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ADAR1 的 Zα 结构域与具有低微摩尔亲和力的 A 型类似的核酸双链结合。

Zα Domain of ADAR1 Binds to an A-Form-like Nucleic Acid Duplex with Low Micromolar Affinity.

机构信息

Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States.

Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.

出版信息

Biochemistry. 2024 Mar 19;63(6):777-787. doi: 10.1021/acs.biochem.3c00636. Epub 2024 Mar 4.

Abstract

The left-handed Z-conformation of nucleic acids can be adopted by both DNA and RNA when bound by Zα domains found within a variety of viral and innate immune response proteins. While Z-form adoption is preferred by certain sequences, such as the commonly studied (CpG) repeats, Zα has been reported to bind to a wide range of sequence contexts. Studying how Zα interacts with B-/A-form helices prior to their conversion to the Z-conformation is challenging as binding coincides with Z-form adoption. Here, we studied the binding of Zα from ADAR1 to a locked "A-type" version of the (CpG) construct (LNA (CpG)) where the sugar pucker is locked into the C3'-/C2'- conformation, which prevents the duplex from adopting the alternating C2'/C3'- sugar puckers found in the Z-conformation. Using NMR and other biophysical techniques, we find that Zα binds to the LNA (CpG) using a similar interface as for Z-form binding, with a dissociation constant () of ∼4 μM. In contrast to Z-DNA/Z-RNA, where two Zα bind to every 6 bp stretch, our data suggests that Zα binds to multiple LNA molecules, indicating a completely different binding mode. Because Zα binds relatively tightly to a non-Z-form model, its binding to B/A-form helices may need to be considered when experiments are carried out which attempt to identify the Z-form targets of Zα domains. The use of LNA constructs may be beneficial in experiments where negative controls for Z-form adoption are needed.

摘要

当结合于各种病毒和先天免疫反应蛋白中的 Zα 结构域时,DNA 和 RNA 都可以采用左手 Z 构象。虽然某些序列(如常见研究的(CpG)重复序列)更喜欢采用 Z 构象,但已有报道称 Zα 可以结合广泛的序列环境。在 Z 构象形成之前,研究 Zα 如何与 B-/A-型螺旋相互作用是具有挑战性的,因为结合与 Z 构象形成同时发生。在这里,我们研究了 ADAR1 中的 Zα 与锁定的“A型”(CpG)构建体(LNA(CpG))的结合,其中糖环被锁定在 C3'-/C2'-构象中,这阻止了双链体采用 Z 构象中发现的交替 C2'/C3'-糖环构象。使用 NMR 和其他生物物理技术,我们发现 Zα 使用与 Z 构象结合相似的界面与 LNA(CpG)结合,解离常数()约为 4 μM。与 Z-DNA/Z-RNA 不同,其中两个 Zα 结合每 6 个 bp 延伸,我们的数据表明 Zα 结合多个 LNA 分子,表明完全不同的结合模式。由于 Zα 相对紧密地结合于非 Z 构象模型,因此在进行尝试鉴定 Zα 结构域的 Z 构象靶标的实验时,可能需要考虑其与 B/A-型螺旋的结合。在需要 Z 构象采用的阴性对照的实验中,LNA 构建体的使用可能是有益的。

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