Effect of Thermodynamic and Environmental Factors on Crystallization of DNA‐Origami Superlattices

Diffraction-quality, ultraflexible protein single crystals engineered with DNA

DNA-functionalized colloidal nanoparticles assemble through flexible, nanoscale DNA hybridization interactions that limit atomic-level structural order. Here, we report a valence-centric strategy that enables DNA-bonded, protein single crystals with unconventional mechanical properties. An octameric enzyme, glutarate L-2-hydroxylase, was site- and number-selectively conjugated with eight self-complementary single-stranded DNA, yielding octavalent molecular bonds. The resulting conjugate assembled into the designed body-centered tetragonal crystals that diffracted to 1.42- to 2.61-angstrom resolution, with contacts mediated by B-form DNA helices spanning 17 to 25 angstroms. Increasing oligonucleotide length induces anisotropic lattice expansion while preserving atomic periodicity, even with partial DNA occupancy. Mechanistic studies suggest that the dynamic motion of unhybridized DNA facilitates crystallization, analogous to fluctuating electron clouds in atomic bonding. Compared with native protein crystals, DNA-hybridized crystals are 23-fold softer. These results challenge the assumption that flexibility is incompatible with structural order and establish a programmable framework for biomolecular crystallization and nanomaterials engineering with atomic precision.

Directing Assembly of Mesoscale Multi‐Shell Morphologies of DNA Origami Crystals

Nature builds hierarchically ordered materials, such as seashells, wood, and bones, through spatially and temporally regulated growth. Mimicking such a level of control in synthetic systems remains challenging, particularly in achieving multiscale organizations with prescribed nanoscale arrangements and desired material morphologies. In this study, we introduce a DNA‐based self‐assembly strategy for constructing diverse multi‐shell mesoscale morphologies from nanoscale lattices, enabling prescribed structural, and compositional 3D material patterns. Using DNA origami frames as modular monomers, we direct anisotropic epitaxial growth through addressable DNA frame binding motifs and encapsulate nanoparticles (NPs) in desired 3D patterns. Sequential monomer addition under thermodynamically favorable conditions enables shell growth through heterogeneous nucleation while minimizing unwanted homogeneous nucleation. We demonstrate that DNA‐encoded addressability enables epitaxial shell growth along specific lattice directions, yielding crystals with multilayered mesoscale organization, including tube‐like (sushi roll) and plate‐like (macaron) morphologies. Shell‐specific NP configurations and compositions are achieved through addressable and differentiated placement of NPs within each shell, as validated by small‐angle x‐ray scattering and cross‐sectional scanning transmission electron microscopy. We further demonstrate addressable NP release and reveal that shells modulate release kinetics. Together, these findings establish a platform for fabricating DNA origami crystals with programmable mesoscale morphologies, nanoscale structure, composition, and transport properties.

Pathway-resolved hierarchical self-assembly of biomimetic double-walled nanotubes.

Self-assembly, the spontaneous organization of molecular components into ordered structures without external intervention, offers a powerful route to complex nanomaterials. Yet the molecular pathways that govern hierarchical assembly, particularly under non-equilibrium conditions, often remain poorly understood. Here we establish an integrated experimental platform that couples microfluidic control of the assembly environment with multi-scale optical and structural probes, enabling direct correlation between morphological evolution and excitonic functionality during supramolecular growth. Using this approach, we track in real time the formation of double-walled nanotubes (DWNTs) from the amphiphilic cyanine dye C8S3, a synthetic analogue of the light-harvesting chlorosomes in green sulfur bacteria. The results show that the outer nanotube structures first, while the inner nanotube follows with a delay, ultimately giving rise to electronically coupled coaxial architectures. While the principal excitonic signatures and morphological motifs emerge within minutes of self-assembly, axial elongation and orientational refinement continue over tens of hours through a nucleation-elongation mechanism. Notably, suppressing local concentration gradients through more efficient mixing abolishes DWNT formation, establishing spatial heterogeneity as a key parameter governing hierarchical self-assembly. By linking structural evolution with excitonic functionality in real time, this combined platform provides a framework for dissecting non-equilibrium pathways in supramolecular materials.

Programmable Functional Silicification of DNA Origami Nanostructures.

The silicification of DNA origami nanostructures offers a powerful strategy for enhancing their mechanical stability and resistance against detrimental environmental conditions. In the past years, several studies have investigated key aspects of the silicification process, resulting in a variety of established protocols. However, until now, the silica coating generally served as a passive protective layer or as the base for the further deposition of inorganic materials, but it did not carry any additional functionality itself. Here, we introduce two complementary, programmable approaches for the direct fabrication of functionalized silica coatings of DNA origami nanostructures. First, we synthesized a fluorescein-bearing silica precursor which imparts fluorescence to the silica coating of both individual DNA origami nanostructures and crystals, enabling intracellular tracking of silica-stabilized structures. Second, we employed a silica precursor containing a disulfide bridge to generate a redox responsive silica coating that degrades in a reducing environment. By introducing functionality at the precursor level, our approach establishes silicification as a modular platform for constructing responsive and traceable DNA-based hybrid materials. These strategies expand the chemical scope of DNA nanotechnology and facilitate future applications in drug delivery and advanced materials science.

Colloidal Crystals Engineered with DNA and Perylenediimide Exhibit Symmetry-Breaking Charge Transfer

Perylenediimide (PDI) and its derivatives are widely studied for their photophysical and photochemical properties, making them promising candidates for photonic materials, organic semiconductors, and molecular qubits. However, the lack of control over their aggregation pathways and charge-transfer coupling severely limits their uses. Here, we report the synthesis of PDI-DNA bioconjugates as a new class of “programmable atom equivalents” (PAEs), in which a single PDI core is covalently linked to two DNA strands. Unlike conventional PAE superlattices formed by slow thermal annealing, the vapor-diffusion crystallization method enables the colloidal crystallization of PDI–DNA conjugates into large single-crystalline superlattices through cooperative DNA hybridization and PDI π–π stacking. The peripheral four sticky ends hybridize into a DNA framework, which serves as a scaffold, organizing the PDI cores into well-defined dimers, rather than disordered aggregates or micelles. The dimeric building units are rigid yet highly dynamic due to the intrinsic flexibility of the linkers, yielding superlattices with programmable PDI packing geometries and adaptiveness upon structural modifications. For most PDI crystals, PDI units stack continuously in one dimension to maximize interactions, which tend to hinder charge separation. Here, DNA not only encodes sequence-specific interactions but also sterically and electrostatically isolates PDI dimers as discrete photonic units into solid-state optically active materials. The structural tunability of the system can be readily adjusted by varying the PDI core or the linker length between the PDI core and the DNA shell. Notably, these superlattices exhibit photoinduced symmetry-breaking charge transfer distinct from that of monomers or micellar aggregates.

Programmable De Novo Design of Mesoporous Protein Crystal Frameworks