Methods for determining the quality of a biomolecular microarray to determine suitability of the microarray for performing specific binding reactions, such as hybridization, are provided. Methods are based on staining a microarray with a solution of detectable nanoparticles that reversibly stain the biomolecules through an electrostatic interaction to select microarrays that meet quality standards for hybridization reactions. A gold nanoparticle solution based staining method for DNA microarrays is provided. Destaining methods allowing multiple rounds of hybridization of nanogold stained microarrays are provided. Microarrays selected by methods of the invention are provided.