d(GC)&amp;lt;italic&amp;gt;&amp;lt;sub&amp;gt;n&amp;lt;/sub&amp;gt;&amp;lt;/italic&amp;gt; repeats form Z-DNA within promoter region and repress the promoter activity in &amp;lt;italic&amp;gt;Escherichia coli&amp;lt;/italic&amp;gt;

Huang, Shenghe; Wu, Chuxin; Li, Dongming; Wang, Haizhou; Ze-chang, Rao; Shen, Qiling; Chen, Chunxiang; Liu, Yong; Xu, Xun; Hu, Chengyu

doi:10.1093/abbs/gmv038

Cited by 4 publications

(2 citation statements)

References 9 publications

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“…It has been repeatedly discussed in literature that antibodies against Z-DNA/RNA detects the nucleic acid only downstream of RNA polymerase moving site (42), possibly indicative of some role for protein in Z-DNA formation and maintenance. This gives rise to the question whether Zα domain containing proteins induce the Z conformation in oligonucleotides with the propensity to form such structures?…”

Section: Discussionmentioning

confidence: 99%

Thermodynamic analysis of Zα domain-nucleic acid interactions

Srinivasan

Kuś

Athanasiadis

2022

Preprint

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DNA/RNA molecules adopting the left-handed conformation (Z-form) have been attributed with immunogenic properties. However, their biological role and importance has been a topic of debate for many years. The discovery of Z-DNA/RNA binding domains (Zα domains) in varied proteins that are involved in the innate immune response, such as the interferon inducible form of the RNA editing enzyme ADAR1 (p150), Z-DNA binding protein 1 (ZBP1), the fish kinase PKZ and the poxvirus inhibitor of interferon response E3L, indicates important roles of Z-DNA/RNA in immunity and self/non-self-discrimination. Such Zα domain-containing proteins recognise left-handed Z-DNA/RNA in a conformation-specific manner. Recent studies have implicated these domains in virus recognition. Given these important emerging roles for the Zα domains, it is pivotal to understand the mechanism of recognition of the Z-DNA/Z-RNA by these domains. To this end, we assessed the binding thermodynamics of Zα domain from ORF112 and ADAR1 on T(CG)3 and T(CG)6 oligonucleotides which have high propensity to adopt the Z-conformation. Our study highlights important differences in the mode of binding by the two Zα domains originating from different proteins. Site-directed mutagenesis was employed together with isothermal titration calorimetry to tease apart finer details of the binding thermodynamics. Our work advances the understanding on binding thermodynamics of Zα domains to their cognate nucleic acid substrates and paves the ground for future efforts to gain a complete appreciation of this process.

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Section: Discussionmentioning

confidence: 99%

Thermodynamic analysis of Zα domain-nucleic acid interactions

Srinivasan

Kuś

Athanasiadis

2022

Preprint

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“…Notably, the major groove is almost non-existent, while the minor groove is narrow. Tracts alternating dinucleotide repeating purine-pyrimidine or pyrimidine-purine (APP) sequences are known to adopt the left-handed conformation [ 16 , 17 ], and are over-represented in higher eukaryotes. In fact, GpC repeats, also named “CpG islands”, show a strong attitude to crystallizing as a Z-structure [ 18 ].…”

Section: Overview Of Nucleic Acidsmentioning

confidence: 99%

DNA Studies: Latest Spectroscopic and Structural Approaches

et al. 2021

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This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

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Thermodynamic analysis of Zα domain-nucleic acid interactions

Srinivasan

Kuś

Athanasiadis

2022

Biochemical Journal

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DNA/RNA molecules adopting the left-handed conformation (Z-form) have been attributed with immunogenic properties. However, their biological role and importance has been a topic of debate for many years. The discovery of Z-DNA/RNA binding domains (Zα domains) in varied proteins that are involved in the innate immune response, such as the interferon inducible form of the RNA editing enzyme ADAR1 (p150), Z-DNA binding protein 1 (ZBP1), the fish kinase PKZ and the poxvirus inhibitor of interferon response E3L, indicates important roles of Z-DNA/RNA in immunity and self/non-self-discrimination. Such Zα domain-containing proteins recognise left-handed Z-DNA/RNA in a conformation-specific manner. Recent studies have implicated these domains in virus recognition. Given these important emerging roles for the Zα domains, it is pivotal to understand the mechanism of recognition of the Z-DNA/Z-RNA by these domains. To this end, we assessed the binding thermodynamics of Zα domain from ORF112 and ADAR1 on T(CG)3 and T(CG)6 oligonucleotides which have high propensity to adopt the Z-conformation. Our study highlights important differences in the mode of oligonucleotide binding by the two Zα domains originating from different proteins. Site-directed mutagenesis was employed together with isothermal titration calorimetry to tease apart finer details of the binding thermodynamics. Our work advances the understanding on binding thermodynamics of Zα domains to their cognate nucleic acid substrates and paves the ground for future efforts to gain a complete appreciation of this process.

show abstract

d(GC)<italic><sub>n</sub></italic> repeats form Z-DNA within promoter region and repress the promoter activity in <italic>Escherichia coli</italic>

Cited by 4 publications

References 9 publications

Thermodynamic analysis of Zα domain-nucleic acid interactions

Thermodynamic analysis of Zα domain-nucleic acid interactions

DNA Studies: Latest Spectroscopic and Structural Approaches

Thermodynamic analysis of Zα domain-nucleic acid interactions

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