Expandable DNA-origami rings as a nanomechanical platform for studying disordered nucleoporins

Cao, E.; Maffeo, C.; Beckert, L.; Kapinos, L.; Malonis, R. J.; Son, D.; Zhou, K.; Wang, Z.; Feng, Q.; Chandra, S.; Shen, Q.; Xiong, Y.; Lusk, C. P.; Lim, R.; Aksimentiev, A.; Lin, C.

doi:10.64898/2026.09.22.753628

bioRxiv · 10.64898/2026.09.22.753628

Expandable DNA-origami rings as a nanomechanical platform for studying disordered nucleoporins

Cao, E.·Maffeo, C.·Beckert, L.·Kapinos, L.·Malonis, R. J.·Son, D.·Zhou, K.·Wang, Z.·Feng, Q.·Chandra, S.·Shen, Q.·Xiong, Y.·Lusk, C. P.·Lim, R.·Aksimentiev, A.·Lin, C.

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Abstract

Phe-Gly-rich nucleoporins (FG-Nups) within the nuclear pore complex (NPC) form a diffusion barrier that controls the exchange of macromolecules between the nucleus and cytoplasm. The behaviors of these intrinsically disordered FG-Nups are fundamental to the NPC function but remain difficult to probe within the dynamic, native nuclear pore. To bridge this knowledge gap, here we build expandable DNA-origami rings with tunable elasticity and study FG-Nups site-specifically tethered in such mechanically responsive NPC mimics. The elastic deformation of DNA rings, measured by single-particle TEM, reveals the type (attraction or repulsion) and strength of FG-Nup interactions that shape the collective morphology of these unstructured proteins. Analyzing homotypic interactions of five FG-Nup species finds diverse FG-Nup behaviors that can be classified as repulsive/extended (Nsp1), moderately cohesive/extended (Nup62, Nup153, and Nup214), and strongly cohesive/compact (Nup98). Furthermore, we examine how FG-Nups' primary sequence, O-glycosylation, grafting density, and binding to nuclear transport receptors (NTRs) impact their biophysical state. For example, O-GlcNAcylation reduced FG-Nup cohesiveness, switching Nup98 from a collapsed state to more extended conformations. Our work thus elucidates spatially confined Nup-Nup and Nup-NTR interactions within an NPC-like nanopore, suggests a previously underappreciated role of FG-Nups in modulating NPC dilation, and establishes a generalizable method for studying multivalent interactions among disordered proteins.

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Cao, E., Maffeo, C., Beckert, L., Kapinos, L., Malonis, R. J., Son, D., Zhou, K., Wang, Z., Feng, Q., Chandra, S., Shen, Q., Xiong, Y., Lusk, C. P., Lim, R., Aksimentiev, A., Lin, C.. 2026-09-24. Expandable DNA-origami rings as a nanomechanical platform for studying disordered nucleoporins. https://doi.org/10.64898/2026.09.22.753628

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