The Mango I and II RNA aptamers have been widely used in vivo and in vitro as genetically encodable fluorogenic markers that undergo large increases in fluorescence upon binding to their ligand, TO1-Biotin. However, while studying nucleic acid sequences, it is often desirable to have trans-acting probes that induce fluorescence upon binding to a target sequence. Here, we rationally design three types of light-up RNA Mango Beacons based on a minimized Mango core that induces fluorescence upon binding to a target RNA strand. Our first design is bimolecular in nature and uses a DNA inhibition strand to prevent folding of the Mango aptamer core until binding to a target RNA. Our second design is unimolecular in nature, and features hybridization arms flanking the core that inhibit G-quadruplex folding until refolding is triggered by binding to a target RNA strand. Our third design builds upon this structure, and incorporates a self-inhibiting domain into one of the flanking arms that deliberately binds to, and precludes folding of, the aptamer core until a target is bound. This design separates G-quadruplex folding inhibition and RNA target hybridization into separate modules, enabling a more universal unimolecular beacon design. All three Mango Beacons feature high contrasts and low costs when compared to conventional molecular beacons, with excellent potential for in vitro and in vivo applications.

中文翻译：

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打开 RNA Mango Beacons 用于反式荧光核酸检测

Mango I 和 II RNA 适体已作为基因可编码荧光标记在体内和体外得到广泛应用，在与其配体 TO1-生物素结合后，荧光会大幅增加。然而，在研究核酸序列时，通常需要具有在与靶序列结合后诱导荧光的反式作用探针。在这里，我们基于最小化的芒果核心合理设计了三种类型的发光 RNA 芒果信标，该核心在与目标 RNA 链结合时诱导荧光。我们的第一个设计本质上是双分子的，并使用 DNA 抑制链来防止 Mango 适体核心折叠，直到与目标 RNA 结合。我们的第二种设计本质上是单分子的，其特征是核心侧翼的杂交臂抑制 G-四链体折叠，直到通过与目标 RNA 链结合触发重折叠。我们的第三种设计建立在这种结构的基础上，并将自我抑制结构域纳入其中一个侧翼臂中，该侧翼臂故意结合并阻止适配体核心的折叠，直到目标被结合。该设计将 G 四链体折叠抑制和 RNA 靶标杂交分离成单独的模块，从而实现更通用的单分子信标设计。与传统分子信标相比，所有三种芒果信标都具有高对比度和低成本的特点，在体外和体内应用方面具有巨大的潜力。