DNA-templated nickel nanostructures and protein assemblies

Dynamic metallization of spherical DNA via conformational transition into gold nanostructures with controlled sizes and shapes

Despite the reversible condensation properties of DNA, DNA metallization during controlled conformational transitions has been rarely investigated. We perform dynamic metallization of spherically condensed DNA nanoparticles (DNA NPs) via a globule-to-coil transition. A positively charged new Au³⁺ reagent is prepared via ligand-exchange of conventional complex Au³⁺ ions, which was used to synthesize spherically condensed DNA NPs simply based on the fundamental electrostatic and coordinative interactions between DNA and Au³⁺ions. Interestingly, the size of the Au³⁺-condensed DNA NPs (Au³⁺-DNA NPs) and the type of reducing agents lead to the formation of different Au nanostructures with unprecedented morphologies (cracked NPs, bowl-shaped NPs, and small NPs), owing to the controlled conformational changes in the Au³⁺-DNA NPs during metallization. The condensed DNA NPs play significant roles for Au nanostructures as (1) the dynamic template for the synthesis, (2) the reservoir and supply of Au³⁺ for the growth, and (3) the surface stabilizer. The synthesized Au nanostructures are remarkably stable against high ionic strength and exhibit catalytic activities and excellent SERS properties. This is the first study on the morphological control and concomitant dynamic metallization of spherically condensed DNA, proposing new synthetic routes for bioinorganic nanomaterials.

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.

Seeding, Plating and Electrical Characterization of Gold Nanowires Formed on Self-Assembled DNA Nanotubes

Self-assembly nanofabrication is increasingly appealing in complex nanostructures, as it requires fewer materials and has potential to reduce feature sizes. The use of DNA to control nanoscale and microscale features is promising but not fully developed. In this work, we study self-assembled DNA nanotubes to fabricate gold nanowires for use as interconnects in future nanoelectronic devices. We evaluate two approaches for seeding, gold and palladium, both using gold electroless plating to connect the seeds. These gold nanowires are characterized electrically utilizing electron beam induced deposition of tungsten and four-point probe techniques. Measured resistivity values for 15 successfully studied wires are between 9.3 × 10-6 and 1.2 × 10-3 Ωm. Our work yields new insights into reproducible formation and characterization of metal nanowires on DNA nanotubes, making them promising templates for future nanowires in complex electronic circuitry.

Alkaline phosphatase determination via regulation of enzymatically generated poly(thymine) as a template for fluorescent copper nanoparticle formation

We propose a new fluorometric method for alkaline phosphatase (ALP) determination. This method is based on the regulation of enzymatically generated poly(thymine) for the preparation of copper nanoparticles (CuNPs). 2'-Deoxythymidine 5'-triphosphate (dTTP) serves as the source for polymerization mediated by terminal deoxynucleotidyl transferase (TdT). This process generates poly(thymine), which acts as the template for synthesis of fluorescent CuNPs. However, if ALP catalyzes the hydrolysis of dTTP, the TdT-mediated polymerization will be disabled. This prevents the formation of CuNPs and causes a drop in fluorescence. The findings were used to design a sensitive and selective fluorometric method for ALP determination. A linear response in the activity range from 0.1 to 20 U L^-1 and a limit of quantification of 0.3 U L^-1 were obtained. The results indicate that the proposed method can be successfully applied to ALP assay in spiked diluted serum. This demonstrates the method's reliability and practicability. Graphical abstract A fluoromoetric method for alkaline phosphatase assay has been developed based on regulation of enzymatically generated poly(thymine) as template for the formation of fluorescent CuNPs.

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.

