X E N O P O R E 

Microarrayer

Microarray Supplies and Services

XENOPORE Corp. has introduced a new product line to bring high quality microarrays at low cost to the scientific community. This product line consists of three parts: an inexpensive manual microarray spotter which can deposit up to 768 six nl spots on a standard 1" x 3" or 25mm x 75 mm glass microscope slide, a family of surface modified glass microscope slides and a custom surface/configuration development program. Consulting service is also available to assist in getting you started producing useable arrays in the minimum time. Thus XENOPORE is your one stop service for all your microarray needs.

I. Manual Microarrayer

The manual microarrayer is a simple bench top device, measuring only 5" x 5" and weighing less than three pounds. It requires no external power source. It consists of three parts: the indexer base/slide holder, the indexing deck and the printer head. They are shown in the attached picture.

The indexer base has slots for two slides and has a spring loaded slide positioner to accommodate variations in slide size. Slides are placed into the holder by pushing lightly on the positioner with the side of the slide and then setting the slide in the groove. The use of the spring loaded device insures that the position of the first spot is consistent on every slide, which allows the reader to have the same starting point on every slide.

The indexer deck contains index holes and pins to move the printing position. Moving the indexing pin one hole in the horizontal direction moves the deck 750 microns and moving the indexing pin one hole in the vertical direction moves the deck 1125 microns. Since the spot size is approximately 500 microns in diameter, the minimum spot spacing is 250 microns in one direction and 625 microns in the other direction.

There are two printer heads available: an eight pin printer with two rows of four pins with spacing to match a 96 well source plate and a 32 pin printer with four rows of eight pins to match a 384 well source plate. The stainless steel guide pins assure accurate placement of the printer head over the slide surface.

A separate wash station with 8 reservoirs for washing the pins in the printer head is also available. The wash station is designed to allow immersion of the pins without the danger of damaging the pins by hitting the bottom of the reservoirs.

Ordering Information

II. Coated Microscope Slides

Using its expertise in surface chemistry, XENOPORE Corp. has developed the new XENOSLIDE family of surface modified glass microscope slides for creating microarrays. Now every laboratory can produce high quality microarrays without spending the time and resources developing their own surface modification procedures. XENOSLIDES come packaged in plastic boxes of five slides separated from each other to prevent scratching. Bulk packaging is also available. Each batch is quality tested to ensure uniformity and reproducibility in your arrays. They are ready to use as received, and no time is wasted prequalifying each batch. The XENOSLIDE family includes:

If there is another surface that you need or a different shape, please contact us. We can probably prepare it for you. Coated cover slips and glass particles are also available.

Typical micro arrays are of two types. Either the target such as cDNA is immobilized onto the surface and analyzed with a labeled probe, or a probe is attached to the surface and hybridized to a labeled target.

The most commonly used slide for binding cDNA is the amino silane slide. While there are several manufacturers of amino silane slides, only XENOSLIDE A combines extremely low autofluorescence with a uniform layer of silanation. Low autofluorescence allows quantitation at very low concentration, in the femtomole range. Monolayer silanation prevents overloading and smearing of the spots to provide accurate quantitation at high concentration. The hydrophobic nature of the surface prevents spot spreading and improves analysis.

The following table compares XENOSLIDE A to several other available slides. The uniformity and capacity difference is obvious from the table:

A suggested binding protocol for use with XENOSLIDE A is given below. There are many modifications of this protocol which have been used depending on the particular circumstance. This protocol is recommended only as a starting point.

Oligo probes are generally immobilized by end labeling the probe with one part of a binding pair and attaching the other part of the binding pair to the slide surface. Amino labeled oligos can be attached to either aldehyde surface (XENOSLIDE D) or epoxy (XENOSLIDE E) slides. Biotinylated probes can be attached to streptavidin slides (XENOSLIDE S). The choice of binding pair depends on steric interference, molecular interferences within the probe and ionic interactions which may affect binding.

Suggested binding protocol for use with XENOSLIDE A (aminosilane):

Prepare a solution of the cDNA to be spotted. Spot size can be controlled by use of solvent mixtures. Correct choice of co-solvent will result in lower surface tension of the mixture compared to water and controlled spreading of the spot. Volatility of the solvent mixture and thus the drying time can also be controlled by solvent composition. Use of a lower volatility co- solvent will increase the drying time. DMSO is frequently use since it is a good solvent for DNA, is miscible with water in all proportions and has lower surface tension and lower volatility than water. Typically, up to 50% DMSO is used. The DNA concentration can be in the range of 1 ng to 1 ug per ml. Alternatively, glycerol can be used in place of DMSO. Spot the solution onto the slide using the microarrayer. If you are using water only, it is helpful to maintain a humidity of 75-80% for a few minutes to allow binding to take place. Some researchers crosslink the DNA to the slide by exposing the slide to UV light for 5 minutes. The slide is now ready for hybridization.

Suggested binding protocol for XENOSLIDES with receptor surfaces.

The receptor surface slides are more hydrophilic than the silanated slides and printing from buffer only is usually satisfactory. However it is beneficial to maintain 70 -80 % relative humidity around the microarrayer and slide for up to 30 minutes to allow attachment to occur.

A solution of 1ng - 1ug of oligo per ml of buffer is a typical starting point. After printing and drying the spots, remove the slide from the holder and rinse the slide with buffer to remove unbound oligo. Rinsing may be done either with a spray bottle or by immersing the slide. The plastic slide holders that the slides are shipped in are a convenient low volume rinsing container.

III. Slide Scanning Service

For research laboratories whose volume of printed slides does not justify the $50,000 to $80,000 cost of a typical fluorescent reader, XENOPORE offers a slide reading service. Using a state of the art scanner, we can provide density scans of Cy3, Cy5, FITC or Texas red. This service is available either on a single slide basis or as a long term contract service based on estimated slide usage.