Programmable Edge-to-Edge Assembly of RNA Nanostructures

Constructing complex three-dimensional RNA nanostructures requires precise molecular connectors for controlled self-assembly. Existing RNA-RNA connectors, such as kissing loops, are restricted to coaxial, end-to-end joining, limiting the range of accessible geometries. Here, we introduce the alpha kissing loop (alphaKL), a compact, sequence-programmable RNA connector that enables edge-to-edge helix association. The alphaKL combines a four-nucleotide kissing loop with minor- and major-groove triplex interactions that pre-organize an -shaped conformation compatible with co-transcriptional folding. Embedded into RNA origami tiles, alphaKLs drive multivalent assembly into filaments and lattices, visualized at nanoscale resolution by atomic force microscopy. All-atom molecular dynamics simulations reveal that triplex occupancy at each sequence position controls the preferred inter-helical angle. Cooperative backbone contacts progressively rigidify the multi-alphaKL interface beyond what individual motifs achieve alone. By linking helices along their edges rather than their ends, the alphaKL expands the structural design space of programmable RNA nanostructures, unlocking previously inaccessible architectures and applications.