Craig A. Kasper, Au.D.

Columbia University Technology: Crossreactive Sensor Arrays Based on DNA Receptors

Drs. Milan N. Stojanovic and Donald W. Landry from Columbia University's Department of Medicine have developed a novel array system for the parallel processing of molecular recognition events via arrays of oligonucleotide-based sensors. The binding domains of these sensors are based on three-way nucleic acid junctions that form at the intersection of three double helixes. The double-helical stems are analogous to antibody framework regions that ensure reliable folding, regardless of variations in or around the binding domain formed by the three-way junction. The sensors are organized into cross-reactive arrays to yield characteristic fingerprints for samples containing hydrophobic molecules.

The principles of this technology draw on the highly cross-reactive design of the mammalian olfactory system which contains approximately one thousand unique receptors. Odorants are characterized by a pattern of massively parallel responses that yield fingerprints that are characteristic of a specific odorant. In the technology developed by Drs. Stojanovic and Landry, analytical samples are similarly matched through their characteristic fingerprints to available standards; incremental structural variations achieve differential cross-reactivity. A reporting domain is introduced by the specific substitution of a single phosphodiester group with a phosphothio, followed by selective functionalization with a fluorophore. Introduction of a fluorophore into the hydrophobic cavity of the junction yields a molecular sensor based on the internal displacement of the fluorophore by a guest molecule.

This sensor array approach can be used to characterize hydrophobic ligands and to fingerprint complex biologic mixtures. Whereas a given sensor may weakly discriminate various hydrophobic ligands, an array of related sensors can achieve considerable specificity. It is anticipated this technology will have research, drug development and clinical applications.

Some advantages of this technology, as detailed by Drs. Stojanovic and Landry include:

• Offers incremental variations of structure to achieve differential cross-reactivity, currently a limiting feature - electronic nose technology 'plus'
• Up to several thousand receptors with similar yet distinctive characteristics can be organized into cross-reactive arrays
• Unique reporter system that utilizes a fluorophore placed in the hydrophobic cavity of the three-way nucleic acid junction - provides immediate readout
• Preparative scale synthesis of sensors can provide standardized extensive arrays

Applications of this technology include:

• Highly sensitive tool for analysis of and distinguishing characteristics of individual ligands with considerable specificity based on fluorescent readouts
• Offers powerful fingerprinting approach for analysis of complex mixtures of hydrophobic molecules - permits unambiguous identification of unknown samples
• Provides capability to systematically construct a series of incrementally varied fluorescent oligonucleotide receptors
• Research-based applications in next-generation drug screening and analog design
• Potential clinical applications - e.g. 'mix and measure' urine assay for diagnosis of gross errors in steroid genesis and similar size biomolecules

To date, a United States Utility patent has been filed. A PCT patent application has also been filed. The technology is available for licensing or sponsored research support. For further information, please contact Jerry Kokoshka, Ph.D., Tel: 212-305-8884 email: jk2108@columbia.edu or Shai Gilad Tel: 212-305-5059 email: sg2230@columbia.edu.