Increasing the stability of DNA nanostructure templates by atomic layer deposition of Al2O3 and its application in imprinting lithography

We present a method to increase the stability of DNA nanostructure templates through conformal coating with a nanometer-thin protective inorganic oxide layer created using atomic layer deposition (ALD). DNA nanotubes and origami triangles were coated with ca. 2 nm to ca. 20 nm of Al₂O₃. Nanoscale features of the DNA nanostructures were preserved after the ALD coating and the patterns are resistive to UV/O₃ oxidation. The ALD-coated DNA templates were used for a direct pattern transfer to poly(L-lactic acid) films.

Directional Growth of DNA-Functionalized Nanorods to Enable Continuous, Site-Specific Metallization of DNA Origami Templates

This work examines the anisotropic electroless plating of DNA-functionalized gold nanorods attached to a DNA origami template to fabricate continuous metal structures of rectanglar, square, and T shapes. DNA origami, a versatile method for assembling a variety of 2- and 3-D nanostructures, is utilized to construct the DNA breadboard template used for this study. Staple strands on selective sites of the breadboard template are extended with an additional nucleotide sequence for the attachment of DNA-functionalized gold nanorods to the template via base pairing. The nanorod-seeded DNA templates are then introduced into an electroless gold plating solution to determine the extent to which the anisotropic growth of the nanorods is able to fill the gaps between seeds to create continuous structures. Our results show that the DNA-functionalized nanorods grow anisotropically during plating at a rate that is approximately 4 times faster in the length direction than in the width direction to effectively fill gaps of up to 11-13 nm in length. The feasibility of using this directional growth at specific sites to enable the fabrication of continuous metal nanostructures with diameters as thin as 10 nm is demonstrated and represents important progress toward the creation of devices and systems based on self-assembled biological templates.

Anisotropic Electroless Deposition on DNA Origami Templates To Form Small Diameter Conductive Nanowires

An improved method for the metallization of DNA origami is examined in this work. DNA origami, a simple and robust method for creating a wide variety of nanostructured shapes and patterns, provides an enabling template for bottom-up fabrication of next-generation nanodevices. Selective metallization of these DNA templates is needed to make nanoelectronic devices. Here, we demonstrate a metallization process that uses gold nanorod seeds followed by anisotropic plating to provide improved morphology and greater control of the final metallized width of the structure. In our approach, gold nanorods are attached to an origami template to create a seed layer. Electroless gold deposition is then used to fill the gaps between seeds in order to create continuous, conductive nanowires. Importantly, growth during electroless deposition occurs preferentially in the length direction at a rate that is approximately 4 times the growth rate in the width direction, which enables fabrication of narrow, continuous wires. The electrical properties of 49 nanowires with widths ranging from 13 to 29 nm were characterized, and resistivity values as low as 8.9 × 10^-7 Ω·m were measured. The anisotropic metallization process presented here represents important progress toward the creation of nanoelectronic devices by molecularly directed placement of functional components onto self-assembled biological templates.

Metallic Nanostructures Based on DNA Nanoshapes

Metallic nanostructures have inspired extensive research over several decades, particularly within the field of nanoelectronics and increasingly in plasmonics. Due to the limitations of conventional lithography methods, the development of bottom-up fabricated metallic nanostructures has become more and more in demand. The remarkable development of DNA-based nanostructures has provided many successful methods and realizations for these needs, such as chemical DNA metallization via seeding or ionization, as well as DNA-guided lithography and casting of metallic nanoparticles by DNA molds. These methods offer high resolution, versatility and throughput and could enable the fabrication of arbitrarily-shaped structures with a 10-nm feature size, thus bringing novel applications into view. In this review, we cover the evolution of DNA-based metallic nanostructures, starting from the metallized double-stranded DNA for electronics and progress to sophisticated plasmonic structures based on DNA origami objects.

