DNA Origami Templates Research Articles

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.

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.

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.

DNA-nanostructure-templated assembly of planar and curved lipid-bilayer membranes.

Lipid-bilayer nanodiscs and liposomes have been developed to stabilize membrane proteins in order to study their structures and functions. Nanodiscs are detergent-free, water-soluble, and size-controlled planar phospholipid-bilayer platforms. On the other hand, liposomes are curved phospholipid-bilayer spheres with an aqueous core used as drug delivery systems and model membrane platforms for studying cellular activities. A long-standing challenge is the generation of a homogenous and monodispersed lipid-bilayer system with a very wide range of dimensions and curvatures (elongation, bending, and twisting). A DNA-origami template provides a way to control the shapes, sizes, and arrangements of lipid bilayers via enforcing the assembly of lipid bilayers within the cavities created by DNA nanostructures. Here, we provide a concise overview and discuss how to design planar and curved lipid-bilayer membranes by using DNA-origami nanostructures as templates. Finally, we will discuss the potential applications of DNA-origami nanostructures in the structural and functional studies of large membrane proteins and their complexes.

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.

Programmed Assembly of DNA Templates by Silver Nanowires.

DNA origami templates are known to exhibit many advantages to integrate functional components at desirable locations for nanoelectronic applications. In order to immobilize conducting or semiconducting species in a bottom-up approach, the programmed assembly of DNA templates is of utmost necessity. This report demonstrates the silver nanowires enabled bridging of two linear DNA origami (DO) nanostructures by utilizing the host-guest interaction of biotin-STV and sequence-specific silver metallization of poly(dG-dC) DNA nanowires (in 10 % yield) using (dA)10 coated AgNPs (15 nm). The enzymatic synthesis of 750 bp, 1500 bp and 3000 bp bis-biotinylated poly(dG-dC), facile synthesis of 1 : 1 biotin-STV and silver-nanowire bridged DNA templates were characterized by gel electrophoresis, atomic force microscope imaging techniques. The strategy utilized here provides a method that can precisely connect heterogeneous templates towards bottom-up fabrication of practical nanoelectronics.

Stimuli-Responsive DNA Origami Nanodevices and Their Biological Applications.

DNA origami nanotechnology has provided predictable static nanoarchitectures and dynamic nanodevices with rationally designed geometries, precise spatial addressability, and marked biocompatibility. Multiple functional elements, such as peptides, aptamers, nanoparticles, fluorescence probes, and proteins, etc. can be easily integrated into DNA origami templates with nanoscale precision, leading to a variety of promising applications. Triggered by chemical/physical stimuli, dynamic DNA origami nanodevices can switch between defined conformations or translocate autonomously, providing powerful tools for intelligent biosensing and drug delivery. In this minireview, we summarize the recent progress of dynamic DNA origami nanodevices with desired reconfigurability and feasibility to perform multiple biological tasks. We introduce varieties of DNA nanodevices that can be controlled by different molecular triggers and external stimuli. Subsequently, we highlight the recent advances in employing DNA nanodevices as biosensors and drug delivery vehicles. At last, future possibilities and perspectives are also discussed.

Programmable and Site-Specific Patterning on DNA Origami Templates with Heterogeneous Condensation of Silver and Silica.

DNA origami has been widely used as a modular platform for condensation of functional molecules to assemble optical, electronic, and biological components. However, the heterogeneous condensation with greater diversities in chemical composition templated with DNA origami is still challenging. Herein, a programmable deposition method is developed to precisely condense silver-silica nanohybrids on DNA origami templates. First, the site-specific metallization of Ag is achieved by thiol group-initiated silver reduction at the designed areas of DNA origami. Next, cysteamine is used to selectively modify the condensed Ag surface with positively charged amino groups for creating an electronically different environment for site-specific placement of silica by a modified Stöber method. Using these strategies, customized patterning of both silver and silica on tubular and rectangular DNA origami nanostructures is successfully achieved with nanoscale spatial resolution. These findings will greatly facilitate the development of DNA nanotechnology-based bottom-up nanofabrication.

Fabrication and temperature-dependent electrical characterization of a C-shape nanowire patterned by a DNA origami

We introduce a method based on directed molecular self-assembly to manufacture and electrically characterise C-shape gold nanowires which clearly deviate from typical linear shape due to the design of the template guiding the assembly. To this end, gold nanoparticles are arranged in the desired shape on a DNA-origami template and enhanced to form a continuous wire through electroless deposition. C-shape nanowires with a size below 150nm on a {hbox {SiO}_2}/hbox {Si} substrate are contacted with gold electrodes by means of electron beam lithography. Charge transport measurements of the nanowires show hopping, thermionic and tunneling transports at different temperatures in the 4.2K to 293K range. The different transport mechanisms indicate that the C-shape nanowires consist of metallic segments which are weakly coupled along the wires.