Biosensors with Low Cross-Reactivity for Waterborne Contaminants

Dr. Philip Borer, CEO of AptaMatrix, Inc. and chemistry professor at Syracuse University (SU), has conducted research to develop a new method to identify nucleic acid sequences—short strands of DNA or RNA—attracted to microorganisms. Borer calls this Direct Sequence Analysis, or the DSA Method. Using this new method, Borer’s team can quickly find the DNA/RNA strands, called “aptamers,” that recognize and bind to chlorine resistant waterborne microorganisms—such as Cryptosporidium and Giardia—which cause debilitating illnesses that can be fatal for infants, senior citizens, or immune-compromised individuals.

The short nucleic acid strands are identified using next-generation technologies that are coming into wide use for determining subtle differences between the DNA genomes of different people. “We are delighted to have two of these next-gen instruments—the first in Syracuse—at AptaMatrix,” says Borer. “The company can sequence nearly a billion DNA fragments per week, which is important because finding aptamers is like searching for a needle in a haystack.” he said. In addition to aptamer discovery, AptaMatrix does sequencing for academic and industrial researchers.

AptMatrix and SU scientists engineered the aptamers that bind directly with a target organism into a “molecular switch.” Thus the outcome of this research—a DNA/RNA molecule that changes its shape on binding with the target—has been dubbed the AlloSwitch™. The shape change is coupled to a change in light output from the switch to provide a biosensor that can detect the target. Because of its selectivity and sensitivity, other non-harmful or beneficial microorganisms in the water will not react to the AlloSwitch™.

Building off his success in capturing aptamers using the DSA method, Borer’s new project aims to discover dozens of high-affinity sequences for each target. Those having the lowest off-target effects will be chosen for commercial biosensors that are specific for Cryptosporidium or Giardia and that do not react with other common components of public water supplies.

“We are especially grateful to SyracuseCoE, NYSTAR, and the SU CASE Center for critical early support for our work,” says Borer. “The techniques developed in this SyracuseCoE funded research project have laid the groundwork for what should become the primary method by which thousands of biosensor targets—proteins, microorganisms, toxins, etc.—are detected.” Borer and his team submitted patent applications in March of 2009 and 2010 for aptamer discovery, and have been awarded three patents on the AlloSwitch™ technology, owned by SU and licensed to AptaMatrix.