BACKGROUND: The fluorescence dye 5-dimethylamino-1-naphthalenesulfonyl chloride (Dansyl chloride) is commonly used for labeling the N-terminus of proteins and peptides. Apart from the fluorescence, the ?SO2?NH?bonds formed are susceptible to photolytic cleavage and will subsequently restore free amines. Consequently, Dansyl amides could act as a fluorescent photoprotecting group with novel application in solid phase synthesis or in microarray technologies. RESULTS: Commercial microscope glass slides were silanized with (3-aminopropyl) triethoxysilane, exposed amines were activated with 1,4-phenylene diisothiocyanate and subsequently reacted with dansylated polyethylene imine (PEI). The resulting fluorescence of the surface was determined and used as a measure of the homogeneity of the introduced functional groups. Using a mask, Dansyl-PEI modified slides were locally exposed to photolytic cleavage within irradiation energy of 100 J cm-2. Inscribed structures would be easily recognized due to their loss of fluorescence. The restored amines in deprotected areas were reacted with phosphorylated capture oligonucleotides followed by hybridization with complementary Cy5-labeled targets. CONCLUSIONS: Capture probes immobilized precisely in structures exposed to UV-light while non-irradiated areas remained blocked. Such pre-structured surfaces allow the production of highly reproducible microarrays without any specific problems of spotting imperfections. Gridding and segmentation of the determined sample allocation facilitate spot finding and spot analysis. Copyright (c) 2012 Society of Chemical Industry