Bottom-Up Fabrication of DNA-Templated Electronic Nanomaterials and Their Characterization

Bottom-up fabrication using DNA is a promising approach for the creation of nanoarchitectures. Accordingly, nanomaterials with specific electronic, photonic, or other functions are precisely and programmably positioned on DNA nanostructures from a disordered collection of smaller parts. These self-assembled structures offer significant potential in many domains such as sensing, drug delivery, and electronic device manufacturing. This review describes recent progress in organizing nanoscale morphologies of metals, semiconductors, and carbon nanotubes using DNA templates. We describe common substrates, DNA templates, seeding, plating, nanomaterial placement, and methods for structural and electrical characterization. Finally, our outlook for DNA-enabled bottom-up nanofabrication of materials is presented.

Reconfiguring DNA Nanotube Architectures via Selective Regulation of Terminating Structures

Molecular assemblies inside cells often undergo structural reconfiguration in response to stimuli to alter their function. Adaptive reconfiguration of cytoskeletal networks, for example, enables cellular shape change, movement, and cargo transport and plays a key role in driving complex processes such as division and differentiation. The cellular cytoskeleton is a self-assembling polymer network composed of simple filaments, so reconfiguration often occurs through the rearrangement of its component filaments' connectivities. DNA nanotubes have emerged as promising building blocks for constructing programmable synthetic analogs of cytoskeletal networks. Nucleating seeds can control when and where nanotubes grow, and capping structures can bind nanotube ends to stop growth. Such seeding and capping structures, collectively called termini, can organize nanotubes into larger architectures. However, these structures cannot be selectively activated or inactivated in response to specific stimuli to rearrange nanotube architectures, a key property of cytoskeletal networks. Here, we demonstrate how selective regulation of the binding affinity of DNA nanotube termini for DNA nanotube monomers or nanotube ends can direct the reconfiguration of nanotube architectures. Using DNA hybridization and strand displacement reactions that specifically activate or inactivate four orthogonal nanotube termini, we demonstrate that nanotube architectures can be reconfigured by selective addition or removal of distinct termini. Finally, we show how terminus activation could be a sensitive detector and amplifier of a DNA sequence signal. These results could enable the development of adaptive and multifunctional materials or diagnostic tools.

On single-electron magnesium bonding formation and the effect of methyl substitution

The complexes formed between MgX₂ (X = F, H) molecules and alkyl radicals Y [Y = CH₃, CH₂CH₃, CH(CH₃)₂, and C(CH₃)₃] have been characterized by using quantum chemical methods. The binding distance in all cases is less than the sum of vdW radii of Mg and C, indicating the formation of a non-covalent interaction, namely single-electron magnesium bond. Energy decomposition analysis reveals that electrostatic and polarization contributions are the major components responsible for the stability of the studied complexes. According to interaction energy, atoms in molecules, and independent gradient model analyses, methyl substitution on electron donor Y imposes a positive effect on its complexation with MgX₂. When compared with other nonbonded interactions, the single-electron magnesium bond is found to have strength comparable to those of the single-electron beryllium bond and π-magnesium bond.

The complexes formed between MgX₂ (X = F, H) molecules and alkyl radicals Y [Y = CH₃, CH₂CH₃, CH(CH₃)₂, and C(CH₃)₃] have been characterized by using quantum chemical methods.

The assemble, grow and lift-off (AGLO) strategy to construct complex gold nanostructures with pre-designed morphologies

The construction of metallic nanostructures with customizable morphologies and complex shapes has been an essential pursuit in nanoscience. DNA nanotechnology has enabled the fabrication of increasingly complex DNA nanostructures with unprecedented specificity, programmability and sub-nanometer precision, which makes it an ideal approach to rationally organize metallic nanostructures. Here we report an Assemble, Grow and Lift-Off (AGLO) strategy to construct robust standalone gold nanostructures with pre-designed customizable shapes in solution, using only a simple 2D DNA origami sheet as a versatile transient template. Gold nanoparticle (AuNP) seeds were firstly assembled onto the pre-designed binding sites of the DNA origami template and then additional gold was slowly deposited onto the AuNP seeds. The growing seed surfaces eventually merge with adjacent seeds to generate one continuous gold nanostructure in a pre-designed shape, which can then be lifted off the origami template. Diverse customized patterns of templated AuNP seeds were successfully transformed into corresponding gold nanostructures with the target structure transformation percentage over 80%. Moreover, the AGLO strategy can be incorporated with a magnetic bead separation platform to enable the easy recycling of the excess AuNP seeds and DNA components.

Fabrication of Metal Nanostructures with Programmable Length and Patterns Using a Modular DNA Platform

Recently introduced DNA nanomolds allow the shape-controlled growth of metallic nanoparticles. Here we demonstrate that this approach can be used to fabricate longer linear metal nanostructures of controlled lengths and patterns. To this end, we establish a set of different interfaces that enable mold interactions with high affinity and specificity. These interfaces enable and control the modular assembly of mold monomers into larger mold superstructure with programmable dimension in which each mold monomer remains uniquely addressable. Preloading the molds with nanoparticle seeds subsequently allows the growth of linear gold nanostructures whose lengths are controlled by the DNA structure. Exploiting the addressability of individual mold monomers furthermore allows achievement of site-specific metallization, that is, to create defined metal patterns. We think that the introduced approach provides a useful basis to fabricate nanomaterials with complex shapes and material composition in a fully programmable and modular fashion.

Aptamer-tagged DNA origami for spatially addressable detection of aflatoxin B1

A DNA origami-based platform for detecting aflatoxin B1 has been constructed with the assistance of aptamer probes and its complementary ssDNA-modified gold nanoparticles. This work may open new horizons for the application of DNA origami in the detection of a variety of small molecules.

