Acoustically shaped DNA-programmable materials

The study addresses the challenge of translating precisely organized DNA-based nanostructures into controlled macroscale morphologies. While DNA-guided self-assembly enables nanoscale ordering and micron-scale crystal domains, thermodynamically governed processes favor equilibrium crystal habits and lose effectiveness as system size grows, limiting shape control at larger scales. The research question is whether combining thermodynamically controlled DNA-programmable assembly with out-of-equilibrium acoustic-field driving can shape materials at the millimeter scale while preserving nanoscale order. The purpose is to use standing surface acoustic waves (SSAW) to direct and enhance nucleation, growth, and fusion of DNA-origami crystal lattices into prescribed macroscale forms, thereby bridging structural control from nanometers to millimeters. This is important for realizing bulk materials and devices that leverage DNA nanotechnology’s precise nano-organization.

DNA-guided self-assembly and DNA origami enable construction of ordered 3D nanomaterials with programmable interactions and diverse inorganic framework architectures. Octahedral DNA frames with sticky ends can form simple cubic lattices whose equilibrium Wulff shape is a cube, and recent work has manipulated domain growth and morphology via differentiated bonds. However, crystal shape is often constrained by lattice type. External fields (light, magnetic, electric) have been used to control macroscale morphology but typically require specific material properties (conductivity, transparency, magnetic susceptibility), limiting applicability. Acoustic fields offer broader compatibility, requiring only an acoustic contrast factor between components and medium. SSAW have been used to align particles, assemble nanoparticles into microstructures, and manipulate reactions with lower power density and scalable working areas. These prior advances motivate applying SSAW to shape DNA-assembled materials at the macroscale while maintaining nanoscale order.

System and building blocks: Two complementary DNA octahedral origami frames (~30 nm edge length; edges are six-helix bundles, 84 bp) bearing four ssDNA sticky ends at each of six vertices self-assemble into a simple cubic lattice via sixfold vertex hybridization. DNA origami were designed in caDNAno, folded with M13mp18 scaffold and staples (TAE/Mg2+ buffer), purified by centrifugal filtration, and combined (20 nM each) to preform lattices via a 50→25 °C, ~72 h anneal.

Acoustic device and setup: Interdigital transducers (IDTs) fabricated by photolithography on a piezoelectric substrate were driven by a function generator to generate SSAW. A borosilicate glass capillary (1 mm inner width, 50 µm height, length 50 mm) containing sample was placed and coupled to the substrate with immersion oil between two IDTs. Operating parameters: sine wave at 19.34 MHz, 20 Vpp, generating SSAW with half-wavelength ~100 µm; nodes are linear regions of minimal pressure, separated by ~50 µm, with node length ~3 mm (set by ~3.5 mm IDT size). The setup was housed in a temperature-controlled stage for in situ optical imaging.

Acoustic pulsing protocol: SSAW applied in pulses to achieve specific spatiotemporal stimulation and induce local heating within the active region. Pulses were 50 ms (≈967k cycles at 19.34 MHz); inter-pulse period varied from 500 to 5000 ms. The ratio τ = period/pulse (values explored: 10, 15, 20, 30, 100; and no-wave control) was used to parameterize conditions.

Experimental workflows:

• Organization of preformed crystals: Preassembled micron-scale crystallites were loaded into the capillary, SSAW applied to translate and align crystallites to nodes, forming linear chains.
• Thermally assisted fusion under SSAW: After alignment, a reannealing protocol was applied—temperature raised to dissolve small crystals/nuclei while retaining larger crystals (narrowing size distribution), then slowly ramped down while maintaining SSAW to promote growth and contact-mediated fusion along nodes into elongated single-lattice entities. SEM verified fused, coherently coordinated lattices spanning multiple initial crystallites; AuNP-loaded lattices were also aligned to demonstrate cargo compatibility.
• Crystallization under acoustic stimulation: During nucleation and growth from monomers, SSAW pulses (fixed 50 ms pulse; varying τ) were applied in combination with thermal anneals at two cooling rates: fast (0.03 °C/min) and slow (0.01 °C/min). Resulting crystals were characterized by optical microscopy; SAXS assessed lattice structure.

Characterization and analysis: Brightfield microscopy tracked organization and morphology; SEM imaged fused structures; SAXS measured structure factors S(q), confirming simple cubic ordering. Crystal edge length was estimated from 2D areas (ImageJ/Fiji) by square-rooting area assuming cubic geometry; only crystals with clear edges were measured, across 5–10 images per condition, with ≥3 independent repeats per τ. A nucleation-and-growth model (Fokker–Planck framework) described distributions without SSAW using parameters derived from DNA thermodynamics and geometry (nucleation rate I as a single fit parameter). An infusion model incorporated SSAW effects: local heating suppressing nucleation by factor e^{−x} in the active region and an influx rate κ of nuclei/clusters from adjacent regions proportional to pulse frequency; the same κ and e^{−x} values were used across cooling rates and τ in fits.

