title: In-depth study of DNA binding of Cys2His2 finger domains in testis zinc-finger protein.
abstract: Previously, we identified that both fingers 1 and 2 in the three Cys2His2 zinc-finger domains (TZD) of testis zinc-finger protein specifically bind to its cognate DNA; however, finger 3 is non-sequence-specific. To gain insights into the interaction mechanism, here we further investigated the DNA-binding characteristics of TZD bound to non-specific DNAs and its finger segments bound to cognate DNA. TZD in non-specific DNA binding showed smaller chemical shift perturbations, as expected. However, the direction of shift perturbation, change of DNA imino-proton NMR signal, and dynamics on the 15N backbone atom significantly differed between specific and non-specific binding. Using these unique characteristics, we confirmed that the three single-finger segments (TZD1, TZD2 and TZD3) and the two-finger segment (TZD23) non-specifically bind to the cognate DNA. In comparison, the other two-finger segment (TZD12) binding to the cognate DNA features simultaneous non-specific and semi-specific binding, both slowly exchanged in terms of NMR timescale. The process of TZD binding to the cognate DNA is likely stepwise: initially TZD non-specifically binds to DNA, then fingers 1 and 2 insert cooperatively into the major groove of DNA by semi-specific binding, and finally finger 3 non-specifically binds to DNA, which promotes the specific binding on fingers 1 and 2 and stabilizes the formation of a specific TZD-DNA complex.
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC.
authors.forename: Chun-Chi
authors.initials: CC
authors.lastname: Chou
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC.
authors.forename: Shu-Yi
authors.initials: SY
authors.lastname: Wei
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC.
authors.forename: Yuan-Chao
authors.initials: YC
authors.lastname: Lou
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC.
authors.forename: Chinpan
authors.initials: C
authors.lastname: Chen
mesh_terms: D000818:Animals; D003545:Cysteine / Q000378:metabolism*; D004247:DNA / Q000378:metabolism*; D006639:Histidine / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D008297:Male; D051379:Mice; D013737:Testis / Q000378:metabolism*; D016335:Zinc Fingers
chemical_list: D006639:Histidine; D004247:DNA; D003545:Cysteine