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