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

Self-Assembled Active Plasmonic Waveguide with a Peptide-Based Thermomechanical Switch

Nanoscale plasmonic waveguides composed of metallic nanoparticles are capable of guiding electromagnetic energy below the optical diffraction limit. Signal feed-in and readout typically require the utilization of electronic effects or near-field optical techniques, whereas for their fabrication mainly lithographic methods are employed. Here we developed a switchable plasmonic waveguide assembled from gold nanoparticles (AuNPs) on a DNA origami structure that facilitates a simple spectroscopic excitation and readout. The waveguide is specifically excited at one end by a fluorescent dye, and energy transfer is detected at the other end via the fluorescence of a second dye. The transfer distance is beyond the multicolor FRET range and below the Abbé limit. The transmittance of the waveguide can also be reversibly switched by changing the position of a AuNP within the waveguide, which is tethered to the origami platform by a thermoresponsive peptide. High-yield fabrication of the plasmonic waveguides in bulk was achieved using silica particles as solid supports. Our findings enable bulk solution applications for plasmonic waveguides as light-focusing and light-polarizing elements below the diffraction limit.

Temperature-Dependent Charge Transport through Individually Contacted DNA Origami-Based Au Nanowires

DNA origami nanostructures have been used extensively as scaffolds for numerous applications such as for organizing both organic and inorganic nanomaterials, studying single molecule reactions, and fabricating photonic devices. Yet, little has been done toward the integration of DNA origami nanostructures into nanoelectronic devices. Among other challenges, the technical difficulties in producing well-defined electrical contacts between macroscopic electrodes and individual DNA origami-based nanodevices represent a serious bottleneck that hinders the thorough characterization of such devices. Therefore, in this work, we have developed a method to electrically contact individual DNA origami-based metallic nanowires using electron beam lithography. We then characterize the charge transport of such nanowires in the temperature range from room temperature down to 4.2 K. The room temperature charge transport measurements exhibit ohmic behavior, whereas at lower temperatures, multiple charge transport mechanisms such as tunneling and thermally assisted transport start to dominate. Our results confirm that charge transport along metallized DNA origami nanostructures may deviate from pure metallic behavior due to several factors including partial metallization, seed inhomogeneities, impurities, and weak electronic coupling among AuNPs. Besides, this study further elucidates the importance of variable temperature measurements for determining the dominant charge transport mechanisms for conductive nanostructures made by self-assembly approaches.

In situ 2D-extraction of DNA wheels by 3D through-solution transport

Controlled transfer of DNA nanowheels from a hydrophilic to a hydrophobic surface was achieved by complexation of the nanowheels with a cationic lipid (2C12N(+)). 2D surface-assisted extraction, '2D-extraction', enabled structure-persistent transfer of DNA wheels, which could not be achieved by simple drop-casting.

Dielectrophoresis of gold nanoparticles conjugated to DNA origami structures

DNA nanostructures are promising construction materials to bridge the gap between self-assembly of functional molecules and conventional top-down fabrication methods in nanotechnology. Their positioning onto specific locations of a microstructured substrate is an important task towards this aim. Here we study manipulation and positioning of pristine and of gold nanoparticle-conjugated tubular DNA origami structures using ac dielectrophoresis. The dielectrophoretic behavior was investigated employing fluorescence microscopy. For the pristine origami, a significant dielectrophoretic response was found to take place in the megahertz range, whereas, due to the higher polarizability of the metallic nanoparticles, the nanoparticle/DNA hybrid structures required a lower electrical field strength and frequency for a comparable trapping at the edges of the electrode structure. The nanoparticle conjugation additionally resulted in a remarkable alteration of the DNA structure arrangement. The growth of linear, chain-like structures in between electrodes at applied frequencies in the megahertz range was observed. The long-range chain formation is caused by a local, gold nanoparticle-induced field concentration along the DNA nanostructures, which in turn, creates dielectrophoretic forces that enable the observed self-alignment of the hybrid structures.

Insight into structural and π–magnesium bonding characteristics of the X2Mg⋯Y (X = H, F; Y = C2H2, C2H4and C6H6) complexes

Quantum chemical calculations have been performed to study the nature of interaction of complexes formed by MgX₂(X = H, F) molecules with acetylene, ethylene, and benzene.

Alignment of Gold Nanoparticle-Decorated DNA Origami Nanotubes: Substrate Prepatterning versus Molecular Combing

DNA origami has become an established technique for designing well-defined nanostructures with any desired shape and for the controlled arrangement of functional nanostructures with few nanometer resolution. These unique features make DNA origami nanostructures promising candidates for use as scaffolds in nanoelectronics and nanophotonics device fabrication. Consequently, a number of studies have shown the precise organization of metallic nanoparticles on various DNA origami shapes. In this work, we fabricated large arrays of aligned DNA origami decorated with a high density of gold nanoparticles (AuNPs). To this end, we first demonstrate the high-yield assembly of high-density AuNP arrangements on DNA origami adsorbed to Si surfaces with few unbound background nanoparticles by carefully controlling the concentrations of MgCl2 and AuNPs in the hybridization buffer and the hybridization time. Then, we evaluate two methods, i.e., hybridization to prealigned DNA origami and molecular combing in a receding meniscus, with respect to their potential to yield large arrays of aligned AuNP-decorated DNA origami nanotubes. Because of the comparatively low MgCl2 concentration required for the efficient immobilization of the AuNPs, the prealigned DNA origami become mobile and displaced from their original positions, thereby decreasing the alignment yield. This increased mobility, on the other hand, makes the adsorbed origami susceptible to molecular combing, and a total alignment yield of 86% is obtained in this way.