Evaluation of substrate performance for a microbial diagnostic microarray using a four parameter ranking

The impact of substrates for probe immobilization was studied using a microbial diagnostic microarray consisting of probes designed against the pmoA genes of methanotrophs and functionally related bacteria. The proprietary ARChip Epoxy was compared to seven epoxy-modified competitor slides, and one porous 3D, furthermore two substrates recommended for oligoprobes without description of the surface chemistry. The diagnostic microarray on Cel silylated aldehyde (CSS) slide was used as a reference for this comparison as it was actually used for assay development and validation. The suitability of binding chemistries for microarrays was evaluated by specificity, signal, and inter- and intra-slide precision and ranked accordingly. The performance of four epoxy substrates (ARChip Epoxy, Cel Epoxy, Corning Epoxy, sciChip) and Spot On slides has proved satisfactory and comparable to the reference Cel CSS in that inter-slide precision was between 8% and 18% CV, intra-slide precision below 30%, respectively. The four parameter ranking shows great promise of providing deeper insight in the performance of materials and protocols tested.