The application of DNA microarrays for high throughput analysis of genetic regulation is often limited by the fluorophores used as markers. The implementation of multi-scan techniques is limited by the fluorophores’ susceptibility to photobleaching when exposed to the scanner laser light. This paper presents combined mechanical and chemical strategies which enhance the photostability of cyanine 3 and cyanine 5 as part of solid state DNA microarrays. These strategies are based on scanning the microarrays while the hybridized DNA is still in an aqueous solution with the presence of a reductive/oxidative system (ROXS). Furthermore, the experimental setup allows for the analysis and eventual normalization of Förster-resonance-energy-transfer (FRET) interaction of cyanine-3/cyanine-5 dye combinations on the microarray. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the comparability of microarray experiment results between labs.

At the variable environmental conditions plant growth and development are under the control of different factors triggered shifts in hormonal balance and followed changes in intensity of hormone-induced gene expression. Root-specific expression of early auxin-regulated genes, belonged to Aux/IAAs, SAURs, ARFs и GH3s gene families, was tested with specially designed chip. An auxin treatment (15, 30 and 60 min) led to increase of IAA1, IAA3, IAA5, IAA11, IAA19 and GH3-1, GH3-3, GH3-5 genes. Intensification of SAUR9 and SAUR10 genes expression was less significant and appeared only at 30 min.