Glen Report 13.14: Polyplex Synthesizer from Genemachines

PolyPlex™ is a fast, cost-effective 96-channel oligonucleotide synthesizer capable of generating a full plate of different 20-mers in less than 3 hours. Synthesis is carried out in a 96-well format, which is amenable to downstream high-throughput processing and handling. Parallel dispensing of reagents reduces both synthesis time and reagent consumption, while also eliminating the flushing of reagent lines. The synthesis chamber provides a unique, inert-gas environment where synthesis progress can be monitored by using full-plate trityl collection after any base addition.

Synthesis scales are in the range 20 - 50 nmole and two additional amidite ports are available for incorporating modified bases. There is flexibility in being able to run partial plates and, if the the trityls are not looking good for a particular well, then that well can be stopped while the others continue. The control software is available in both Apple and Windows formats.

In parallel synthesizers, there is a good possibility that tetrazole will crystallize on tips. This situation would lead to termination of flow which is bad in itself but, even worse, the blockage may be temporary. A solution to this problem is to use 4,5-dicyanoimidazole (DCI) as activator. DCI is typically used at a concentration of 0.25M in acetonitrile which is far below its saturation level at greater than 1.1M.

Regular 500Å supports may be used to fill the wells. However, a universal support clearly removes the need for four specific supports and makes preparing plates straightforward. The conditions to eliminate the terminal phosphodiester linkage entirely to 3'-OH are very forcing in our current universal support. However, the use of ammonium hydroxide for 6 hours at 55°C gives around 50% 3'-OH and oligos prepared this way are perfectly usable sequencing primers. For more stringent applications, the use of 0.4M sodium hydroxide in aqueous methanol gives 100% 3'-OH in 0.5 hours at 80°C. The universal Q support allows cleavage of the oligos from the plate in 2 minutes.