Custom-shaped metal nanostructures based on DNA origami silhouettes

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DNA-Based Enzyme Reactors and Systems

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Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering

The study of biologically relevant molecules and their interaction with external stimuli on a single molecular scale is of high importance due to the availability of distributed rather than averaged information. Surface enhanced Raman scattering (SERS) provides direct chemical information, but is rather challenging on the single molecule (SM) level, where it is often assumed to require a direct contact of analyte molecules with the metal surface. Here, we detect and investigate the molecular states of single hemin by SM-SERS. A DNA aptamer based G-quadruplex mediated recognition of hemin directs its placement in the SERS hot-spot of a DNA Origami Nanofork Antenna (DONA). The configuration of the DONA structure allows the molecule to be trapped at the plasmonic hot-spot preferentially in no-contact configuration with the metal surface. Owing to high field enhancement at the plasmonic hot spot, the detection of a single folded G-quadruplex becomes possible. For the first time, we present a systematic study by SM-SERS where most hemin molecule adopt a high spin and oxidation state (III) that showed state crossover to low spin upon strong-field-ligand binding. The present study therefore, provides a platform for studying biologically relevant molecules and their properties at SM sensitivity along with demonstrating a conceptual advancement towards successful monitoring of single molecular chemical interaction using DNA aptamers

Plasmonic nanostructures through DNA-assisted lithography

Programmable self-assembly of nucleic acids enables the fabrication of custom, precise objects with nanoscale dimensions. These structures can be further harnessed as templates to build novel materials such as metallic nanostructures, which are widely used and explored because of their unique optical properties and their potency to serve as components of novel metamaterials. However, approaches to transfer the spatial information of DNA constructions to metal nanostructures remain a challenge. We report a DNA-assisted lithography (DALI) method that combines the structural versatility of DNA origami with conventional lithography techniques to create discrete, well-defined, and entirely metallic nanostructures with designed plasmonic properties. DALI is a parallel, high-throughput fabrication method compatible with transparent substrates, thus providing an additional advantage for optical measurements, and yields structures with a feature size of ~10 nm. We demonstrate its feasibility by producing metal nanostructures with a chiral plasmonic response and bowtie-shaped nanoantennas for surface-enhanced Raman spectroscopy. We envisage that DALI can be generalized to large substrates, which would subsequently enable scale-up production of diverse metallic nanostructures with tailored plasmonic features.Peer reviewe

Itsejärjestäytyvä DNA-kultananopartikkeli-rakenne yhden elektronin transistorina

Tässä tutkielmassa selvitettiin kultananopartikkelien ja itsejärjestäytyvän DNA-järjestelmän soveltuvuutta nanoteknologian komponenttina. Työssä yhdistetään funktionalisoituja kultapartikkeleita jo valmiiksi tutkittuun itsejärjestäytyvään DNA-rakenteeseen työnimeltään BAB. Se muodostuu kolmen TX-tiilen ketjusta, johon suunnittelin kandidaatin tutkinnossani kiinnityskohdat kultapartikkeleille. Yhdistämällä kultapartikkelit ja BAB-rakenne saadaan muodostettua kolmen partikkelin ketju, ja tällä rakenteella pyritään muodostamaan yhden elektronin transistori: Toiminta yhden elektronin transistorina pyrittiin havainnoimaan Coulombin saarron avulla mittaamalla differentiaalista konduktanssia sekä tasavirtakäyttäytymistä huoneenlämpötilasta aina nestemäisen heliumin lämpötilaan asti. Tutkittavat rakenteet eivät johda ilman mitään erillisiä käsittelyjä johtuen liian suuresta aukosta kultapartikkelien välillä. Näytteitä kasvatettiin kemiallisella kultakasvatuksella. Kolmelle näytteelle havaittiin Coulombin saarto huoneenlämpötilassa. Havaittiin myös, että rakenteen läpi menevä virta oskilloi tai hyppii eri johtavuuksien välillä jopa matalilla jännitteillä ja lämpötiloilla johtuen todennäköisesti piioksidi alustan varausten liikkeestä. Nämä taustavaraukset pystyvät muuttamaan SET:n kantajännitettä, jolloin myös näytteen johtavuus muuttuisi. Muita mahdollisia syitä oskillaatiolle ovat resonanssitunneloituminen kultapartikkelien läpi ja kultapartikkelien liike sähkökentän mukana. Kantajännitteen muutos on kuitenkin todennäköisin syy, sillä kultapartikkelien liike havaittiin varmasti vain yhden näytteen kohdalla ja havaitut oskillaatiot ja hypyt riippuivat lämpötilasta, eikä resonanssitunneloitumisen pitäisi riippua lämpötilasta