Biomimetic and Bioinspired Synthesis of Nanomaterials/Nanostructures

In recent years, due to its unparalleled advantages, the biomimetic and bioinspired synthesis of nanomaterials/nanostructures has drawn increasing interest and attention. Generally, biomimetic synthesis can be conducted either by mimicking the functions of natural materials/structures or by mimicking the biological processes that organisms employ to produce substances or materials. Biomimetic synthesis is therefore divided here into "functional biomimetic synthesis" and "process biomimetic synthesis". Process biomimetic synthesis is the focus of this review. First, the above two terms are defined and their relationship is discussed. Next different levels of biological processes that can be used for process biomimetic synthesis are compiled. Then the current progress of process biomimetic synthesis is systematically summarized and reviewed from the following five perspectives: i) elementary biomimetic system via biomass templates, ii) high-level biomimetic system via soft/hard-combined films, iii) intelligent biomimetic systems via liquid membranes, iv) living-organism biomimetic systems, and v) macromolecular bioinspired systems. Moreover, for these five biomimetic systems, the synthesis procedures, basic principles, and relationships are discussed, and the challenges that are encountered and directions for further development are considered.

DNA-templated nanowires: morphology and electrical conductivity

DNA-templating has been used to create nanowires from metals, compound semiconductors and conductive polymers. The mechanism of growth involves nucleation at binding sites on the DNA followed by growth of spherical particles and then, under favourable conditions, a slow transformation to a smooth nanowire. The final transformation is favoured by restricting the amount of templated material per unit length of template and occurs most readily for materials of low surface tension. Electrical measurements on DNA-templated nanowires can be facilitated using three techniques: (i) standard current-voltage measurements with contact electrodes embedded in a dielectric so that there is a minimal step height at the dielectric/electrode boundary across which nanowires may be aligned by molecular combing, (ii) the use of a dried droplet technique and conductive AFM to determine contact resistance by moving the tip along the length of an individual nanowire and (iii) non-contact assessment of conductivity by scanned conductance microscopy on Si/SiO2 substrates.

Fabrication of DNA-templated Te and Bi2Te3 nanowires by galvanic displacement

This paper demonstrates the use of galvanic displacement to form continuous tellurium-based nanowires on DNA templates, enabling the conversion of metals, which can be deposited site-specifically, into other materials needed for device fabrication. Specifically, galvanic displacement reaction of copper and nickel nanowires is used to fabricate tellurium and bismuth telluride nanowires on λ-DNA templates. The method is simple, rapid, highly selective, and applicable to a number of different materials. In this study, continuous Ni and Cu nanowires are formed on DNA templates by seeding with Ag followed by electroless plating of the desired metal. These wires are then displaced by a galvanic displacement reaction where either Te or Bi2Te3 is deposited from an acidic solution containing HTeO2(+) ions or a combination of HTeO2(+) and Bi(3+) ions, and the metal wire is simultaneously dissolved due to oxidation. Both tellurium and bismuth telluride wires can be formed from nickel templates. In contrast, copper templates only form tellurium nanowires under the conditions considered. Therefore, the composition of the metal being displaced can be used to influence the chemistry of the resulting nanowire. Galvanic displacement of metals deposited on DNA templates has the potential to enable site-specific fabrication of a variety of materials and, thereby, make an important contribution to the advancement of useful devices via self-assembled nanotemplates.

Electrically conductive gold- and copper-metallized DNA origami nanostructures

This work demonstrates the use of a circuit-like DNA origami structure as a template to fabricate conductive gold and copper nanostructures on Si surfaces. We improved over previous results by using multiple Pd seeding steps to increase seed uniformity and density. Our process has also been characterized through atomic force microscopy, particle size distribution analysis, and scanning electron microscopy. We found that four successive Pd seeding steps yielded the best results for electroless metal plating on DNA origami. Electrical resistance measurements were done on both Au- and Cu-metallized nanostructures, with each showing ohmic behavior. Gold-plated DNA origami structures made under optimal conditions had an average resistivity of 7.0 × 10(-5) Ω·m, whereas copper-metallized structures had a resistivity as low as 3.6 × 10(-4) Ω·m. Importantly, this is the first demonstration of electrically conductive Cu nanostructures fabricated on either DNA or DNA origami templates. Although resistivities for both gold and copper samples were larger than those of the bulk metal, these metal nanostructures have the potential for use in electrically connecting small structures. In addition, these metallized objects might find use in surface-enhanced Raman scattering experiments.

