title: NMR investigation on the DNA binding and B-Z transition pathway of the Zα domain of human ADAR1.
abstract: Human ADAR1, which has two left-handed Z-DNA binding domains, preferentially binds Z-DNA rather than B-DNA with a high binding affinity. Z-DNA can be induced in long genomic DNA by Z-DNA binding proteins through the formation of two B-Z junctions with the extrusion of one base pair from each junction. We performed NMR experiments on complexes of Zα(ADAR1) with three DNA duplexes at a variety of protein-to-DNA molar ratios. This study confirmed that the Zα(ADAR1) first binds to an 8-bp CG-rich DNA segment via a unique conformation during B-Z transition and the neighboring AT-rich region becomes destabilized. We also found that, when DNA duplexes have only 6-bp CG-rich segment, the interaction with Zα(ADAR1) did not affect the thermal stabilities of the 6-bp CG-rich segment as well as the neighboring two A·T base pairs. These results indicate that four Zα(ADAR1) proteins interact with the 8-bp DNA sequence containing a 6-bp CG-repeat segment as well as a dinucleotide step, even though the dinucleotid step contains A∙T base pairs. Thus this study suggests that the length of the CG-rich region is more important than the specific DNA sequence for determining which base-pair is extruded from the B-Z junction structure. This study also found that the Zα(ADAR1) in complex with a 11-bp DNA duplex exhibits a Z-DNA-bound conformation distinct from that of free Zα(ADAR1) and the initial contact conformations of Zα(ADAR1) complexed with 13-bp DNA duplexes.
authors: Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 660-701, Republic of Korea.
authors: Yeon-Mi
authors: YM
authors: Lee
authors: Hee-Eun
authors: HE
authors: Kim
authors: Eun-Hae
authors: EH
authors: Lee
authors: Yeo-Jin
authors: YJ
authors: Seo
authors: Ae-Ree
authors: AR
authors: Lee
authors: Joon-Hwa
authors: JH
authors: Lee
mesh_terms: D000243:Adenosine Deaminase / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D059371:DNA, B-Form / Q000737:chemistry / Q000378:metabolism*; D043542:DNA, Z-Form / Q000737:chemistry / Q000378:metabolism*; D020862:GC Rich Sequence / Q000235:genetics; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016601:RNA-Binding Proteins
chemical_list: D059371:DNA, B-Form; D043542:DNA, Z-Form; D016601:RNA-Binding Proteins; C567955:ADARB1 protein, human; D000243:Adenosine Deaminase