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bioRxiv · 10.64898/2026.09.26.754601

De novo design of functional RNAs through higher-order interactions

Yuan, T.·Wang, D.·Chen, X.-L.·Tao, H.-L.·Zheng, C.-C. Z.·Zhao, X.-C.·Tan, Y.-L.·Zhang, X.-H.·Tan, Z.-J.
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Abstract

Designing RNA sequences that reliably adopt functional three-dimensional structures remains a central challenge in RNA engineering because folding depends on cooperative interactions beyond canonical base pairing. Here we present DS3dRNA, an interaction-based framework for de novo RNA sequence design that combines a three-body statistical potential with physics-guided sequence sampling and supports design against multiple conformations. Across the evaluated benchmarks, DS3dRNA outperformed representative RNA inverse-design methods in native-sequence recovery and agreement between predicted and target structures. Energy-sequence-quality analyses further showed that lower design energies generally accompanied higher sequence recovery and macro-averaged F1 scores (MacroF1). Experimentally tested Mango II designs retained high-affinity fluorogenic activity, and five twister ribozyme designs yielded mean endpoint cleavage fractions of 37.7-50.6%, compared with 23.5% for the wild type. These results establish explicit higher-order interaction scoring as a complementary approach to emerging data-driven RNA design methods and provide a framework for designing functional RNAs from experimental or predicted structural ensembles.

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Yuan, T., Wang, D., Chen, X.-L., Tao, H.-L., Zheng, C.-C. Z., Zhao, X.-C., Tan, Y.-L., Zhang, X.-H., Tan, Z.-J.. 2026-09-26. De novo design of functional RNAs through higher-order interactions. https://doi.org/10.64898/2026.09.26.754601

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