Origami Templates Research Articles

Precision fabrication of polymer nanostructures on recyclable DNA template

AbstractThe fabrication of precisely patterned polymers at the nanoscale is of critical importance. We have previously succeeded in creating various nanopatterned polymers with nanoscale resolution through the use of in situ atom transfer radical polymerization (ATRP) techniques on deoxyribonucleic acid (DNA) origami. However, separating nanopatterned polymers from the origami template without damaging the origami presents a significant challenge, thereby increasing costs and limiting the development of applications involving nanopatterned polymers. Here, we achieved spatially and temporally controlled release of DNA origami templates through photo‐regulation by incorporating azobenzene‐modified DNA into the initiator. Under UV exposure, azobenzene isomerization rapidly induces the disassociation of patterned polymers from the origami template at ambient temperatures, without damaging the DNA origami. Additionally, the released origami template can be reused as a template for the cyclic production of nanopatterned polymers. This method provides a pathway for the large‐scale production of patterned polymers at reduced costs and facilitates dynamic control over the polymer‐DNA complex, with potential applications in both the biomedical and chemical fields.

Controlling Nanoparticle Distance by On-Surface DNA-Origami Folding.

DNA origami is a flexible platform for the precise organization of nano-objects, enabling numerous applications from biomedicine to nano-photonics. Its huge potential stems from its high flexibility that allows customized structures to meet specific requirements. The ability to generate diverse final structures from a common base by folding significantly enhances design variety and is regularly occurring in liquid. This study describes a novel approach that combines top-down lithography with bottom-up DNA origami techniques to control folding of the DNA origami with the adsorption on pre-patterned surfaces. Using this approach, tunable plasmonic dimer nano-arrays are fabricated on a silicon surface. This involves employing electron beam lithography to create adsorption sites on the surface and utilizing self-organized adsorption of DNA origami functionalized with two gold nanoparticles (AuNPs). The desired folding of the DNA origami helices can be controlled by the size and shape of the adsorption sites. This approach can for example be used to tune the center-to-center distance of the AuNPs dimers on the origami template. To demonstrate this technique's efficiency, the Raman signal of dye molecules (carboxy tetramethylrhodamine, TAMRA) coated on the AuNPs surface are investigated. These findings highlight the potential of tunable DNA origami-based plasmonic nanostructures for many applications.

Direct Measurement of Optical Resonance Modes in Gold Meta-Atoms Fabricated by Metallization of Triangle- and V-Shaped DNA Origami Templates

Direct Measurement of Optical Resonance Modes in Gold Meta-Atoms Fabricated by Metallization of Triangle- and V-Shaped DNA Origami Templates

Planar oligomerization of reconfigurable gold nanorod dimers.

Reconfigurable chiral plasmonic complexes are fabricated by planar assembly of multiple individual gold nanorod dimers using DNA origami templates. Additionally, each chiral center can be controlled to switch among achiral, left-handed, and right-handed states. We demonstrate that their overall circular dichroism is determined by the coupling of individual chiral centers and is heavily influenced by the precise number and arrangement of these centers. Our study offers a novel self-assembly method for constructing intricate and dynamic chiral plasmonics as well as investigating the interactions among several plasmonic chiral centers.

Accessible hotspots for single-protein SERS in DNA-origami assembled gold nanorod dimers with tip-to-tip alignment

The label-free identification of individual proteins from liquid samples by surface-enhanced Raman scattering (SERS) spectroscopy is a highly desirable goal in biomedical diagnostics. However, the small Raman scattering cross-section of most (bio-)molecules requires a means to strongly amplify their Raman signal for successful measurement, especially for single molecules. This amplification can be achieved in a plasmonic hotspot that forms between two adjacent gold nanospheres. However, the small (≈1−2 nm) gaps typically required for single-molecule measurements are not accessible for most proteins. A useful strategy would thus involve dimer structures with gaps large enough to accommodate single proteins, whilst providing sufficient field enhancement for single-molecule SERS. Here, we report on using a DNA origami scaffold for tip-to-tip alignment of gold nanorods with an average gap size of 8 nm. The gaps are accessible to streptavidin and thrombin, which are captured at the plasmonic hotspot by specific anchoring sites on the origami template. The field enhancement achieved for the nanorod dimers is sufficient for single-protein SERS spectroscopy with sub-second integration times. This design for SERS probes composed of DNA origami with accessible hotspots promotes future use for single-molecule biodiagnostics in the near-infrared range.

