Engineering Cell Surface Function with DNA Origami

A specific and reversible method is reported to engineer cell‐membrane function by embedding DNA‐origami nanodevices onto the cell surface. Robust membrane functionalization across epithelial, mesenchymal, and nonadherent immune cells is achieved with DNA nanoplatforms that enable functions including the construction of higher‐order DNA assemblies at the cell surface and programed cell–cell adhesion between homotypic and heterotypic cells via sequence‐specific DNA hybridization. It is anticipated that integration of DNA‐origami nanodevices can transform the cell membrane into an engineered material that can mimic, manipulate, and measure biophysical and biochemical function within the plasma membrane of living cells.     

Controlling the formation of DNA origami structures with external signals

Degradable Newkome-type and polylysine dendrons functionalized with spermine surface units are used to control the formation of DNA origami structures. The intact dendrons form polyelectrolyte complexes with the scaffold strands, therefore blocking the origami formation. Degradation of the dendron with an optical trigger or chemical reduction leads to the release of the DNA scaffold and efficient formation of the desired origami structure. These results provide new insights towards realizing responsive materials with DNA origami.     

Synthetic Transient Crosslinks Program the Mechanics of Soft,Biopolymer‐Based Materials

Actin networks are adaptive materials enabling dynamic and static functions of living cells. A central element for tuning their underlying structural and mechanical properties is the ability to reversibly connect, i.e., transiently crosslink, filaments within the networks. Natural crosslinkers, however, vary across many parameters. Therefore, systematically studying the impact of their fundamental properties like size and binding strength is unfeasible since their structural parameters cannot be independently tuned. Herein, this problem is circumvented by employing a modular strategy to construct purely synthetic actin crosslinkers from DNA and peptides. These crosslinkers mimic both intuitive and noncanonical mechanical properties of their natural counterparts. By isolating binding affinity as the primary control parameter, effects on structural and dynamic behaviors of actin networks are characterized. A concentration‐dependent triphasic behavior arises from both strong and weak crosslinkers due to emergent structural polymorphism. Beyond a certain threshold, strong binding leads to a nonmonotonic elastic pulse, which is a consequence of self‐destruction of the mechanical structure of the underlying network. The modular design also facilitates an orthogonal regulatory mechanism based on enzymatic cleaving. This approach can be used to guide the rational design of further biomimetic components for programmable modulation of the properties of biomaterials and cells.     

Interfacing DNA hydrogels with ceramics for biofunctional architectural materials

The development of architectural components with the capabilities of biological systems could lead to the realization of biofunctional, dynamic, interactive, and self-sustaining “living” architecture. One route to interfacing biological systems with architectural materials is functionalization with biomolecules. In particular, functionalization of surfaces with DNA incorporates both informational and active properties such as the ability to produce proteins. However, direct conjugation to surfaces can degrade biomolecule activity, reduce reaction kinetics, and limit available binding sites. Integration of DNA into a hydrogel matrix that is conjugated to the surface can overcome these limitations. Here, DNA encoding genetic information is converted into a hydrogel matrix, termed Meta P-gel. The unique mechanical properties of Meta P-gel allow it to adsorb to patterned ceramic surfaces in a spatially controlled manner. Simultaneously, Meta P-gel retains the biological ability to produce proteins, achieving spatial control over protein synthesis for potential applications in living architecture. Finally, Meta P-gel-based functionalization is applied to create stable protein gradients in situ, further exemplifying its applicability beyond architecture. These experiments are a first step toward continuous and stable protein expression from spatially controlled DNA hydrogels that would enable applications in biotechnological fields such as biosensor development and screening, and more broadly, in architectural fields such as fabrication of bioactive and bio-responsive ceramics for building façade design.     

结构DNA纳米技术:利用链霉亲和素-生物素相互作用增强DNA纳米结构的稳定性(英文)

实现纳米尺寸物体的合理设计与组装是纳米技术与精密工程的主要目标之一.DNA因其双链相互作用和螺旋几何构型的可预测性而使其成为构建纳米尺度结构的优秀建筑基元.DNA纳米结构在溶液状况改变时易分解.为提高DNA纳米结构的稳定性,一个链霉亲和素-生物素复合单元被引入到该纳米结构中.凝胶测试与熔点测试均证实链霉亲和素-生物素复合有助于提高DNA纳米结构的稳定性.该方法可广泛用于解决结构DNA纳米技术中的类似问题.     

