To evaluate the effect of synthetic DNA oligomers on regulation of bacterial genes in vivo, we tested 63 oligomers of variable length and chemistry for their ability to selectively suppress light production in the bioluminescent marine organism, Vibrio fischeri. Phosphodiester, phosphorothioate, and mixed backbone oligomers were designed to be lux gene targeted or nontargeted (negative) controls. Although significant suppression of luminescence was observed, most notably with the phosphorothioate oligomers, there was no correlation between inhibitory activity and oligomer sequence. The phosphorothioate oligomer that was most potent for inhibition of luminescence in bacterial culture had no effect on the activity of purified luciferase. Mechanisms other than sequence-specific inhibition of gene expression or direct interaction with luciferase are discussed.