CiTCOM, Cibles Thérapeutiques et Conception de Médicaments, UMR8038 CNRS, Université Paris Cité, Paris, France.
Methods Mol Biol. 2025;2847:177-191. doi: 10.1007/978-1-0716-4079-1_12.
RNA design is a major challenge for the future development of synthetic biology and RNA-based therapy. The development of efficient and accurate RNA design pipelines is based on trial and error strategies. The fast progression of such algorithms requires assaying the properties of many RNA sequences in a short time frame. High throughput RNA structure chemical probing technologies such as SHAPE-MaP allow for assaying RNA structure and interaction rapidly and at a very large scale. However, the promiscuity of the designed sequences that may differ only by one nucleotide requires special care. In addition, it necessitates the analysis and evaluation of many experimental results that may reveal to be very tedious. Here we propose an experimental and analytical workflow that eases the screening of thousands of designed RNA sequences at once. In particular, we have developed shapemap tools a customized software suite available at https://github.com/sargueil-citcom/shapemap-tools .
RNA 设计是合成生物学和基于 RNA 的治疗未来发展的主要挑战。高效准确的 RNA 设计管道的开发基于反复试验的策略。此类算法的快速发展需要在短时间内测定许多 RNA 序列的特性。高通量 RNA 结构化学探测技术（如 SHAPE-MaP）允许快速、大规模地测定 RNA 结构和相互作用。然而，设计序列的混杂性可能仅相差一个核苷酸，这需要特别注意。此外，还需要分析和评估许多可能非常繁琐的实验结果。在这里，我们提出了一种实验和分析工作流程，可方便地同时筛选数千个设计的 RNA 序列。特别是，我们开发了 shapemap 工具，这是一个定制的软件套件，可在 https://github.com/sargueil-citcom/shapemap-tools 上获得。
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