Nanodevices by DNA based gold nanostructures

In this thesis DNA based structures were utilized to create gold nanostructures for nanosensing and nanoelectronic applications. In the past, both of these fields have been dominated by the conventional lithography methods, e.g., electron beam lithography and UV-lithography, but more recently scaling down the components by these techniques has become increasingly more complex and costly. Especially in the micro- and nanoelectronics, the increase in the component density and thus computational power would require fabrication of sub-10-nm components, which is challenging for the top-down approaches. Aforementioned developments have led researchers to seek alternative methods to fabricate these components using so-called bottom-up approaches, that could offer less complex, faster and cost-efficient ways to fabricate the desired structures. Two of the most promising candidates for this task have been the deoxyribonucleic acid and metallic nanoparticles due to their unique optical, mechanical and chemical properties, which allow almost seamless interfacing between the two, yet still incorporate their essential optical and electrical properties, that is typically more difficult to achieve using other pairs of organic and inorganic compounds. Three distinct fabrication methods were investigated to create three different nanodevices. The new DNA assisted lithography method was used to create meta- surfaces covered with arbitrary, highly defined metallic shapes, e.g., nanoantenna bowties. The more traditional hybridization based patterning of gold nanoparticles on DNA template was used to create DNA and gold nanoparticle assemblies, which applicability as a single electron transistor was demonstrated. Finally, DNA and gold nanoparticle based assembly was utilized as an electric field controllable probe to investigate the folding and unfolding properties of a hairpin-DNA molecule. Metallic bowtie antennas have interested researchers due to the high field enhancement between the two triangles, which could be used in e.g. surface-enhanced Raman spectroscopy. However, the current fabrication techniques have been mostly limited to infrared region due to the size and shape restrictions. By using dark field microscopy, we have showed that the new fabrication method is able to produce highly defined structures in a wafer scale and having their desired optical properties at visible regions even on high-refractive index substrates, where both of the features have not been feasible to accomplice before. Single stranded DNA functionalized gold nanoparticles are one of the standard tools to develop nanoscale applications, from nanopatterning to diagnostic detection. Functionalization scheme using DNA and AuNPs was utilized to fabricate two vastly different assemblies: pearl-like, three gold nanoparticle linear chain on DNA template and AuNPs coated with biotinylated DNA strands, which were further immobilized to chimeric avidin coated gold surface via strong biotin-avidin interaction. For the former case, dielectrophoresis trapping was employed to position these pearl-like DNA-AuNP assemblies between a fingertip electrode structure for current-voltage characterization. It was observed that the plain, pearl-like DNA-AuNP assemblies did not conduct a current, which was most probably due to too large air gaps between the AuNPs. Thus the structures were extruded larger by chemical gold growth process. After that the current started to flow when a threshold voltage was reached, i.e, where after the Coulomb blockade was observed for a few samples from 4.2 K up to room temperature. For the latter case, the sandwich assembly of gold surface-avidin-DNA-AuNP was used to study the conformational changes of a hairpin-DNA by electric field induced motion of the AuNP, where the motion of gold nanoparticles either caused the DNA to stretch and unfold or relax and fold back