Multicomponent DNA Polymerization Motor Gels

Hydrogels with the ability to change shape in response to biochemical stimuli are important for biosensing, smart medicine, drug delivery, and soft robotics. Here, a family of multicomponent DNA polymerization motor gels with different polymer backbones is created, including acrylamide‐co‐bis‐acrylamide (Am‐BIS), poly(ethylene glycol) diacrylate (PEGDA), and gelatin‐methacryloyl (GelMA) that swell extensively in response to specific DNA sequences. A common mechanism, a polymerization motor that induces swelling is driven by a cascade of DNA hairpin insertions into hydrogel crosslinks. These multicomponent hydrogels can be photopatterned into distinct shapes, have a broad range of mechanical properties, including tunable shear moduli between 297 and 3888 Pa and enhanced biocompatibility. Human cells adhere to the GelMA‐DNA gels and remain viable during ≈70% volumetric swelling of the gel scaffold induced by DNA sequences. The results demonstrate the generality of sequential DNA hairpin insertion as a mechanism for inducing shape change in multicomponent hydrogels, suggesting widespread applicability of polymerization motor gels in biomaterials science and engineering.     

Smart Drug Delivery Nanocarriers with Self‐Assembled DNA Nanostructures

Self‐assembled DNA nanostructures have emerged as a type of nano‐biomaterials with precise structures, versatile functions and numerous applications. One particularly promising application of these DNA nanostructures is to develop universal nanocarriers for smart and targeted drug delivery. DNA is the genetic material in nature, and inherently biocompatible. Nevertheless, cell membranes are barely permeable to naked DNA molecules, either single‐ or double‐ stranded; transport across the cell membrane is only possible with the assistance of transfection agents. Interestingly, recent studies revealed that many DNA nanostructures could readily go into cells with high cell uptake efficiency. In this Progress Report, we will review recent advances on using various DNA nanostructures, e.g., DNA nanotubes, DNA tetrahedra, and DNA origami nanorobot, as drug delivery nanocarriers, and demonstrate several examples aiming at therapeutic applications with CpG‐based immunostimulatory and siRNA‐based gene silencing oligonucleotides.     

硼基材料在表面工程上应用的潜力

全面阐述了硼基材料适于表面工程上应用的各种潜在性能与特点，并分析了其在表面工程上的各种应用前景。     

Programming Motions of DNA Origami Nanomachines

DNA nanotechnology enables the precise fabrication of DNA‐based machines with nanoscale dimensions. A wide range of DNA nanomachines are designed, which can be activated by specific inputs to perform various movement and functions. The excellent rigidity and unprecedented addressability of DNA origami have made it an excellent platform for manipulating and investigating the motion behaviors of DNA machines at single‐molecule level. In this Concept, power supply, machine actuation, and motion behavior of DNA machines on origami platforms are summarized and classified. The strategies utilized for programming motion behavior of DNA machines on DNA origami are also discussed with representative examples. The challenges and outlook for future development of manipulating DNA nanomachines at the single molecule level are presented and discussed.     

Self-Assembly of DNA Nanostructures in Different Cations

The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions that restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions are used so far (typically Mg²⁺ and Na⁺). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (~134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca²⁺, Ba²⁺, Na⁺, K⁺ and Li⁺ and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na⁺, K⁺ and Li⁺) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg²⁺, Ca²⁺ and Ba²⁺). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.     

Rhombic‐Shaped Nanostructures and Mechanical Properties of 2D DNA Origami Constructed with Different Crossover/Nick Designs

DNA origami methods enable the fabrication of various nanostructures and nanodevices, but their effective use depends on an understanding of their structural and mechanical properties and the effects of basic structural features. Frequency‐modulation atomic force microscopy is introduced to directly characterize, in aqueous solution, the crossover regions of sets of 2D DNA origami based on different crossover/nick designs. Rhombic‐shaped nanostructures formed under the influence of flexible crossovers placed between DNA helices are observed in DNA origami incorporating crossovers every 3, 4, or 6 DNA turns. The bending rigidity of crossovers is determined to be only one‐third of that of the DNA helix, based on interhelical electrostatic forces reported elsewhere, and the measured pitches of the 3‐turn crossover design rhombic‐shaped nanostructures undergoing negligible bending. To evaluate the robustness of their structural integrity, they are intentionally and simultaneously stressed using force‐controlled atomic force microscopy. DNA crossovers are verified to have a stabilizing effect on the structural robustness, while the nicks have an opposite effect. The structural and mechanical properties of DNA origami and the effects of crossovers and nicks revealed in this paper can provide information essential for the design of versatile DNA origami structures that exhibit specified and desirable properties.     

Orthogonal protein decoration of DNA nanostructures

The development of robust DNA-protein coupling techniques is mandatory for applications of DNA nanostructures in biomedical diagnostics, fundamental biochemistry, and other fields in biomolecular nanosciences. The use of self-labeling fusion proteins, which are orthogonal to biotin-streptavidin and antibody-antigen interactions, is described for the site-selective protein decoration of two exemplary DNA nanostructures: a four-way junction X-tile motif and a 3D DNA tetrahedron. Multifunctional DNA superstructures bearing up to four different proteins are generated and characterized by electrophoresis and microplate-based functionality assays. Steric and electrostatic interactions are identified as critical parameters controlling the efficiency of DNA-protein ligation. The results indicate that this method is versatile and broadly applicable, not only for the functionalization of DNA architectures but also for the site-specific decoration of other molecular materials and devices containing several different proteins.     

