Targeting a conserved structural element from the SARS-CoV-2 genome using l-DNA aptamers.
Targeting a conserved structural element from the SARS-CoV-2 genome using l-DNA aptamers.
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DOI：
10.1039/d1cb00172h
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发表时间：
2022-01-05
影响因子：
4.1
通讯作者：
Sczepanski JT
中科院分区：
文献类型：
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作者：
Li J;Sczepanski JT
严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 是导致 COVID-19 的病毒，已导致一场持续的全球大流行，已夺去了超过 400 万人的生命。虽然大多数抗病毒工作都集中在必需的 SARS-CoV-2 蛋白上，但病毒基因组内的 RNA 结构元件也是引人注目的目标。在这项研究中，我们鉴定了针对 SARS-CoV-2 茎环 II 样基序 (s2m) 的高亲和力 l-DNA 适体，s2m 是一种高度保守的 RNA 结构，具有良好的诊断和治疗潜力。优化的 l-C1t 和 l-C3t 适配体选择性结合 s2m RNA，Kd 值在纳摩尔范围内，并且能够区分单体 s2m 茎环与所提出的同二聚体双链体。这种结构特异性的识别模式还允许 l-C1t 和 l-C3t 区分来自 SARS-CoV-2 和 SARS-CoV-1 的 s2m RNA，它们仅相差两个核苷酸。最后，我们证明 l-C1t 和 l-C3t 在结合后会诱导 s2m 结构发生显着的构象变化，因此有可能阻断蛋白质-s2m 相互作用。总体而言，这些结果证明了使用 l-适体靶向 SARS-CoV-2 RNA 的可行性，这对 COVID-19 的诊断和治疗具有重要意义。此外，l-C1t 和 l-C3t 的高亲和力和选择性，加上 l-DNA 固有的核酸酶抗性，为生成新工具和探针来研究 SARS-CoV-2 和相关病毒中的 s2m 功能提供了机会。 采用体外选择来鉴定对 SARS-CoV-2 基因组中的 s2m RNA 结构具有高亲和力和选择性的 L-DNA 适体。
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has resulted in an ongoing global pandemic that has already claimed more than 4 million lives. While most antiviral efforts have focused on essential SARS-CoV-2 proteins, RNA structural elements within the viral genome are also compelling targets. In this study, we identified high-affinity l-DNA aptamers against a SARS-CoV-2 stem-loop II-like motif (s2m), a highly conserved RNA structure with promising diagnostic and therapeutic potential. Optimized l-C1t and l-C3t aptamers bind selectively to s2m RNA with Kd values in the nanomolar range, and are capable of differentiating the monomeric s2m stem-loop from the proposed homodimer duplex. This structure-specific mode of recognition also allows l-C1t and l-C3t to discriminate between s2m RNAs from SARS-CoV-2 and SARS-CoV-1, which differ by just two nucleotides. Finally, we show that l-C1t and l-C3t induce dramatic conformational changes in s2m structure upon binding, and thus, have the potential to block protein–s2m interactions. Overall, these results demonstrate the feasibility of targeting SARS-CoV-2 RNA using l-aptamers, which has important implications in the diagnosis and treatment of COVID-19. Moreover, the high affinity and selectivity of l-C1t and l-C3t, coupled with the intrinsic nuclease resistance of l-DNA, present an opportunity for generating new tools and probes for interrogating s2m function in SARS-CoV-2 and related viruses. In vitro selection was used to identify L-DNA aptamers with high affinity and selectivity for the s2m RNA structure in the SARS-CoV-2 genome.