosens, which manufactures both the chips and the instruments. A generic chip with about 750 human kinases and phosphatases will be available in September, and other pre-spotted arrays for different gene families are in the works, according to Qiagen.
Affymetrix Issues
The main application for the SensiChip is gene expression profiling when the number of relevant genes has already been winnowed down to a few hundred, yet high sensitivity is required. However, sensitivity has its price: The DNA chip system costs around Euro150,000 excluding the chips. It is currently available in Europe, Asia, and Canada but not the US, because of Affymetrix patents that require a license, said Martin Potgeter, who added that Qiagen is in discussions with Affy. Meanwhile, the first systems have been sold to “some” customers, he said, but declined to give a specific number.
Zeptosens on its part has already been adapting the technology for protein chips, which are “close to commercialization,” said Ehrat. The first product is likely to be a customized protein-ligand interaction array, which could be either marketed through a partner or Zeptosens’ own channels. The company is currently running feasibility studies with three pharmaceutical and biotech companies and one academic partner, he added. However, “on the protein side, the market really needs to be developed,” Ehrat noted.
— JK