title: Specific DNA-RNA hybrid recognition by TAL effectors.
abstract: The transcription activator-like (TAL) effector targets specific host promoter through its central DNA-binding domain, which comprises multiple tandem repeats (TALE repeats). Recent structural analyses revealed that the TALE repeats form a superhelical structure that tracks along the forward strand of the DNA duplex. Here, we demonstrate that TALE repeats specifically recognize a DNA-RNA hybrid where the DNA strand determines the binding specificity. The crystal structure of a designed TALE in complex with the DNA-RNA hybrid was determined at a resolution of 2.5 Å. Although TALE repeats are in direct contact with only the DNA strand, the phosphodiester backbone of the RNA strand is inaccessible by macromolecules such as RNases. Consistent with this observation, sequence-specific recognition of an HIV-derived DNA-RNA hybrid by an engineered TALE efficiently blocked RNase H-mediated degradation of the RNA strand. Our study broadens the utility of TALE repeats and suggests potential applications in processes involving DNA replication and retroviral infections.
authors.affiliation: State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Yin
authors.forename: Dong
authors.initials: D
authors.lastname: Deng
authors.forename: Chuangye
authors.initials: C
authors.lastname: Yan
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Pan
authors.forename: Jianzhong Jeff
authors.initials: JJ
authors.lastname: Xi
authors.forename: Nieng
authors.initials: N
authors.lastname: Yan
authors.forename: Yigong
authors.initials: Y
authors.lastname: Shi
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D006678:HIV / Q000235:genetics; D006801:Humans; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D016914:Ribonuclease H / Q000378:metabolism; D020080:Tandem Repeat Sequences
chemical_list: D004268:DNA-Binding Proteins; D009692:Nucleic Acid Heteroduplexes; D012313:RNA; D004247:DNA; D016914:Ribonuclease H