BiodegChip : a DNA microarray to study the catabolic genes of aromatic "BTEX" pollutants in complex microbial communities

Different tools have been proposed to detect, characterize and quantify genes responsible for degradation of different pollutants in environmental samples such us PCR-SSCP DNA fingerprinting, PCR DNA clone libraries and microarrays. In the present work, we developed a custom array system termed BiodegChip to assess functional BTEX (Benzene, Toluene, Ethylbenzene, Xylene) catabolic gene diversity in contaminated environments. A custom CDS database was created including all catabolic genes encoding key activities in BTEX degradation pathways based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, containing >15,000 genes in >30 functional groups (EC number). Resulting gene database were subjected to probe design (50 mer) using the software Oligoarrays 2.1 with a selection parameter of GC content between 35 and 50% and Tm range 80 and 88°C. The verification of specificity of all probes was used using BLASTTN database. Printing and experimental procedures for application in environmental analyses are in progress.