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The use of the restriction enzyme EcoRI for the manipulation of double-stranded DNA on microarrays is introduced. Gold nanoparticles are attached to a microarray via base pairing between complementary DNA sequences on the array and on the particles. These particles could be detected by light scattering measurements following an enhancement step, in which silver islands were deposited on top of the gold particles. This deposition of silver could be completely suppressed if the particles were removed by enzymatic cleavage of their DNA linker molecules. This cleavage step critically depends on the presence of a specific enzyme recognition site.