Spiral Patterning of Au Nanoparticles on Au Nanorod Surface to Form Chiral AuNR@AuNP Helical Superstructures Templated by DNA Origami

Plasmonic motifs with precise surface recognition sites are crucial for assembling defined nanostructures with novel functionalities and properties. In this work, a unique and effective strategy is successfully developed to pattern DNA recognition sites in a helical arrangement around a gold nanorod (AuNR), and a new set of heterogeneous AuNR@AuNP plasmonic helices is fabricated by attaching complementary‐DNA‐modified gold nanoparticles (AuNPs) to the predesigned sites on the AuNR surface. AuNR is first assembled to one side of a bifacial rectangular DNA origami, where eight groups of capture strands are selectively patterned on the other side. The subsequently added link strands make the rectangular DNA origami roll up around the AuNR into a tubular shape, therefore giving birth to a chiral patterning of DNA recognition sites on the surface of AuNR. Following the hybridization with the AuNPs capped with the complementary strands to the capture strands on the DNA origami, left‐handed and right‐handed AuNR@AuNP helical superstructures are precisely formed by tuning the pattern of the recognition sites on the AuNR surface. Our strategy of nanoparticle surface patterning innovatively realizes hierarchical self‐assembly of plasmonic superstructures with tunable chiroptical responses, and will certainly broaden the horizon of bottom‐up construction of other functional nanoarchitectures with growing complexity.     

Solution‐Controlled Conformational Switching of an Anchored Wireframe DNA Nanostructure

Self‐assembled DNA origami nanostructures have a high degree of programmable spatial control that enables nanoscale molecular manipulations. A surface‐tethered, flexible DNA nanomesh is reported herein which spontaneously undergoes sharp, dynamic conformational transitions under physiological conditions. The transitions occur between two major macrostates: a spread state dominated by the interaction between the DNA nanomesh and the BSA/streptavidin surface and a surface‐avoiding contracted state. Due to a slow rate of stochastic transition events on the order of tens of minutes, the dynamic conformations of individual structures can be detected in situ with DNA PAINT microscopy. Time series localization data with automated imaging processing to track the dynamically changing radial distribution of structural markers are combined. Conformational distributions of tethered structures in buffers with elevated pH exhibit a calcium‐dependent domination of the spread state. This is likely due to electrostatic interactions between the structures and immobilized surface proteins (BSA and streptavidin). An interaction is observed in solution under similar buffer conditions with dynamic light scattering. Exchanging between solutions that promote one or the other state leads to in situ sample‐wide transitions between the states. The technique herein can be a useful tool for dynamic control and observation of nanoscale interactions and spatial relationships.     

Self‐Assembly of DNA Origami Heterodimers in High Yields and Analysis of the Involved Mechanisms

Efficient fabrication of structurally and functionally diverse nanomolecular devices and machines by organizing separately prepared DNA origami building blocks into a larger structure is limited by origami attachment yields. A general method that enables attachment of origami building blocks using ‘sticky ends' at very high yields is demonstrated. Two different rectangular origami monomers are purified using agarose gel electrophoresis conducted in solute containing 100 × 10^?3 m NaCl, a treatment that facilitates the dissociation of most of the incorrectly hybridized origami structures that form through blunt‐end interactions during the thermal annealing process and removes these structures as well as excess strands that otherwise interfere with the desired heterodimerization reaction. Heterodimerization yields of gel‐purified monomers are between 98.6% and 99.6%, considerably higher than that of monomers purified using the polyethylene glycol (PEG) method (88.7–96.7%). Depending on the number of PEG purification rounds, these results correspond to about 4‐ to 25‐fold reduction in the number of incorrect structures observed by atomic force microscopy. Furthermore, the analyses of the incorrect structures observed before and after the heterodimerization reactions and comparison of the purification methods provide valuable information on the reaction mechanisms that interfere with heterodimerization.     

3D Lattice Engineering of Nanoparticles by DNA Shells

With the development of structural DNA nanotechnology, DNA has now far exceeded its original function: as a genetic code. It can, in principle, self‐assemble into desired shapes with accurate size. Moreover, it can perform as a functional linker to program other materials by grafting DNA onto these materials. Nanoparticles, both inorganic and organic, can now be programmatically assembled into complex 3D superlattices with high order when guided by DNA. By encoding functions into the as‐assembled nanoparticles, materials with excellent collective effects may be invented. Here, how nanoparticles with different shapes or functions are successfully fabricated into 3D lattices with the help of DNA shells coated on the surface and how scientists can produce desired lattices by design are reviewed. The cases to achieve dynamic superlattices of nanoparticles by affecting the environment where DNA survives are also discussed.