Inhibitory effect of a short Z-DNA forming sequence on transcription elongation by T7 RNA polymerase

Abstract

DNA sequences capable of forming unusual secondary structures can be a source of genomic instability. In some cases that instability might be affected by transcription, as recently shown for the Z-DNA forming sequence (CG) ₁₄ , which causes genomic instability both in mammalian cells and in bacteria, and this effect increases with its transcription. We have investigated the effect of this (CG) ₁₄ sequence on transcription with T7 RNA polymerase in vitro . We detected partial transcription blockage within the sequence; the blockage increased with negative supercoiling of the template DNA. This effect was not observed in a control self-complementary sequence of identical length and base composition as the (CG) ₁₄ sequence, when the purine–pyrimidine alternation required for Z-DNA formation was disrupted. These findings suggest that the inhibitory effect on T7 transcription results from Z-DNA formation in the (CG) ₁₄ sequence rather than from an effect of the sequence composition or from hairpin formation in either the DNA or the RNA product.