Multimodal characterization of a linear DNA-based nanostructure

Designer DNA structures have garnered much interest as a way of assembling novel nanoscale architectures with exquisite control over the positioning of discrete molecules or nanoparticles. Exploiting this potential for a variety of applications such as light-harvesting, molecular electronics, or biosensing is contingent on the degree to which various nanoarchitectures with desired molecular functionalizations can be realized, and this depends critically on characterization. Many techniques exist for analyzing DNA-organized nanostructures; however, these are almost never used in concert because of overlapping concerns about their differing character, measurement environments, and the disparity in DNA modification chemistries and probe structure or size. To assess these concerns and to see what might be gleaned from a multimodal characterization, we intensively study a single DNA nanostructure using a multiplicity of methods. Our test bed is a linear 100 base-pair double-stranded DNA that has been modified by a variety of chemical handles, dyes, semiconductor quantum dots, gold nanoparticles, and electroactive labels. To this we apply a combination of physical/optical characterization methods including electrophoresis, atomic force microscopy, transmission electron microscopy, dynamic light scattering, Förster resonance energy transfer, voltammetry, and structural modeling. In general, the results indicate that the differences among the techniques are not so large as to prevent their effective use in combination, that the data tend to be corroborative, and that differences observed among them can actually be quite informative.

Metallization of branched DNA origami for nanoelectronic circuit fabrication

This work examines the metallization of folded DNA, known as DNA origami, as an enabling step toward the use of such DNA as templates for nanoelectronic circuits. DNA origami, a simple and robust method for creating a wide variety of shapes and patterns, makes possible the increased complexity and flexibility needed for both the design and assembly of useful circuit templates. In addition, selective metallization of the DNA template is essential for circuit fabrication. Metallization of DNA origami presents several challenges over and above those associated with the metallization of other DNA templates such as λ-DNA. These challenges include (1) the stability of the origami in the processes used for metallization, (2) the enhanced selectivity required to metallize small origami structures, (3) the increased difficulty of adhering small structures to the surface so that they will not be removed when subject to multiple metallization steps, and (4) the influence of excess staple strands present with the origami. This paper describes our efforts to understand and address these challenges. Specifically, the influence of experimental conditions on template stability and on the selectivity of metal deposition was investigated for small DNA origami templates. These templates were seeded with Ag and then plated with Au via an electroless deposition process. Both staple strand concentration and the concentration of ions in solution were found to have a significant impact. Selective continuous metal deposition was achieved, with an average metallized height as small as 32 nm. The shape of branched origami was also retained after metallization. These results represent important progress toward the realization of DNA-templated nanocircuits.

Hydrogen enhances nickel tolerance in the purple sulfur bacterium Thiocapsa roseopersicina

A common microbial strategy for detoxifying metals involves redox transformation which often results in metal precipitation and/or immobilization. In the present study, the influence of ionic nickel [Ni(II)] on growth of the purple sulfur bacterium Thiocapsa roseopersicina was investigated. The results suggest that Ni(II) in the bulk medium at micromolar concentrations results in growth inhibition, specifically an increase in the lag phase of growth, a decrease in the specific growth rate, and a decrease in total protein concentration when compared to growth controls containing no added Ni(II). The inhibitory effects of Ni(II) on the growth of T. roseopersicina could be partially overcome by the addition of hydrogen (H(2)) gas. However, the inhibitory effects of Ni(II) on the growth of T. roseopersicina were not alleviated by H(2) in a strain containing deletions in all hydrogenase-encoding genes. Transmission electron micrographs of wild-type T. roseopersicina grown in the presence of Ni(II) and H(2) revealed a significantly greater number of dense nanoparticulates associated with the cells when compared to wild-type cells grown in the absence of H(2) and hydrogenase mutant strains grown in the presence of H(2). X-ray diffraction and vibrating sample magnetometry of the dense nanoparticles indicated the presence of zerovalent Ni, suggesting Ni(II) reduction. Purified T. roseopersicina hyn-encoded hydrogenase catalyzed the formation of zerovalent Ni particles in vitro, suggesting a role for this hydrogenase in Ni(II) reduction in vivo. Collectively, these results suggest a link among H(2) metabolism, Ni(II) tolerance, and Ni(II) reduction in T. roseopersicina .

