Blocking Polylysines on Homemade Microarrays

Homemade microarrays are printed on polylysine-coated slides. The lysines form a positively charged surface that can bind nonspecifically to the acidic nucleic acids during hybridization, resulting in significant background fluorescence. Thus, a key step in microarray processing is blocking all of the surface lysines not associated with the oligonucleotides in the microarray spots. In this protocol, the ε-amino group of lysine is succinylated by reacting with succinic anhydride. The procedure is straightforward. Microarrays are, if necessary, rehydrated; excess liquid is removed by drying at a moderate temperature; and the succinylation reaction is performed. After the reaction is complete, the slides are washed and dried with ethanol, at which point they are ready for hybridization or they can be stored in a desiccator.