Compatible solutes from hyperthermophiles improve the quality of DNA microarrays

We report here that compatible solutes from hyperthermophiles increased the performance of the hybridization buffer for Affymetrix GeneChip？ arrays. The experimental setup included independent hybridizations with constant RNA over a wide range of compatible solute concentrations. The dependence of array quality and compatible solute was assessed using specialized statistical tools provided by both the proprietary Affymetrix quality control system and the open source Bioconductor suite.Low concentration (10 to 25 mM) of hydroxyectoine, potassium mannosylglycerate and potassium diglycerol phosphate in hybridization buffer positively affected hybridization parameters and enhanced microarrays outcome. This finding harbours a strong potential for the improvement of DNA microarray experiments.In recent years DNA microarrays as other high throughput molecular techniques became first choice investigation methods for DNA and RNA studies. Early applications included expression profiling and DNA mutation analysis [1]. Recently, single nucleotide polymorphisms (SNPs) and comparative genomics hybridization also found widespread solutions in microarray based assays [2-4]. The optimization of the microarray workflow, including the hybridization step, is thus a primary target for the evolution of more efficient protocols.The identification of compatible solutes in hyperthermophilic microorganisms, and of their stabilization effect, prompted us to test their effectiveness in microarray protocols. The accumulation of low molecular mass compounds is known to be a common strategy used by microorganisms to survive in environmental and stressful conditions [5]. Hyperthermophiles accumulate compatible solutes (the so-called hypersolutes) rarely encountered in mesophiles. These solutes are generally negatively charged, whereas mesophiles accumulate primarily neutral solutes.Mannosyl glycerate (MG) is a compatible solute accumulated by some thermophiles and hyperthermophiles in answering to