Zhi-Jie Tan

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.

Multivalent cations are essential for DNA and RNA structures and their functions. However, how multivalent cations and their accompanying anions jointly reshape nucleic-acid mechanics, and why DNA and RNA respond so differently, remain unclear. Here we show using single-molecule magnetic tweezers that increasing multivalent cation concentrations first softens and then stiffens DNA due to charge inversion, whereas RNA first stiffens and then softens by over twofold. Our all-atom simulations reproduce these effects and reveal a physical mechanism: at low concentrations, multivalent cations clamp the RNA major groove, stiffening RNA; at higher concentrations, anions disrupt this groove clamping and promote local cation-clamping that distorts and softens RNA. The mechanism also explains changes in stretching modulus, contour length, and twist-stretch coupling. Our findings reveal that local cation-clamping sharply softens RNA and highlight the significant roles of anions in modulating RNA structure, providing a framework for tuning nucleic-acid mechanics in vitro for RNA-related applications.

RNAs play crucial roles in various important biological functions such as gene regulation and catalysis. The functions of RNAs are generally coupled to their structures as well as to the stability of the structure, which can strongly depend on ionic conditions. However, it is still a challenge to make reliable predictions for the structures and stability of RNAs in ion solutions. In this work, we developed a coarse-grained method involving temperature and ion effects for simulating RNA folding and three-dimensional (3D) structure prediction, named TiRNA. Extensive tests demonstrate that TiRNA can make successful predictions for 3D structures of RNAs, including pseudoknots and multi-way junctions, and for thermal stability of RNAs in ion solutions solely from sequences, as compared with the top existing methods. Moreover, TiRNA can also make reliable predictions for 3D structures and stability of RNAs in ion solutions based on inputting secondary structures.

The elasticities of RNAs are generally essential for their biological functions, and RNAs often become functional when interacting with their binding proteins. However, the effects of binding proteins on the elasticities of double-stranded (ds) RNAs, such as twist–stretch coupling, still remain little understood. Here, our extensive all-atom molecular dynamics simulations show that the twist–stretch coupling of dsRNAs can be reversed from positive to negative by their binding proteins. Our analyses revealed that such a reversing effect of binding proteins is attributed to the protein anchoring across the major groove of dsRNAs, which alters the dominating deformation pathway from a major-groove-mediated one to a helical-radius-mediated one through two base-pair parameters of slide and inclination. Meanwhile, the anchoring effect from binding proteins on dsRNAs is further ascribed to the strong electrostatic attractions between dsRNAs and the positively charged binding domain of the proteins.