Many functions of ribonucleic acid (RNA) rely on its ability to assume specific sequence-structure motifs. Packaging signals found in certain RNA viruses are one such prominent example of functional RNA motifs. These signals are short hairpin loops that interact with coat proteins and drive viral self-assembly. As they are found in different positions along the much longer genomic RNA, the formation of their correct structure occurs as a part of a larger context. Any changes to this context can consequently lead to changes in the structure of the motifs themselves. In fact, previous studies have shown that structure and function of RNA motifs can be highly context sensitive to the flanking sequence surrounding them. However, in what ways different flanking sequences influence the structure of an RNA motif they surround has yet to be studied in detail. We focus on a hairpin-rich region of the RNA genome of bacteriophage MS2—a well-studied RNA virus with a wide potential for use in biotechnology—and systematically examine context-dependent structural stability of 14 previously identified hairpin motifs, which include putative and confirmed packaging signals. Combining secondary and tertiary RNA structure prediction of the hairpin motifs placed in different contexts, ranging from the native genomic sequence to random RNA sequences and unstructured poly-U sequences, we determine different measures of motif structural stability. In this way, we show that while some motif structures can be stable in any context, others require specific context provided by the genome. Our results demonstrate the importance of context in RNA structure formation and how changes in the flanking sequence of an RNA motif sometimes lead to drastic changes in its structure. Structural stability of a motif in different contexts could provide additional insights into its functionality as well as assist in determining whether it remains functional when intentionally placed in other contexts.

中文翻译：

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噬菌体 MS2 基因组 RNA 中发夹基序的上下文依赖性结构形成


核糖核酸 （RNA） 的许多功能依赖于其承担特定序列结构基序的能力。在某些 RNA 病毒中发现的包装信号是功能性 RNA 基序的一个突出例子。这些信号是与外壳蛋白相互作用并驱动病毒自组装的短发夹环。由于它们位于更长的基因组 RNA 上的不同位置，因此它们正确结构的形成是更大背景的一部分。因此，对这个上下文的任何更改都可能导致主题本身结构的变化。事实上，以前的研究表明，RNA 基序的结构和功能对周围的侧翼序列高度敏感。然而，不同的侧翼序列以何种方式影响它们周围的 RNA 基序的结构还有待详细研究。我们专注于噬菌体 MS2（一种经过充分研究的 RNA 病毒，在生物技术中具有广泛应用潜力）的 RNA 基因组中富含发夹的区域，并系统地检查了 14 个先前确定的发夹基序的上下文依赖性结构稳定性，其中包括推定和确认的包装信号。结合放置在不同环境中的发夹基序的二级和三级 RNA 结构预测，从天然基因组序列到随机 RNA 序列和非结构化 poly-U 序列，我们确定了基序结构稳定性的不同测量方法。通过这种方式，我们表明，虽然一些基序结构可以在任何环境中保持稳定，但其他基序结构需要基因组提供的特定上下文。我们的结果证明了环境在 RNA 结构形成中的重要性，以及 RNA 基序侧翼序列的变化有时如何导致其结构的剧烈变化。 一个基体在不同语境中的结构稳定性可以提供对其功能的额外见解，并有助于确定它在有意放置在其他语境中时是否仍然有效。