• SSAW directs preformed DNA crystallites to standing-wave nodes, forming linear chains with node spacing ~50 µm and node lengths ~3 mm. Crystallites exhibit some facet alignment parallel to the transducer surface, likely minimizing cross-section to SSAW.
• Under a thermal reanneal while SSAW is applied, closely packed crystals within nodes fuse during regrowth into single, elongated entities composed of coherently coordinated lattices spanning multiple initial crystallites (confirmed by SEM). Linear assemblies of AuNP-loaded lattices were also formed.
• Applying SSAW pulses during nucleation and growth yields elongated morphologies at nodes and significantly increases crystal sizes for specific pulse regimes. Crystal size exhibits a non-monotonic dependence on τ = period/pulse; distributions broaden compared to no-wave controls.
• An optimal pulse regime at τ = 20 (1000 ms period, 50 ms pulse) produced the largest crystals, with edge lengths nearly doubling relative to no-wave controls. This optimum held across both fast (0.03 °C/min) and slow (0.01 °C/min) cooling rates.
• With fast cooling plus SSAW (τ = 20), followed by reanneal, elongated macroscale crystalline structures up to ~2 mm in length were obtained and could move between nodes as intact units, indicating fused single entities.
• SAXS showed that crystals formed under SSAW maintain the same simple cubic lattice as untreated crystals, indicating acoustic driving shapes mesoscale/millimeter-scale morphology without altering nanoscale organization.
• Mechanism: SSAW introduces (i) local heating in the active region that suppresses homogeneous nucleation and (ii) an influx of nuclei/small clusters from adjacent regions into the active region. The interplay of suppression and infusion explains the non-monotonic size vs. τ behavior: initial suppression reduces crystal number and increases size; stronger infusion at lower τ increases crystal number and reduces size.
• A simplified infusion model (suppression factor e^{−x}, infusion rate κ) coupled to a Fokker–Planck nucleation/growth framework quantitatively captured the observed distributions near optimal conditions, using the same κ and e^{−x} across cooling rates and τ.

The results demonstrate that out-of-equilibrium acoustic driving can deterministically shape macroscale morphology of DNA-programmable materials while preserving their DNA-encoded nanoscale order. SSAW aligns preformed crystallites and, with controlled reannealing, fuses them into coherent, elongated single-lattice entities. When applied during nucleation and growth, SSAW modulates the effective number of nuclei via local heating and influx from adjacent regions, which in turn controls final crystal sizes and morphology. The non-monotonic dependence of size on τ and the existence of an optimal pulsing window underscore the importance of spatiotemporal control of the acoustic field. SAXS confirms that acoustic shaping does not perturb the simple cubic nano-architecture, decoupling nanoscale ordering from macroscale morphology. Because acoustic manipulation requires only an acoustic contrast between components and medium, the approach is broadly applicable and offers a route to bridge structural control across six orders of magnitude (nm to mm), enabling device-scale architectures from precisely organized DNA-based building blocks.

Acoustic fields with tailored spatiotemporal profiles, combined with DNA-programmable assembly, enable control of material structure from nanometers to millimeters. SSAW directs, enhances, and fuses DNA-origami crystal lattices into elongated macroscale morphologies, with optimal pulsing (τ ≈ 20) producing markedly larger crystals across cooling rates while maintaining simple cubic nanoscale order. The method supports integration of functional cargo (e.g., AuNPs). Future directions include shaping beyond linear morphologies by modifying boundary conditions and transducer geometries to create complex 2D/3D patterns (e.g., Chladni-like patterns, acoustic holography), and integrating inorganic templating to realize device-scale materials for photonics, mechanics, electronics, and biomaterials.

• Current demonstrations primarily produce linear structures defined by SSAW node geometry; extending to more complex patterns requires different boundary conditions or transducer arrangements.
• Crystal size measurements were biased toward larger, well-defined crystals due to selection of objects with clear edges.
• The theoretical infusion model is intentionally simplified (acknowledged as oversimplified), though it captures trends near optimal conditions; parameters κ and e^{−x} are phenomenological.
• Local heating and influx of nuclei are inferred as the dominant SSAW effects and modeled accordingly; direct, spatially resolved quantification within the active region is limited to supplementary measurements of heating.
• Results were obtained for a specific DNA-origami octahedral system and device configuration (frequency, voltage, capillary dimensions), which may require adaptation for other systems.