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Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers
Analytical Chemistry ( IF 6.7 ) Pub Date : 2023-09-18 , DOI: 10.1021/acs.analchem.3c02477 Yuzhe Ding 1 , Juewen Liu 1
Analytical Chemistry ( IF 6.7 ) Pub Date : 2023-09-18 , DOI: 10.1021/acs.analchem.3c02477 Yuzhe Ding 1 , Juewen Liu 1
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Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.
中文翻译：
Capture-SELEX、GO-SELEX 和 Gold-SELEX 富集适体的定量比较
自 1990 年以来，已经开发了多种适体选择方法，但缺乏对其序列富集的定量比较。在本研究中，我们比较了三种文库固定化 SELEX 方法（capture-SELEX、GO-SELEX 和 gold-SELEX）的富集因子。我们使用了一个包含多个对腺苷具有不同亲和力的 DNA 适体的加标文库。使用 qPCR 测量适配体分离效率，所有三种方法在 100 μM 腺苷存在下均显示出非常低的 DNA 释放 (<1%)。其中，几乎没有任何DNA从金纳米颗粒中释放出来。使用深度测序来比较三种适配体的富集：Ade1301、Ade1304和经典适配体。仅在 capture-SELEX 方法中观察到高达 30 至 50 倍的富集，而其他两种方法显示的富集因子低于 1。通过封闭文库的引物结合区域，GO-SELEX 达到了高达 14% 的富集。最后，讨论了基于非特异性释放和靶标诱导释放的适配体富集，并合理化了capture-SELEX的优势。综上所述，这些结果表明 capture-SELEX 是一种更有效的富集适体的方法。
更新日期：2023-09-18
中文翻译：
Capture-SELEX、GO-SELEX 和 Gold-SELEX 富集适体的定量比较
自 1990 年以来，已经开发了多种适体选择方法，但缺乏对其序列富集的定量比较。在本研究中，我们比较了三种文库固定化 SELEX 方法（capture-SELEX、GO-SELEX 和 gold-SELEX）的富集因子。我们使用了一个包含多个对腺苷具有不同亲和力的 DNA 适体的加标文库。使用 qPCR 测量适配体分离效率，所有三种方法在 100 μM 腺苷存在下均显示出非常低的 DNA 释放 (<1%)。其中，几乎没有任何DNA从金纳米颗粒中释放出来。使用深度测序来比较三种适配体的富集：Ade1301、Ade1304和经典适配体。仅在 capture-SELEX 方法中观察到高达 30 至 50 倍的富集，而其他两种方法显示的富集因子低于 1。通过封闭文库的引物结合区域，GO-SELEX 达到了高达 14% 的富集。最后，讨论了基于非特异性释放和靶标诱导释放的适配体富集，并合理化了capture-SELEX的优势。综上所述，这些结果表明 capture-SELEX 是一种更有效的富集适体的方法。
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