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Nucleic Acids Research Advance Access originally published online on April 9, 2008
Nucleic Acids Research 2008 36(10):3163-3170; doi:10.1093/nar/gkn136
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Nucleic Acids Research, 2008, Vol. 36, No. 10 3163-3170
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

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

Jennifer V. Ditlevson1, Silvia Tornaletti1, Boris P. Belotserkovskii1, Virginia Teijeiro1, Guliang Wang2, Karen M. Vasquez2 and Philip C. Hanawalt1,*

1Department of Biological Sciences, Stanford University, Stanford, CA, 94305 and 2Department of Carcinogenesis, University of Texas, M. D. Anderson Cancer Center, Science Park-Research Division, Smithville, TX, 78957, USA

*To whom correspondence should be addressed. Tel: +1 650 723 2424; Fax: +1 650 725 1848; Email: hanawalt{at}stanford.edu

Received January 17, 2008. Revised February 15, 2008. Accepted March 12, 2008.

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.

Present address: Silvia Tornaletti, Department of Anatomy and Cell Biology, University of Florida, USA


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