POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer.

A DNA array, or gene chip, is an ordered arrangement of known nucleic acid sequences.  Based on the matching known with unknown sequences, it enables the large-scale analysis of genes and their products.

There are three varieties of DNA arrays: macroarrays (nylon filters - plasmid clones - radioactive report groups), microarrays (glass - PCR or cDNA - fluorescent reporters), and oligonucleotide arrays (glass - oligonucleotides - fluorescent reporters). Oligonucleotide array advantages include high specificity (the ability to distinguish closely-related members of gene families or alternatively spliced RNAs, gene insertions, gene deletions, and SNPs) and relatively simple construction (there is no need for the creation and maintainance of libraries of cDNAs or PCR products).  Inkjet arrays are special oligonucleotide arrays in which the sequences are synthesized in situ, chemically, on the surface of the chip.

The inkjet array synthesizer produces custom arrays by combining phosphoramidite DNA synthesis chemistry with commercial ink-jet technology. The machine uses a six-channel piezoelectric print head with 32 nozzles per channel to quickly deliver DNA monomers and activator to thousands of reaction sites on a silanized glass slide. Each bank of the piezoelectric printer is attached to a pressurized reservoir containing one phosphoramidite monomer. The fifth bank delivers activator to the slide, and the sixth bank can be used for modified phosphoramidite monomers (such as phosphorylated or fluorescently labeled monomers). The current design permits the addition of a second 6-channel print head if necessary. Droplet volume is less than 10 pL and feature size can be less than 40 microns in diameter with a pitch (center-to-center distance) of less than 150 microns. Typically, features are 150 microns in diameter, have a pitch of 280 microns, and are printed in numbers of 4900 per chip.  The array substrate is a 25x76mm glass slide.  Synthesis occurs inside a dry, nitrogen-filled chamber.

The Piezoelectric Oligonucleotide Synthesizer And Microarrayer (POSAM) was developed in the Hood Laboratory to give researchers access to customizeable DNA microarrays.  The result is an "open source" platform.  The hardware design and protocols are being made available freely to the public and the control software is released under the GPL license.  Version 0.6 of Pogo, the control software, is available below.  (Click here for a screenshot.)  The latest version is available through CVS at Bioinformatics.org. 

Requirements:

• Pentium III 500MHz PC
• MS Windows NT 4.0 or later
• Visual Basic Runtime libraries v.6.0
• National Instruments NIDAQ v.6.9.1
• Compumotor Com6srvr v.3.3.1
• POSAM software (one of the following):
  • Pogo CVS repository
  • Pogo version 0.6.

Resources for building your own POSAM

• User manual chapter 1: Assembly
  Updated May 2005
  New: IEEE-1394 camera for imaging droplets; linear encoders for precision; fewer parts for droplet detector.
• User manual chapter 2: Operation
  
• Slide holder DWG/DXF files
• Acrylic cover DXF files
• Circuit board design/ordering software
• Circuit board 1503 rev 1.2
  Updated April 2005
  Changes: Holes added for standoffs; traces made thicker.
• Circuit board 1804 rev 1.2 
  Updated: Aug 2004. 
  Changes: Missing 30VDC line to pin 15 of DB15 connector added; part number for 68-pin connector updated; several connector labels added.
  
• Circuit board 1902 rev 1.2
  Updated April 2005
  Changes: Photodiode signals at screw terminals; short between hygrometer and solenoid relay fixed;
  7408 chip added to protect LS7183 chip; more labeling on top conductor layer.
  

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