title: Interaction of the Zalpha domain of human ADAR1 with a negatively supercoiled plasmid visualized by atomic force microscopy.
abstract: Interest to the left-handed DNA conformation has been recently boosted by the findings that a number of proteins contain the Zalpha domain, which has been shown to specifically recognize Z-DNA. The biological function of Zalpha 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 Zalpha domain in isolation. We have hypothesized that the recognition of a Z-DNA sequence by the Zalpha(ADAR1) 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 Zalpha(ADAR1) complexed with supercoiled plasmid DNAs. We have demonstrated that the Zalpha(ADAR1) 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 Zalpha binding to d(GC)(13) or d(GC)(2)C(GC)(10) inserts is observed when DNA supercoiling is insufficient to induce Z-DNA formation. These results indicate that Zalpha(ADAR1) 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.
authors.affiliation: School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
authors.forename: Alexander Y
authors.initials: AY
authors.lastname: Lushnikov
authors.forename: Bernard A
authors.initials: BA
authors.lastname: Brown
authors.forename: Elena A
authors.initials: EA
authors.lastname: Oussatcheva
authors.forename: Vladimir N
authors.initials: VN
authors.lastname: Potaman
authors.forename: Richard R
authors.initials: RR
authors.lastname: Sinden
authors.forename: Yuri L
authors.initials: YL
authors.lastname: Lyubchenko
mesh_terms: D000243:Adenosine Deaminase / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D004278:DNA, Superhelical / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure*; D043542:DNA, Z-Form / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure*; D006801:Humans; D018625:Microscopy, Atomic Force; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000737:chemistry / Q000648:ultrastructure; D017434:Protein Structure, Tertiary; D016601:RNA-Binding Proteins
chemical_list: D004278:DNA, Superhelical; D043542:DNA, Z-Form; D016601:RNA-Binding Proteins; C567955:ADARB1 protein, human; D000243:Adenosine Deaminase