Instrumentation

OmniGrid 100 Microarrayer

Stealth Printhead

We use this high-throughput contact microarrayer for printing small molecules. The arrayer is outfitted with a 48-pin printhead containing Telechem SMP3 pins and has the capacity to print 100 replicate slides in a single print run. For more information, see http://www.genomicsolutions.com and http://www.arrayit.com.

Axon GenePix 4000B and 4200A Scanners

We use the Axon 4000B dual-laser scanner for imaging standard 2-color microarrays at 532 nm and 635 nm. We use the 4200A four-laser scanner to scan for fluorescence at 488 nm, 532 nm, 594 nm, and 635nm. Both scanners are capable of scans at resolutions between 5 and 100 µm. High speed, simultaneous dual-channel scanning allows the user to acquire data for two wavelengths at 10 µm resolution in 5 minutes. Genepix software allows the user to adjust scan area and resolution. In addition, the software enables automated spot finding and identification.

For more information, see http://www.moleculardevices.com

Biacore S51 HT-Biosensor

We use this high-throughput surface plasmon resonance instrument to study biomolecular interactions involving small molecules, proteins, and nucleic acids without the need for labels. The quantitative data obtained using the S51 provides insight into binding kinetics, affinity, concentration, and specificity of the interaction. For more information, see http://www.biacore.com.

Stratagene Mx3005P QPCR System

We use the real-time quantitative PCR instrument to perform fluorescence-based thermal-shift assays. The assay benefits from the phenomenon of ligand-induced conformational stabilization. The midpoint of the melting curve of a protein will increase in the presence of ligands that bind more tightly to the native state than the unfolded state. The assay involves the use of an environmentally sensitive fluorescent dye, such as SYPRO Orange, to monitor the protein’s thermal unfolding. The plate-based assay format allows quick and qualitative evaluation of microarray positives in a secondary binding assay. The kinetic parameters of selected promising interactions are characterized using surface plasmon resonance. For more information, see Anal. Biochem. 332, 153-159, 2004 or http://www.stratagene.com.

To learn about using any of these instruments, contact Anna Borodovsky (borodov@broad.harvard.edu).