Development of a new electrochemical chip technology for gastrointestinal biopsy specimen cDNA analysis

Background: DNA microarray technology provides an efficient method for the detection of multiple gene polymorphisms at the same time. However, the combination of high number of measured polymorphisms necessary to reach statistical significance with today's high cost for a single measurements makes population-wide studies impossible.

Aim: The goal of our project was to develop a new method to reduce time and cost of the DNA array measurements.

Methods and results: The basis of a new array is a glass-slide sized alcali-free silicium dioxide slide. Here an Au coated chrome-dioxide base is fixed. Using photolythography we establish 200 um diameter electric pads on the coating artificial rosin insulation. To these Au pads we deliver thiol-marked oligonucleotide sequences using a newly developed automatic pipetting system. These sequences are bind to the Au via sulphide bridges. The probe sequences are designed to detect various polymorphisms associated with gastrointestinal diseases. DNA is isolated from gastrointestinal biopsy specimens with standard phenol-cholophorm extraction and ethanol precipitation. The DNA samples are then electronically hybridized to the firm probe DNA within a few minutes. Finally the detection is performed in an automatic scanner using fluorescent labeling.

Conclusion: Our new method provides a fast and cost-efficient custom DNA array technology, thus allowing the screening of large patient populations, and detection of even very small effects of gene polymorphisms.