Journal Article

The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZα<sub>ADAR1</sub>

Sung Chul Ha, Jongkeun Choi, Hye-Yeon Hwang, Alexander Rich, Yang-Gyun Kim and Kyeong Kyu Kim

in Nucleic Acids Research

Volume 37, issue 2, pages 629-637
Published in print February 2009 | ISSN: 0305-1048
Published online December 2008 | e-ISSN: 1362-4962 | DOI: http://dx.doi.org/10.1093/nar/gkn976

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The Z-DNA conformation preferentially occurs at alternating purine-pyrimidine repeats, and is specifically recognized by Zα domains identified in several Z-DNA-binding proteins. The binding of Zα to foreign or chromosomal DNA in various sequence contexts is known to influence various biological functions, including the DNA-mediated innate immune response and transcriptional modulation of gene expression. For these reasons, understanding its binding mode and the conformational diversity of Zα bound Z-DNAs is of considerable importance. However, structural studies of Zα bound Z-DNA have been mostly limited to standard CG-repeat DNAs. Here, we have solved the crystal structures of three representative non-CG repeat DNAs, d(CACGTG)2, d(CGTACG)2 and d(CGGCCG)2 complexed to hZαADAR1 and compared those structures with that of hZαADAR1/d(CGCGCG)2 and the Zα-free Z-DNAs. hZαADAR1 bound to each of the three Z-DNAs showed a well conserved binding mode with very limited structural deviation irrespective of the DNA sequence, although varying numbers of residues were in contact with Z-DNA. Z-DNAs display less structural alterations in the Zα-bound state than in their free form, thereby suggesting that conformational diversities of Z-DNAs are restrained by the binding pocket of Zα. These data suggest that Z-DNAs are recognized by Zα through common conformational features regardless of the sequence and structural alterations.

Journal Article.  4510 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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