IMPROVING THE IMMOBILIZATION OF DNA TO A NOVEL GLASS SOLID SUPPORT Instructor: Dr. Claude E. Gagna Student Presenters: Amy Law, Craig Spergel, Tina Law, Pooja Mody, Jason Rotunno, Kevin Schlatmann, Joseph Cherian

Introduction: What are DNA Microarrays? A collection of microscopic DNA spots arrayed on a solid surface (e.g., microscope slide). The DNA is bound to the surface of the solid support. With this, experiments can be run to see the effect a possible drug used for gene expression studies may have on DNA and/or a gene. The more tightly bound the DNA is to the surface, the more experiments can be run.

Glass Slide: 1 x 3 in

Problems with Characterizing the Surface of DNA Microarrays Requires the use of either an electron or confocal microscope. Examination of the microscope slide requires much time and money. Electron microscopes can cost over a million dollars. Investigators must wait for a long time to gain access to the microscope. Reagents are expensive.

Our Goals Reduce the time and money needed by using a light microscope. Light microscopes are a common piece of equipment in a laboratory and thus easy to access. Light microscopes cost much less than either an electron or a confocal microscope. Allows for a quick examination of the glass surface, so the lower quality etched slides can be discarded. To develop novel solid support surfaces.

The Process Plain microscope slides are etched using a Dremel rotary tool. A drop of a tissue stain, either hematoxylin or eosin (at varied concentrations), is placed on the etched surface with or without a coverslip and allowed to dry. A picture of the etched surface is taken using a digital camera attached to a light microscope.

Preliminary Results: Control (No Tissue Stain)

Preliminary Results, continued: Eosin, full concentration

Preliminary Results, continued: Eosin, 1/5 full concentration

Preliminary Results, continued: Hematoxylin, full concentration

Preliminary Results, continued: Hematoxylin, 1/5 full concentration

Summary of Results Hematoxylin at full concentration allowed for enhanced resolution of the surface of the glass slide, compared to the diluted (1/5 concentration) hematoxylin. In contrast, eosin at 1/5 of its full strength allowed for better visualization of the etched glass surface compared to eosin at its full strength. Overall, hematoxylin was the better tissue stain in allowing us to see more intricate details of the etched slide.

Where are we headed? This is the beginning of a long process to simplify the examination of the surface of the glass slide. We plan to use ultrafine sandpaper to smooth down the nicks and grooves produced by the Dremel rotary tool. As the experiments become increasingly complex, we will remove the particle debris using pressurized air.

Conclusion Analyzing the surface of microarrays is timely and costly due to the equipment used. Using a light microscope can reduce the time and money spent. This research will help in developing superior DNA immobilizing techniques. It will also help other investigators with their DNA microarray projects.