Environmental Sample Processor (ESP)

Printing probe arrays

The “ink” of the probe array is made up of a single-stranded DNA probe, complementary to a unique rRNA sequence in the organisms of interest. These probes are chemically linked to biotin and mixed with the protein streptavidin, which binds the whole to the surface of the filter support. Electrostatic charges force the probes to stand upright, ready to attach to any complimentary sequence of nucleic acid. The support is a 25-millimeter circle of filter material that fits in the puck, where the analysis takes place.

To print probe arrays, an XYZ translation gantry positions four piezoelectric-actuated nozzles over the spotting area and delivers 6nL of probe solution per spot.  Each of those probes targets a specific species or group of species. The probes can be printed on the substrate in any shape or pattern, as long as you keep track of the “map”.  Below are two typical maps generated with various printers we have used over the years. Note a target might have 5-8 dedicated spots to provide a pseudo-replicated response of the sample to this array print.

Left, early printing (2000–2013); right, current printing (2014–present).

Left, early printing (2000–2013); right, current printing (2014–present).

With better printing technology, we now can lay down 300+ spots on a 25mm disk.

With better printing technology, we now can lay down more than 300 spots on a 25-millimeter disk.

Using a Scienion sciFlexarrayer S3, we lay down 6nL of probe “ink” on a nitrocellulose membrane. It takes about two hours to print 63 arrays for detecting harmful algae targets.