The effects of organic and inorganic mercury ions on gene expression were studied by in vitro cell-free assays for transcription and translation. While organic mercury (methylmercury chloride, MeHgCl) showed no effects, treatment of template DNA with inorganic mercury (HgCl₂) inhibited mRNA synthesis in a bacteriophage T7 RNA polymerase transcription system. The inhibited transcription resulted in reduced protein synthesis after the subsequent application of the transcripts to a translation system consisting of Sf21 insect cell lysate. Treatment of mRNA with inorganic mercury also reduced translation, although this inhibitory effect was weaker than the effect produced by DNA exposure. Treatment of DNA and RNA with mercury did not increase oxidative damage such as strand cleavage and base oxidation. Instead, circular dichroism spectrometry demonstrated that mercury ions, not methyl mercury, drastically changed strand conformation of DNA and RNA. Therefore, the gene expression inhibition observed in this study was thought to be caused by crossbridging of DNA bases with mercury ions, which blocked the transcriptional machinery. Taken together with reports on biological conversion of organic mercury to inorganic forms in animals, our results show that transcriptional inhibition via conformational changes in DNA could be a toxic mechanism involved in mercury poisoning.