Profile and relaxation of sequence-specificity of DNA sulfur binding domains facilitate new nucleic acid detection platform

Shuai, Yuting; Xu, Anan; Li, Jiayi; Han, Zhaoxi; Ma, Dini; Duan, Hairong; Jiang, Lan; Zhang, Jingyu; Tan, Gao-Yi; Liu, Xueting; Zhao, Yi‐Lei; Tong, Yaojun; Wang, Shenlin; He, Xinyi; Deng, Zixin; Liu, Guang; Zhang, Lixin

doi:10.1016/j.scib.2023.07.012

Cited by 3 publications

(1 citation statement)

References 14 publications

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“…We also tested the chiral PT-modifications at the upstream and downstream backbone positions to understand the recent experiments with multiple PT-modifications. 26 SBD Spr and SBD Sco were found to prefer additional R p-PT modifications at 5′-II because the S P2 atom interacts with SBD Spr -T100 or SBD Sco -R190, whereas additional S p PT-modifications do not interact with SBD Spr and eliminate the salt bridge with R171 in SBD Sco (Fig. S23, ESI†).…”

Section: Resultsmentioning

confidence: 99%

Understanding base and backbone contributions of phosphorothioate DNA for molecular recognition with SBD proteins

Li,

Luo,

Ouyang

et al. 2023

Phys. Chem. Chem. Phys.

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Section: Resultsmentioning

confidence: 99%

Understanding base and backbone contributions of phosphorothioate DNA for molecular recognition with SBD proteins

Li,

Luo,

Ouyang

et al. 2023

Phys. Chem. Chem. Phys.

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Characterization of a promiscuous DNA sulfur binding domain and application in site-directed RNA base editing

Hu,

Yang,

Xiao

et al. 2023

Nucleic Acids Research

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Phosphorothioate (PT)-modification was discovered in prokaryotes and is involved in many biological functions such as restriction-modification systems. PT-modification can be recognized by the sulfur binding domains (SBDs) of PT-dependent restriction endonucleases, through coordination with the sulfur atom, accompanied by interactions with the DNA backbone and bases. The unique characteristics of PT recognition endow SBDs with the potential to be developed into gene-targeting tools, but previously reported SBDs display sequence-specificity for PT-DNA, which limits their applications. In this work, we identified a novel sequence-promiscuous SBDHga from Hahella ganghwensis. We solved the crystal structure of SBDHga complexed with PT-DNA substrate to 1.8 Å resolution and revealed the recognition mechanism. A shorter L4 loop of SBDHga interacts with the DNA backbone, in contrast with previously reported SBDs, which interact with DNA bases. Furthermore, we explored the feasibility of using SBDHga and a PT-oligonucleotide as targeting tools for site-directed adenosine-to-inosine (A-to-I) RNA editing. A GFP non-sense mutant RNA was repaired at about 60% by harnessing a chimeric SBD-hADAR2DD (deaminase domain of human adenosine deaminase acting on RNA), comparable with currently available RNA editing techniques. This work provides insights into understanding the mechanism of sequence-specificity for SBDs and for developing new tools for gene therapy.

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Profiling and application of the sequence-specificity of DNA sulfur binding domains

Shuai,

He,

Deng

et al. 2024

Chin. Sci. Bull.

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Profile and relaxation of sequence-specificity of DNA sulfur binding domains facilitate new nucleic acid detection platform

Cited by 3 publications

References 14 publications

Understanding base and backbone contributions of phosphorothioate DNA for molecular recognition with SBD proteins

Understanding base and backbone contributions of phosphorothioate DNA for molecular recognition with SBD proteins

Characterization of a promiscuous DNA sulfur binding domain and application in site-directed RNA base editing

Profiling and application of the sequence-specificity of DNA sulfur binding domains

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