Interaction of the Zα domain of human ADAR1 with a negatively supercoiled plasmid visualized by atomic force microscopy

• Published in: Nucleic acids research 2004, Vol.32 (15), p.4704-4712
• Main Authors: Lushnikov, Alexander Y., Brown, Bernard A., Oussatcheva, Elena A., Potaman, Vladimir N., Sinden, Richard R., Lyubchenko, Yuri L.
• Format: Article
• Language: English
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkh810

Interest to the left-handed DNA conformation has been recently boosted by the findings that a number of proteins contain the Zα domain, which has been shown to specifically recognize Z-DNA. The biological function of Zα is presently unknown, but it has been suggested that it may specifically direct protein regions of Z-DNA induced by negative supercoiling in actively transcribing genes. Many studies, including a crystal structure in complex with Z-DNA, have focused on the human ADAR1 Zα domain in isolation. We have hypothesized that the recognition of a Z-DNA sequence by the ZαADAR1 domain is context specific, occurring under energetic conditions, which favor Z-DNA formation. To test this hypothesis, we have applied atomic force microscopy to image ZαADAR1 complexed with supercoiled plasmid DNAs. We have demonstrated that the ZαADAR1 binds specifically to Z-DNA and preferentially to d(CG)n inserts, which require less energy for Z-DNA induction compared to other sequences. A notable finding is that site-specific Zα binding to d(GC)13 or d(GC)2C(GC)10 inserts is observed when DNA supercoiling is insufficient to induce Z-DNA formation. These results indicate that ZαADAR1 binding facilities the B-to-Z transition and provides additional support to the model that Z-DNA binding proteins may regulate biological processes through structure-specific recognition.