Detection of SARS-CoV-2 RNA with a plasmonic chiral biosensor

The detection of SARS-CoV-2 infection is crucial for effective prevention and surveillance of COVID-19. In this study, we report the development of a novel detection assay named CENSOR that enables sensitive and specific detection of SARS-CoV-2 RNA using a plasmonic chiral biosensor in combination with CRISPR-Cas13a. The chiral biosensor was designed by assembling gold nanorods (AuNR) into three-dimensional plasmonic architectures of controllable chirality on a DNA origami template. This modular assembly mode enhances the flexibility and adaptability of the sensor, thereby improving its universality as a sensing platform. In the presence of SARS-CoV-2 RNA, the CRISPR-Cas13a enzyme triggers collateral cleavage of RNA molecules, resulting in a differential chiral signal readout by the biosensor compared to when there are no RNA targets present. Notably, even subtle variations in the concentration of SARS-CoV-2 RNA can provoke significant changes in chiral signals after preamplification of RNA targets (calculated LOD: 0.133 aM), which establishes the foundation for quantitative detection. Furthermore, CENSOR demonstrated high sensitivity and accuracy in detecting SARS-CoV-2 RNA from clinical samples, suggesting its potential application in clinical settings for viral detection beyond SARS-CoV-2.

Reconfigurable pH-Responsive DNA Origami Lattices.

DNA nanotechnology enables straightforward fabrication of user-defined and nanometer-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows for encoding of the DNA object shape but also it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these "robotic" features of DNA nanostructures are usually demonstrated for only small, discrete, and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami-based lattice can be assembled into two different configurations ("open" and "closed" states) on a mica substrate and further switched from one to the other distinct state upon a pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with "pH-latches" that form Hoogsteen-type triplexes at low pH. In short, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice. To further emphasize the feasibility of the method, we also demonstrate the formation of pH-responsive 2D gold nanoparticle lattices. We believe this work can bridge the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity.

High-entropy alloy nanopatterns by prescribed metallization of DNA origami templates

High-entropy multimetallic nanopatterns with controlled morphology, composition and uniformity hold great potential for developing nanoelectronics, nanophotonics and catalysis. Nevertheless, the lack of general methods for patterning multiple metals poses a limit. Here, we develop a DNA origami-based metallization reaction system to prescribe multimetallic nanopatterns with peroxidase-like activities. We find that strong coordination between metal elements and DNA bases enables the accumulation of metal ions on protruding clustered DNA (pcDNA) that are prescribed on DNA origami. As a result of the condensation of pcDNA, these sites can serve as nucleation site for metal plating. We have synthesized multimetallic nanopatterns composed of up to five metal elements (Co, Pd, Pt, Ag and Ni), and obtained insights on elemental uniformity control at the nanoscale. This method provides an alternative pathway to construct a library of multimetallic nanopatterns.

Additively Manufactured Mechanical Metamaterial‐Based Pressure Sensor with Tunable Sensing Properties for Stance and Motion Analysis

Mechanical metamaterials are attracting considerable attention due to their unique properties not found in natural materials. Advanced geometrical shapes such as Menger cubes, origami templates, and gyroids offer exciting avenues for device engineering. In addition, the recent developments of various additive manufacturing technologies have expanded materials selection and geometrical complexities. Herein, a piezoresistive pressure sensor based on a 3D‐printed gyroid structure with a conformal coating of carbon nanotubes (CNTs) is presented. The gyroid structures are printed using fused deposition modeling (FDM) 3D printing with thermoplastic polyurethane (TPU), providing mechanical robustness even at low densities. By altering the relative density of the gyroid structure, Young's modulus can be tailored, ranging from 0.32 MPa at 30% relative density and 3.61 MPa at 80% relative density. The presented gyroid‐based pressure sensor achieves a wide sensing range of up to 1.45 MPa and a high sensitivity of 2.68 MPa−1. The sensor is integrated into a shoe for wearable applications, demonstrating its mechanical robustness and potential for human stance and motion monitoring.

Recent Advances of DNA Origami Technology and Its Application in Nanomaterial Preparation

In recent years, the unrivalled self‐assembly properties of DNA molecules have driven the rapid development of a new class of DNA self‐assembly technology—DNA origami technology. Over the past decade, this technology has enabled the construction of DNA nanostructures with different shapes, such as 2D and 3D structures. Meanwhile, the application of DNA origami are also developed rapidly. DNA origami structures are widely used in nanomaterial preparation and drug delivery due to their characteristics of accurate addressability, excellent programmability, and good biocompatibility, especially in the field of nanomaterial preparation. Such structures provide a new platform to construct nanomaterials with high precision. Herein, the development of DNA origami technology is introduced, and the research progress of 2D and 3D DNA origami in the past two decades is systematically summarized. Then, the application of DNA origami template in nanomaterial preparation is emphasized. Finally, the main challenges and opportunities for nanomaterials fabrication based on DNA origami technology are illustrated.

