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Lattice Engineering Through Nanoparticle–DNA Frameworks BNL-112667-2016-JA Lattice engineering through nanoparticle–DNA frameworks Ye Tian, Yugang Zhang, Tong Wang, Huolin L. Xin, Huilin Li and Oleg Gang Submitted to Nature Materials February 2016 Center for Functional Nanomaterials Brookhaven National Laboratory U.S. Department of Energy USDOE Office of Science (SC), Basic Energy Sciences (SC-22) Notice: This manuscript has been authored by employees of Brookhaven Science Associates, LLC under Contract No. DE- SC0012704 with the U.S. Department of Energy. The publisher by accepting the manuscript for publication acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. DISCLAIMER This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, nor any of their contractors, subcontractors, or their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or any third party’s use or the results of such use of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof or its contractors or subcontractors. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. Lattice engineering through nanoparticle–DNA frameworks Ye Tian1,Yugang Zhang1,Tong Wang2, Huolin L. Xin1, Huilin Li2,3 and Oleg Gang1* Advances in self-assembly over the past decade have demonstrated that nano- and microscale particles can be organized into a large diversity of ordered three-dimensional (3D) lattices. However, the ability to generate dierent desired lattice types from the same set of particles remains challenging. Here, we show that nanoparticles can be assembled into crystalline and open 3D frameworks by connecting them through designed DNA-based polyhedral frames. The geometrical shapes of the frames, combined with the DNA-assisted binding properties of their vertices, facilitate the well-defined topological connections between particles in accordance with frame geometry. With this strategy, dierent crystallographic lattices using the same particles can be assembled by introduction of the corresponding DNA polyhedral frames. This approach should facilitate the rational assembly of nanoscale lattices through the design of the unit cell. he progress in nanomaterial fabrication methods was for a powerful approach for 3D crystallization14,15,38, where phases can a long time motivated by the idea that self-assembly will be controlled by means of particle sizes, shapes, tailoring of DNA endow us with the ability to organize nanoparticles (NPs) shells23,33, and even in a dynamic manner by selective interaction T 39 in designed arrays. In reality, the particle characteristics have a triggering . Despite these significant advances, assembled phases profound effect on the assembled structure thus, a little room remain determined by particle details. Here, we propose a remains for structural design. Yet, it would be far more powerful conceptually different approach, in which we shift the problem of to have the ability to generate the different desired types of 3D lattice design from tailoring nanoscale particles, into forcing the lattice from the same particles. Such freedom of lattice engineering connection between isotropic particles by precisely engineered will permit the fabrication of targeted materials, with properties anisotropic linkages. Specifically, polyhedral 3D DNA origami40,41 that can be enhanced and manipulated by precise organization of frames, whose vertices connect DNA-encoded NPs (refs 42,43), functional components1–5. facilitate the establishment of local particle coordination that Colloids, often presented as a model of atomic systems, results in the formation of 3D ordered NP–DNA frameworks have revealed great insight into the fundamentals of crystal (Fig. 1). We demonstrate that the same kind of NPs can be formation6–9 and the role of particle nature10–12. Although an assembled into different types of lattice by employing appropriately extremely rich variety of lattices have been demonstrated12–15, the designed polyhedral frames. Moreover, the crystallographic type particular particle characteristics—such as sizes13,16,17, interactions, of the assembled lattice (framework) is correlated with the frame entropic and many-body effects18–21, and shape22–24—dominate geometry. Thus, our strategy potentially permits the deliberate lattice formation. These dependences are both natural and useful; engineering of the unit cell by controlling the shape of the particle- numerous investigations have detailed how particle characteristics connecting frames and does not require particle modifications. drive structure formation12,24–28. Whereas these studies uncovered This approach addresses the challenge articulated by Ned Seaman a great depth of physical insight, the goal of lattice `engineering' in his visionary work, more than three decades ago, that led to the remains elusive, owing to the complex dependences between the rise of the field of DNA nanotechnology44: how to create 3D lattices structural and energetic parameters of particles and lattices, and the that position guest species in a predetermined, regular manner. In necessity to tailor particles for each target lattice. this work, we designed45 five different DNA origami polyhedral Anisotropic interparticle interactions, induced by precise frames, including octahedron, cube, elongated square bipyramid arrangement of binding patches or by particle shaping, were (ESB), prism and triangular bipyramid (TBP) geometries, built considered as a means to simplify the lattice design. These using six-helix-bundle edges with lengths (depending on the particles have been extensively investigated for regulating phase frame shape) from 30 to 45 nm, as shown in Fig. 1 and detailed formation11,29,30, and diverse phases were predicted29. Several in Supplementary Methods. Every bundle has one single-stranded recent studies exploited directional interactions to create particle DNA chain extending from each of its ends. This chain can further clusters and arrays13,31–34. However, such approaches require hybridize with complementary DNA, which coats NPs uniformly. ample efforts in fabrication of building blocks with sophisticated Thus, for all our designs, the number of strands linking a frame anisotropic interactions. High-fidelity and high-yield fabrication of vertex to an individual NP is equal to the number of edges at these elaborate particles remains challenging, particularly on the the given vertex. The designed DNA frames thus connect NPs at nanoscale32,35–37. Besides, the resultant lattices are still determined by their vertices, establishing the overall lattice topology based on the specific particle design. DNA-based methods have emerged as frame geometry. 1 * ARTICLES Frames Nanoparticle−DNA framework Nanoparticle Particle−frame Framework assembly formation + Figure 1 | Lattice assembly through NP–DNA frameworks. NPs (yellow ball) capped with oligonucleotides (blue curves) are mixed with polyhedral DNA frames (from top to bottom): cube, octahedron, elongated square bipyramid (ESB), prism, triangular bipyramid (TBP). The frames are designed to have complementary strands at the vertices for NP binding. An aggregation (framework formation) is expected when NPs and the correspondingly encoded polyhedral frames are allowed to mix and to hybridize. NP–DNA frameworks might exhibit an ordered lattice for optimized NP sizes, linking motif and annealing process. The crystallographic symmetry of the assembled lattice is controlled by the shape of the interparticle linking frames, but not by the NPs themselves. This strategy thus enables ‘engineering’ the lattice and its unit cell. Polyhedral frames as topological linkers NP–DNA framework assembly Assembly of polyhedral origami frames was carried out using We first discuss the assembly of a 3D lattice using an octahedral M13mp18 DNA and staple strands (1:10 ratio) in 1×TAE frame46. To prepare the assembled system, DNA octahedra and buffer with 12.5 mM Mg2C, annealed slowly from 90 ◦C to room NPs (10 nm core) were mixed at a ratio of 1:2. To explore the temperature (see Supplementary Information). Proper assembly role of particle–vertex linkages on the phase formation, we studied was confirmed using gel electrophoresis45 (Supplementary the assembly behaviour as a function of the length, d, of the Fig. 1), and negative-staining transmission electron microscopy DNA motifs connecting the frame vertices to the NP. Partially (Supplementary Fig. 3). Cryo-electron microscopy (EM) with complementary single-stranded (ss) DNA strands extend from 3D reconstruction, as described previously46, was also applied to the octahedra vertices and particles respectively—so-called `sticky visualize the assembled DNA frames (Supplementary Figs 4–7). ends’—providing attachment of NPs to frames. We regulate the We probed the ability of the frame to
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