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. 2025:2847:177-191.
doi: 10.1007/978-1-0716-4079-1_12.

SHAPE Probing to Screen Computationally Designed RNA

Pierre Hardouin #  1 , Francois-Xavier Lyonnet du Moutier #  1 , Bruno Sargueil  2
Affiliations

SHAPE Probing to Screen Computationally Designed RNA

Pierre Hardouin et al. Methods Mol Biol. 2025.

Abstract

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 .

Keywords: Chemical probing; Footprint; IPANEMAP; RNA structure prediction.

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References

    1. Smola MJ, Rice GM, Busan S, Siegfried NA, Weeks KM (2015) Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nat Protoc 10:1643. https://doi.org/10.1038/nprot.2015.103 - DOI - PubMed - PMC
    1. Siegfried NA, Busan S, Rice GM, Nelson JAE, Weeks KM (2014) RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat Methods 11:959–965. https://doi.org/10.1038/nmeth.3029 - DOI - PubMed - PMC
    1. Frezza E, Courban A, Allouche D, Sargueil B, Pasquali S (2019) The interplay between molecular flexibility and RNA chemical probing reactivities analyzed at the nucleotide level via an extensive molecular dynamics study. Methods 162–163:108–127. https://doi.org/10.1016/j.ymeth.2019.05.021 - DOI - PubMed
    1. Steen K-A, Rice GM, Weeks KM (2012) Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. J Am Chem Soc 134:13160–13163. https://doi.org/10.1021/ja304027m - DOI - PubMed - PMC
    1. Mlýnský V, Bussi G (2018) Molecular dynamics simulations reveal an interplay between SHAPE reagent binding and RNA flexibility. J Phys Chem Lett 9:313–318. https://doi.org/10.1021/acs.jpclett.7b02921 - DOI - PubMed

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