One-Step Ligand-Exchange Method to Produce Quantum Dot-DNA Conjugates for DNA-Directed Self-Assembly.

To address the current challenges in making bright, stable, and small DNA-functionalized quantum dots (QDs), we have developed a one-step ligand-exchange method to produce QD-DNA conjugates from commonly available hydrophobic QDs. We show that by systematically adjusting the reaction conditions such as ligand-to-nanoparticle molar ratio, pH, and solvent composition, stable and highly photoluminescent water-soluble QD-DNA conjugates with relatively high ligand loadings can be produced. Moreover, by site specifically binding these QD-DNA conjugates to a DNA origami template, we demonstrate that these bioconjugates have sufficient colloidal stability for DNA-directed self-assembly. Fluorescence quenching by an adjacent gold nanoparticle (AuNP) was demonstrated. Such QD-AuNP dimers may serve as biosensors with improved sensitivity and reproducibility. Moreover, our simple method can facilitate the assembly of QDs into more complex superlattices and discrete clusters that may enable novel photophysical properties.

A Reconfigurable Nanophotonic Heterostructure Engineered by a DNA Origami Switch.

DNA origami has been widely used to construct nanophotonic structures due to its unparallel capability in assembling photonic nanomaterials with nanometer precision. Nevertheless, the majority of fabricated fluorescence-based nanophotonic systems so far operate in the ultraviolet-visible (UV-Vis) region, which are accompanied by limitations of shallow penetration and potential light damage. Herein, we constructed a reconfigurable nanophotonic heterostructure by integrating an upconversion nanoparticle (UCNP) and a gold nanorod (AuNR) on a DNA origami switch (DOS) template. With the unique anti-Stokes luminescence of UCNP whose excitation wavelength is mostly located in the near-infrared (NIR) region, the obtained reconfigurable nanophotonic system can be excited by 980 laser light and generates visible light emission. In our nanophotonic system, the DNA origami template serves as a switch to reversibly tune the optical properties of UCNP. The construction of this nanophotonic heterostructure expands the toolbox of DNA origami-based nanophotonic systems that may hold great potential in optical biosensing and imaging.

Pattern Recognition Directed Assembly of Plasmonic Gap Nanostructures for Single-Molecule SERS.

Gold nanocubes (AuNCs) with tunable localized surface plasmon resonance properties are good candidates for plasmonic gap nanostructures (PGNs) with hot spots (areas with intense electric field localization). Nevertheless, it remains challenging to create shape-controllable nanogaps between AuNCs. Herein, we report a DNA origami directed pattern recognition strategy to assemble AuNCs into PGNs. By tuning the position and number of capture strands on the DNA origami template, different geometrical configurations of PGNs with nanometer-precise and shape-controllable gaps are created. The localized field enhancement in these gaps can generate hot spots that are in accordance with finite difference time domain simulations. Benefiting from the single Raman probe molecule precisely anchored at these nanogaps, the dramatic enhanced electromagnetic fields localized in hot spots arouse stronger single-molecule SERS (SM-SERS) signals. This method can be utilized in the design of ultrahigh-sensitivity photonic devices with tailored optical properties and SERS-based applications.

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching.

Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.

A DNA‐Based Plasmonic Nanodevice for Cascade Signal Amplification

AbstractHere, we describe a DNA circuit‐aided, origami nanodevice‐based plasmonic system, which performs DNA‐regulated, cascade amplification of faint chemical/biological signals. In this system, two gold‐nanorods (GNRs) are co‐assembled onto a DNA lock‐containing, tweezer‐like DNA origami template. Logic circuits serve as recognition and amplification elements for specific messengers, producing DNA keys for driving conformational changes of the plasmonic nanodevices. In the presence of input signals including nucleic acids, adenosines, chiral tyrosinamides or specific receptors expressed by tumor cells, the plasmonic nanodevices can be activated to perform dynamic structural motions, reporting robust responses via plasmonic circular dichroism (CD) spectral changes. This DNA nanodevice‐based system provides a different design to enrich the strategies for constructing synthetic nanomachines, enabling the customized bottom‐up nanostructure construction for sensitive biological signaling.

A DNA-Based Plasmonic Nanodevice for Cascade Signal Amplification.

