Confocal scanning microscopy in microarray detection

Abstract All microarrays require fluorescence scanning to extract their experimental results. The confocal laser scanner delivers the highest image and data quality, a significant performance advantage. This chapter will describe the scanning process from an instrument point of view. It is divided into three parts. Sections 1 and 2 will describe the relevant characteristics of microarrays and all types of microarray scanners. Sections 3– 7 will describe the design options and critical characteristics of confocal scanners. Finally, Section 8 will describe one commercial confocal implementation, the ScanArray®. This section will describe the aspects of microarrays that are most relevant from the point of view of a scanning instrument. Microarrays consist of small samples of DNA or other biological matter arranged on a flat surface. The DNA or other material is tagged with a fluorescent probe so that a fluorescence measurement will reveal the concentration of the sample, with a typical fluorescence dynamic range of between about 400:1 and 4000:1 limited by background fluorescence. The flat substrate is generally made of chemically treated glass, and is often in the form of a 25 mm × 75 mm microscope slide. Microarrays are described at length in several other chapters; this chapter will confine itself to the aspects of microarrays related to fluorescence detection.