title: NMR study on the B-Z junction formation of DNA duplexes induced by Z-DNA binding domain of human ADAR1.
abstract: Z-DNA is produced in a long genomic DNA by Z-DNA binding proteins, through formation of two B-Z junctions with the extrusion of one base pair from each junction. To answer the question of how Z-DNA binding proteins induce B-Z transitions in CG-rich segments while maintaining the B-conformation of surrounding segments, we investigated the kinetics and thermodynamics of base-pair openings of a 13-bp DNA in complex with the Z-DNA binding protein, Zα(ADAR1). We also studied perturbations in the backbone of Zα(ADAR1) upon binding to DNA. Our study demonstrates the initial contact conformation as an intermediate structure during B-Z junction formation induced by Zα(ADAR1), in which the Zα(ADAR1) protein displays unique backbone conformational changes, but the 13-bp DNA duplex maintains the B-form helix. We also found the unique structural features of the 13-bp DNA duplex in the initial contact conformation: (i) instability of the AT-rich region II and (ii) longer lifetime for the opening state of the CG-rich region I. Our findings suggest a three-step mechanism of B-Z junction formation: (i) Zα(ADAR1) specifically interacts with a CG-rich DNA segment maintaining B-form helix via a unique conformation; (ii) the neighboring AT-rich region becomes very unstable, and the CG-rich DNA segment is easily converted to Z-DNA; and (iii) the AT-rich regions are base-paired again, and the B-Z junction structure is formed.
authors.affiliation: Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 660-701, Republic of Korea.
authors.forename: Yeon-Mi
authors.initials: YM
authors.lastname: Lee
authors.forename: Hee-Eun
authors.initials: HE
authors.lastname: Kim
authors.forename: Chin-Ju
authors.initials: CJ
authors.lastname: Park
authors.forename: Ae-Ree
authors.initials: AR
authors.lastname: Lee
authors.forename: Hee-Chul
authors.initials: HC
authors.lastname: Ahn
authors.forename: Sung Jae
authors.initials: SJ
authors.lastname: Cho
authors.forename: Kwang-Ho
authors.initials: KH
authors.lastname: Choi
authors.forename: Byong-Seok
authors.initials: BS
authors.lastname: Choi
authors.forename: Joon-Hwa
authors.initials: JH
authors.lastname: Lee
mesh_terms: D000243:Adenosine Deaminase / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D006801:Humans; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D016601:RNA-Binding Proteins
chemical_list: D016601:RNA-Binding Proteins; D004247:DNA; C567955:ADARB1 protein, human; D000243:Adenosine Deaminase