Here, we describe a DNA circuit-aided, origami nanodevice-based plasmonic system, which performs DNA-regulated, cascade amplification of faint chemical/biological signals. In this system, two gold-nanorods (GNRs) are co-assembled onto a DNA lock-containing, tweezer-like DNA origami template. Logic circuits serve as recognition and amplification elements for specific messengers, producing DNA keys for driving conformational changes of the plasmonic nanodevices. In the presence of input signals including nucleic acids, adenosines, chiral tyrosinamides or specific receptors expressed by tumor cells, the plasmonic nanodevices can be activated to perform dynamic structural motions, reporting robust responses via plasmonic circular dichroism (CD) spectral changes. This DNA nanodevice-based system provides a different design to enrich the strategies for constructing synthetic nanomachines, enabling the customized bottom-up nanostructure construction for sensitive biological signaling.

Polarization-dispersive imaging spectrometer for scattering circular dichroism spectroscopy of single chiral nanostructures

Circular dichroism spectroscopy is one of the most important tools in nanoscopic chiroptics. However, there is lack of simple, fast and reliable method for measuring the circular dichroism responses of single nanostructures. To tackle this issue, we report a polarization-dispersive imaging spectrometer which is capable of measuring the scattering circular dichroism response of a single chiral nanostructure with a single shot. Using this technique, we studied the scattering circular dichroism spectra of a model system, the vertically coupled plasmonic nanorod pair. Both experimental and theoretical results indicate that the polarization-dispersive spectrometer measures the imaginary part of nonlocal susceptibility of the structure. We further applied the technique to 3-dimensional Au nanorod structures assembled on DNA origami templates together with correlated scanning electron microscopic measurements. Rich chiroptical phenomena were unveiled at the single nanostructure level.

DNA Origami-Encoded Integration of Heterostructures.

Integrating dissimilar materials at the nanoscale is crucial for modern electronics and optoelectronics. The structural DNA nanotechnology provides a universal platform for precision assembly of materials; nevertheless, heterogeneous integration of dissimilar materials with DNA nanostructures has yet to be explored. We report a DNA origami-encoded strategy for integrating silica-metal heterostructures. Theoretical and experimental studies reveal distinctive mechanisms for the binding and aggregation of silica and metal clusters on protruding double-stranded DNA (dsDNA) strands that are prescribed on the DNA origami template. In particular, the binding energy differences of silica/metal clusters and DNA molecules underlies the accessibilities of dissimilar material areas on DNA origami. By programming the densities and lengths of protruding dsDNA strands on DNA origami, silica and metal materials can be independently deposited at their predefined areas with a high vertical precision of 2 nm. We demonstrate the integration of silica-gold and silica-silver heterostructures with high site addressability. This DNA nanotechnology-based strategy is thus applicable for integrating various types of dissimilar materials, which opens up new routes to bottom-up electronics.

DNA Origami‐Encoded Integration of Heterostructures

AbstractIntegrating dissimilar materials at the nanoscale is crucial for modern electronics and optoelectronics. The structural DNA nanotechnology provides a universal platform for precision assembly of materials; nevertheless, heterogeneous integration of dissimilar materials with DNA nanostructures has yet to be explored. We report a DNA origami‐encoded strategy for integrating silica‐metal heterostructures. Theoretical and experimental studies reveal distinctive mechanisms for the binding and aggregation of silica and metal clusters on protruding double‐stranded DNA (dsDNA) strands that are prescribed on the DNA origami template. In particular, the binding energy differences of silica/metal clusters and DNA molecules underlies the accessibilities of dissimilar material areas on DNA origami. By programming the densities and lengths of protruding dsDNA strands on DNA origami, silica and metal materials can be independently deposited at their predefined areas with a high vertical precision of 2 nm. We demonstrate the integration of silica‐gold and silica‐silver heterostructures with high site addressability. This DNA nanotechnology‐based strategy is thus applicable for integrating various types of dissimilar materials, which opens up new routes to bottom‐up electronics.

Multiple Wavelength Photopolymerization of Stable Poly(Catecholamines)-DNA Origami Nanostructures.

The synthesis of multicomponent polymer hybrids with nanometer precision is chemically challenging in the bottom‐up synthesis of complex nanostructures. Here, we leverage the fidelity of the DNA origami technique to install a multiple wavelength responsive photopolymerization system with nanometer resolution. By precisely immobilizing various photosensitizers on the origami template, which are only activated at their respective maximum wavelength, we can control sequential polymerization processes. In particular, the triggered photosensitizers generate reactive oxygen species that in turn initiate the polymerization of the catecholamines dopamine and norepinephrine. We imprint polymeric layers at designated positions on DNA origami, which modifies the polyanionic nature of the DNA objects, thus promoting their uptake into living cells while preserving their integrity. Our herein proposed method provides a rapid platform to access complex 3D nanostructures by customizing material and biological interfaces.