Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia.
Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow 119071, Russia.
Org Biomol Chem. 2024 Jul 24;22(29):5936-5947. doi: 10.1039/d4ob00645c.
DNA aptamers are oligonucleotides that specifically bind to target molecules, similar to how antibodies bind to antigens. We identified an aptamer named MEZ that is highly specific to the receptor-binding domain, RBD, of the SARS-CoV-2 spike protein from the Wuhan-Hu-1 strain. The SELEX procedure was utilized to enrich the initial 31-mer oligonucleotide library with the target aptamer. The aptamer identification was performed using the novel protocol based on nanopore sequencing developed in this study. The MEZ aptamer was chemically synthesized and tested for binding with the SARS-CoV-2 RBD of the spike protein from different strains. The is 6.5 nM for the complex with the RBD from the Wuhan-Hu-1 strain, which is comparable with known aptamers; the advantage is that the MEZ aptamer is smaller than known analogs. The proposed aptamer is highly selective for the RBD protein from the Wuhan-Hu-1 strain and does not form complexes with the RBD from Beta, Delta and Omicron strains. Experimental and theoretical studies together revealed the molecular mechanism of aptamer binding. The aptamer occupies the same binding site as ACE2 when bound to the RBD. The 3'-end of the MEZ aptamer is important for complex formation and is responsible for the discrimination of the RBD protein from a specific strain. The 5'-end is responsible for the formation of a loop in the 3D structure of the aptamer, which is important for proper binding.
DNA 适体是能够特异性结合靶分子的寡核苷酸，类似于抗体与抗原的结合方式。我们从武汉株的 SARS-CoV-2 刺突蛋白中鉴定出一种名为 MEZ 的适体，它对受体结合域（RBD）具有高度特异性。SELEX 程序用于富集初始的 31 个核苷酸文库中的目标适体。适体的鉴定是使用本研究中开发的基于纳米孔测序的新方案进行的。MEZ 适体被化学合成，并测试了与不同株系刺突蛋白 RBD 的结合能力。该适体与武汉株 RBD 的复合物的 Kd 值为 6.5 nM，与已知的适体相当；其优势在于 MEZ 适体比已知的类似物更小。该拟议的适体对武汉株 RBD 蛋白具有高度选择性，并且不会与 Beta、Delta 和 Omicron 株系的 RBD 形成复合物。实验和理论研究共同揭示了适体结合的分子机制。当结合到 RBD 时，适体占据与 ACE2 相同的结合位点。MEZ 适体的 3'-端对于形成复合物很重要，并且负责区分来自特定株系的 RBD 蛋白。5'-端负责形成适体 3D 结构中的环，这对于正确结合很重要。