Polymerase chain reaction based scaffold preparation for the production of thin, branched DNA origami nanostructures of arbitrary sizes

Designs for DNA origami have previously been limited by the size of the available single-stranded genomes for scaffolds. Here we present a straightforward method for the production of scaffold strands having various lengths, using polymerase chain reaction amplification followed by strand separation via streptavidin-coated magnetic beads. We have applied this approach in assembling several distinct DNA nanostructures that have thin ( approximately 10 nm) features and branching points, making them potentially useful templates for nanowires in complex electronic circuitry.

Self-assembly from milli- to nanoscales: methods and applications

The design and fabrication techniques for microelectromechanical systems (MEMS) and nanodevices are progressing rapidly. However, due to material and process flow incompatibilities in the fabrication of sensors, actuators and electronic circuitry, a final packaging step is often necessary to integrate all components of a heterogeneous microsystem on a common substrate. Robotic pick-and-place, although accurate and reliable at larger scales, is a serial process that downscales unfavorably due to stiction problems, fragility and sheer number of components. Self-assembly, on the other hand, is parallel and can be used for device sizes ranging from millimeters to nanometers. In this review, the state-of-the-art in methods and applications for self-assembly is reviewed. Methods for assembling three-dimensional (3D) MEMS structures out of two-dimensional (2D) ones are described. The use of capillary forces for folding 2D plates into 3D structures, as well as assembling parts onto a common substrate or aggregating parts to each other into 2D or 3D structures, is discussed. Shape matching and guided assembly by magnetic forces and electric fields are also reviewed. Finally, colloidal self-assembly and DNA-based self-assembly, mainly used at the nanoscale, are surveyed, and aspects of theoretical modeling of stochastic assembly processes are discussed.

Fabrication of DNA nanowires by orthogonal self-assembly and DNA intercalation on a Au patterned Si/SiO2 surface

A novel Ru complex bearing both an acridine group and anchoring phosphonate groups was immobilized on a surface in order to capture double-stranded DNAs (dsDNAs) from solution. At low surface coverage, the atomic force microscopy (AFM) image revealed the "molecular dot" morphology with the height of the Ru complex ( approximately 2.5 nm) on a mica surface, indicating that four phosphonate anchor groups keep the Ru complex in an upright orientation on the surface. Using a dynamic molecular combing method, the DNA capture efficiency of the Ru complex on a mica surface was examined in terms of the effects of the number of molecular dots and surface hydrophobicity. The immobilized surface could capture DNAs; however, the optimal number of molecular dots on the surface as well as the optimal pull-up speed exist to obtain the extended dsDNAs on the surface. Applying this optimal condition to a Au-patterned Si/SiO 2 (Au/SiO 2) surface, the Au electrode was selectively covered with the Ru complex by orthogonal self-assembly of 4-mercaptbutylphosphonic acid (MBPA), followed by the formation of a Zr (4+)-phosphonate layer and the Ru complex. At the same time, the remaining SiO 2 surface was covered with octylphosphonic acid (OPA) by self-assembly. The selective immobilization of the Ru complex only on the Au electrode was identified by time-of-flight secondary-ion mass spectrometry (TOF-SIMS) imaging on the chemically modified Au/SiO 2 surface. The construction of DNA nanowires on the Au/SiO 2 patterned surface was accomplished by the molecular combing method of the selective immobilized Ru complex on Au electrodes. These interconnected nanowires between Au electrodes were used as a scaffold for the modification of Pd nanoparticles on the DNA. Furthermore, Cu metallization was achieved by electroless plating of Cu metal on a priming of Pd nanoparticles on the Pd-covered DNA nanowires. The resulting Cu nanowires showed a metallic behavior with relatively high resistance.

