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

• Published in: Nucleic acids research 2008-06, Vol.36 (10), p.3163-3170
• Main Authors: Ditlevson, Jennifer V, Tornaletti, Silvia, Belotserkovskii, Boris P, Teijeiro, Virginia, Wang, Guliang, Vasquez, Karen M, Hanawalt, Philip C
• Format: Article
• Language: English
• Subjects: Base Sequence; DNA, Superhelical - chemistry; DNA, Z-Form - chemistry; DNA-Directed RNA Polymerases - antagonists & inhibitors; Models, Genetic; Molecular Biology; Purines - chemistry; Pyrimidines - chemistry; RNA, Catalytic - chemistry; Transcription, Genetic; Viral Proteins - antagonists & inhibitors
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkn136

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.