DNA microarrays based on polymer brushes

One of the key problems in the development of a DNA chip for a given analytical problem is the determination of suitable chip parameters: the correct DNA probe sequences need to be found, different types of buffers are to be tested at different buffer concentrations and the optimum temperatures for, both, hybridization and melting need to be determined. This list is by no means exhaustive but already demonstrates that the development and optimization of a chip requires thousands of experiments and test chips leading to often unacceptable development times and costs.

In our labs we currently develop a chip analysis platform technique that addresses this problem. The entire system consists of two key features:

A total internal reflectance fluorescence (TIRF) readout system in which the fluorescence is excited through the chip itself which acts as a waveguide. The exciting light is such provided through the evanscent wave travelling along the chip surface. This mode of excitation allows for the fluorescence readout in the presence of the analyte solution and a flow cell with heating / cooling devices can be used to follow the hybridization and to reset the chip by melting/washing protocols without the need to take the chip out of the detector.
The second key feature of this system is the chip itself. We have developed a polymer chip made from PMMA or cyclic olefin copolymers (COCs) onto which the probes are printed together with a photocrosslinkable polymer. Upon illumination the polymer forms a three dimensional hydrogel that acts as a carrier for the probes. This “skyscraper” approach allows for the deposition of a higher probe concentration per surface area leading to an enhanced chip sensitivity and selectivity.

In further work we currently use this technology platform to address questions such as:

Development of a biochip for simultaneous SNP- and gene expression analysis
Chip assisted search for biomarkers that are responsible for femal incontience
Extension of the concept to protein analysis.

Figure: Photographs of the printer used to manufacture DNA microarrays