Synthesis of nanostructured protein–mineral-microcapsules by sonication

We propose a simple and eco-friendly method for the formation of composite protein–mineral-microcapsules induced by ultrasound treatment. Protein- and nanoparticle-stabilized oil-in-water (O/W) emulsions loaded with different oils are prepared using high-intensity ultrasound. The formation of thin composite mineral proteinaceous shells is realized with various types of nanoparticles, which are pre-modified with Bovine Serum Albumin (BSA) and subsequently characterized by EDX, TGA, zeta potential measurements and Raman spectroscopy. Cryo-SEM and EDX mapping visualizations show the homogeneous distribution of the densely packed nanoparticles in the capsule shell. In contrast to the results reported in our previous paper,1 the shell of those nanostructured composite microcapsules is not cross-linked by the intermolecular disulfide bonds between BSA molecules. Instead, a Pickering-Emulsion formation takes place because of the amphiphilicity-driven spontaneous attachment of the BSA-modified nanoparticles at the oil/water interface. Using colloidal particles for the formation of the shell of the microcapsules, in our case silica, hydroxyapatite and calcium carbonate nanoparticles, is promising for the creation of new functional materials. The nanoparticulate building blocks of the composite shell with different chemical, physical or morphological properties can contribute to additional, sometimes even multiple, features of the resulting capsules. Microcapsules with shells of densely packed nanoparticles could find interesting applications in pharmaceutical science, cosmetics or in food technology.peerReviewe

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.peerReviewe

Raman Enhancement of Nanoparticle Dimers Self-Assembled Using DNA Origami Nanotriangles

Surface-enhanced Raman scattering is a powerful approach to detect molecules at very low concentrations, even up to the single-molecule level. One important aspect of the materials used in such a technique is how much the signal is intensified, quantified by the enhancement factor (EF). Herein we obtained the EFs for gold nanoparticle dimers of 60 and 80 nm diameter, respectively, self-assembled using DNA origami nanotriangles. Cy5 and TAMRA were used as surface-enhanced Raman scattering (SERS) probes, which enable the observation of individual nanoparticles and dimers. EF distributions are determined at four distinct wavelengths based on the measurements of around 1000 individual dimer structures. The obtained results show that the EFs for the dimeric assemblies follow a log-normal distribution and are in the range of 106 at 633 nm and that the contribution of the molecular resonance effect to the EF is around 2, also showing that the plasmonic resonance is the main source of the observed signal. To support our studies, FDTD simulations of the nanoparticle’s electromagnetic field enhancement has been carried out, as well as calculations of the resonance Raman spectra of the dyes using DFT. We observe a very close agreement between the experimental EF distribution and the simulated values

One-step large-scale deposition of salt-free DNA origami nanostructures

DNA origami nanostructures have tremendous potential to serve as versatile platforms in selfassembly -based nanofabrication and in highly parallel nanoscale patterning. However, uniform deposition and reliable anchoring of DNA nanostructures often requires specific conditions, such as pre-treatment of the chosen substrate or a fine-tuned salt concentration for the deposition buffer. In addition, currently available deposition techniques are suitable merely for small scales. In this article, we exploit a spray-coating technique in order to resolve the aforementioned issues in the deposition of different 2D and 3D DNA origami nanostructures. We show that purified DNA origamis can be controllably deposited on silicon and glass substrates by the proposed method. The results are verified using either atomic force microscopy or fluorescence microscopy depending on the shape of the DNA origami. DNA origamis are successfully deposited onto untreated substrates with surface coverage of about 4 objects/mm2 . Further, the DNA nanostructures maintain their shape even if the salt residues are removed from the DNA origami fabrication buffer after the folding procedure. We believe that the presented one-step spray-coating method will find use in various fields of material sciences, especially in the development of DNA biochips and in the fabrication of metamaterials and plasmonic devices through DNA metallisation.peerReviewe