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TitleMeasuring multisubunit mechanics of geometrically programmed colloidal assemblies via cryo-EM multi-body refinement.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 122, Issue 37, Page e2500716122, Year 2025
Publish dateSep 16, 2025
AuthorsThomas E Videbæk / Daichi Hayakawa / Michael F Hagan / Gregory M Grason / Seth Fraden / W Benjamin Rogers /
PubMed AbstractProgrammable self-assembly has recently enabled the creation of complex structures through precise control of the interparticle interactions and the particle geometries. Targeting ever more ...Programmable self-assembly has recently enabled the creation of complex structures through precise control of the interparticle interactions and the particle geometries. Targeting ever more structurally complex, dynamic, and functional assemblies necessitates going beyond the design of the structure itself, to the measurement and control of the local flexibility of the intersubunit connections and its impact on the collective mechanics of the entire assembly. In this study, we demonstrate a method to infer the mechanical properties of multisubunit assemblies using cryogenic electron microscopy (cryo-EM) and RELION's multi-body refinement. Specifically, we analyze the fluctuations of pairs of DNA-origami subunits that self-assemble into tubules. By measuring the fluctuations of dimers using cryo-EM, we extract mechanical properties such as the bending modulus and interparticle spring constant. These properties are then applied to elastic models to predict assembly outcomes, which align well with experimental observations. This approach not only provides a deeper understanding of nanoparticle mechanics but also opens pathways to refining subunit designs to achieve precise assembly behavior. This methodology could have broader applications in the study of nanomaterials, including protein assemblies, where understanding the interplay of mechanical properties and subunit geometry is essential for controlling complex self-assembled structures.
External linksProc Natl Acad Sci U S A / PubMed:40924447 / PubMed Central
MethodsEM (single particle)
Resolution24.63 - 39.07 Å
Structure data

EMDB-48633: DNA-origami colloid for self-assembly of tubules: (10,0) monomer, bound pair from side 1 interaction
Method: EM (single particle) / Resolution: 24.63 Å

EMDB-48634: DNA-origami colloid for self-assembly of tubules: (10,0) monomer, bound pair from side 2 interaction
Method: EM (single particle) / Resolution: 27.58 Å

EMDB-48635: DNA-origami colloid for self-assembly of tubules: (10,0) monomer, bound pair from side 3 interaction
Method: EM (single particle) / Resolution: 28.78 Å

EMDB-48636: DNA-origami colloid for self-assembly of tubules: (10,0) monomer, bound hexamer
Method: EM (single particle) / Resolution: 39.07 Å

EMDB-48637: DNA-origami colloid for self-assembly of tubules: (10,0) monomer, twist corrected
Method: EM (single particle) / Resolution: 25.32 Å

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