Applied chemistry of natural DNA

Recently, natural DNA has emerged as an appealing biomacromolecule for functional materials. It is abundant and renewable, and possesses the well known double helix structure that promises many unique properties difficult to find in other polymers. Natural DNA has been applied in electronic, optical and biomaterials, as a catalyst for enantioselective reactions, and as a material for cleaning the environment. Most of the applications are based on combining DNA with other chemicals or nanoparticles by electrostatic binding, intercalation or groove binding. In this critical review article, recent developments in utilizing natural DNA are reviewed by focusing on three basic properties of DNA: the electrostatic property as a polyelectrolyte, selective affinity for small molecules, and biocompatibility (128 references).

Structure and activity of apoferritin-stabilized gold nanoparticles

A simple method for synthesizing gold nanoparticles stabilized by horse spleen apoferritin (HSAF) is reported using NaBH(4) or 3-(N-morpholino)propanesulfonic acid (MOPS) as the reducing agent. AuCl(4)(-) reduction by NaBH(4) was complete within a few seconds, whereas reduction by MOPS was much slower; in all cases, protein was required during reduction to keep the gold particles in aqueous solution. Transmission electron microscopy (TEM) showed that the gold nanoparticles were associated with the outer surface of the protein. The average particle diameters were 3.6 and 15.4 nm for NaBH(4)-reduced and MOPS-reduced Au-HSAF, respectively. A 5-nm difference in the UV-Vis absorption maximum was observed for NaBH(4)-reduced (530 nm) and MOPS-reduced Au-HSAF (535 nm), which was attributed to the greater size and aggregation of the MOPS-reduced gold sample. NaBH(4)-reduced Au-HSAF was much more effective than MOPS-reduced Au-HSAF in catalyzing the reduction of 4-nitrophenol by NaBH(4), based on the greater accessibility of the NaBH(4)-reduced gold particle to the substrate. Rapid reduction of AuCl(4)(-) by NaBH(4) was determined to result in less surface passivation by the protein. Methods for studying ferritin-gold nanoparticle assemblies may be readily applied to other protein-metal colloid systems.

Preparation of DNA-silver nanohybrids in multilayer nanoreactors by in situ electrochemical reduction, characterization, and application

Novel nanocomposite films containing DNA-silver nanohybrids have been successfully fabricated by combined use of the layer-by-layer self-assembly technique and an in situ electrochemical reduction method with the DNA-Ag+ complex as one of the building blocks. UV-vis absorption spectroscopy was employed to monitor the buildup of the multilayer films, which suggested a progressive deposition with almost an equal amount of the DNA-Ag+ complex in each cycle. The following electrochemical reduction of silver resulted in the formation of metal nanoparticles in the film, which was evidenced by the evolution of the intense plasmon absorption band originating from silver. Scanning electron microscopy indicated that the particles formed in the multilayer films possessed good monodispersity and stability, thanks to the surrounding polymers. X-ray photoelectron spectroscopy further confirmed the presence of the main components (such as DNA and metallic silver) of the nanocomposite films. In addition, we show that the size of the metal nanoparticles and the optical property of the film could be readily tuned by manipulating the assembly conditions. Furthermore, the feasibility of the as-prepared nanocomposite films functioning as a surface-enhanced Raman scattering active substrate for sensing purposes was investigated, and the results showed great enhancement of the Raman signal of two probe molecules, Rhodamine 6G and 4-aminothiophenol.