Antiviral action of a functionalized plastic surface against human coronaviruses

Viruses may persist on solid surfaces for long periods, which may contribute to indirect transmission. Thus, it is imperative to develop functionalized surfaces that will lower the infectious viral load in everyday life. Here, we have tested a plastic surface functionalized with tall oil rosin against the seasonal human coronavirus OC43 as well as severe acute respiratory syndrome coronavirus 2. All tested non-functionalized plastic surfaces showed virus persistence up to 48 h. In contrast, the functionalized plastic showed good antiviral action already within 15 min of contact and excellent efficacy after 30 min over 90% humidity. Excellent antiviral effects were also observed at lower humidities of 20% and 40%. Despite the hydrophilic nature of the functionalized plastic, viruses did not adhere strongly to it. According to helium ion microscopy, viruses appeared flatter on the rosin-functionalized surface, but after flushing away from the rosin-functionalized surface, they showed no apparent structural changes when imaged by transmission electron microscopy of cryogenic or negatively stained specimens or by atomic force microscopy. Flushed viruses were able to bind to their host cell surface and enter endosomes, suggesting that the fusion with the endosomal membrane was halted. The eluted rosin from the functionalized surface demonstrated its ability to inactivate viruses, indicating that the antiviral efficacy relied on the active leaching of the antiviral substances, which acted on the viruses coming into contact. The rosin-functionalized plastic thus serves as a promising candidate as an antiviral surface for enveloped viruses.IMPORTANCEDuring seasonal and viral outbreaks, the implementation of antiviral plastics can serve as a proactive strategy to limit the spread of viruses from contaminated surfaces, complementing existing hygiene practices. In this study, we show the efficacy of a rosin-functionalized plastic surface that kills the viral infectivity of human coronaviruses within 15 min of contact time, irrespective of the humidity levels. In contrast, non-functionalized plastic surfaces retain viral infectivity for an extended period of up to 48 h. The transient attachment on the surface or the leached active components do not cause major structural changes in the virus or prevent receptor binding; instead, they effectively block viral infection at the endosomal stage.

Creation of ordered 3D tubes out of DNA origami lattices

Hierarchical self-assembly of nanostructures with addressable complexity has been a promising route for realizing novel functional materials. Traditionally, the fabrication of such structures on a large scale has been achievable using top-down methods but with the cost of complexity of the fabrication equipment versus resolution and limitation mainly to 2D structures. More recently bottom-up methods using molecules like DNA have gained attention due to the advantages of low fabrication costs, high resolution and simplicity in an extension of the methods to the third dimension. One of the more promising bottom-up techniques is DNA origami due to the robust self-assembly of arbitrarily shaped nanostructures with feature sizes down to a few nanometers. Here, we show that under specific ionic conditions of the buffer, the employed plus-shaped, blunt-ended Seeman tile (ST) origami forms elongated, ordered 2D lattices, which are further rolled into 3D tubes in solution. Imaging structures on a surface by atomic force microscopy reveals ribbon-like structures, with single or double layers of the origami lattice. Further studies of the double-layered structures in a liquid state by confocal microscopy and cryo-TEM revealed elongated tube structures with a relatively uniform width but with a varying length. Through meticulous study, we concluded that the assembly process of these 3D DNA origami tubes is heavily dependent on the concentration of both mono- and divalent cations. In particular, nickel seems to act as a trigger for the formation of the tubular assemblies in liquid.

Elongation and plasmonic activity of embedded metal nanoparticles following heavy ion irradiation

Shape modification of embedded nanoparticles by swift heavy ion (SHI) irradiation is an effective way to produce nanostructures with controlled size, shape, and orientation. In this study, randomly oriented gold nanorods embedded in SiO₂ are shown to re-orient along the ion beam direction. The degree of orientation depends on the irradiation conditions and the nanorod's initial size. SHI irradiation was also applied to modify spherical metallic nanoparticles embedded in Al₂O₃. The results showed that they elongate due to the irradiation comparably to those embedded in SiO₂. Metallic nanostructures embedded in dielectric matrices can exhibit localized surface plasmon (LSP) modes. The elongated nanoparticles investigated by means of dark-field spectroscopy showed two discrete peaks which correspond to longitudinal and transverse modes.

Identifying Vibrations that Control Non-adiabatic Relaxation of Polaritons in Strongly Coupled Molecule-Cavity Systems

The strong light-matter coupling regime, in which excitations of materials hybridize with excitations of confined light modes into polaritons, holds great promise in various areas of science and technology. A key aspect for all applications of polaritonic chemistry is the relaxation into the lower polaritonic states. Polariton relaxation is speculated to involve two separate processes: vibrationally assisted scattering (VAS) and radiative pumping (RP), but the driving forces underlying these two mechanisms are not fully understood. To provide mechanistic insights, we performed multiscale molecular dynamics simulations of tetracene molecules strongly coupled to the confined light modes of an optical cavity. The results suggest that both mechanisms are driven by the same molecular vibrations that induce relaxation through nonadiabatic coupling between dark states and polaritonic states. Identifying these vibrational modes provides a rationale for enhanced relaxation into the lower polariton when the cavity detuning is resonant with specific vibrational transitions.

Effect of molecular Stokes shift on polariton dynamics

When the enhanced electromagnetic field of a confined light mode interacts with photoactive molecules, the system can be driven into the regime of strong coupling, where new hybrid light-matter states, polaritons, are formed. Polaritons, manifested by the Rabi split in the dispersion, have shown potential for controlling the chemistry of the coupled molecules. Here, we show by angle-resolved steady-state experiments accompanied by multi-scale molecular dynamics simulations that the molecular Stokes shift plays a significant role in the relaxation of polaritons formed by organic molecules embedded in a polymer matrix within metallic Fabry-Pérot cavities. Our results suggest that in the case of Rhodamine 6G, a dye with a significant Stokes shift, excitation of the upper polariton leads to a rapid localization of the energy into the fluorescing state of one of the molecules, from where the energy scatters into the lower polariton (radiative pumping), which then emits. In contrast, for excitonic J-aggregates with a negligible Stokes shift, the fluorescing state does not provide an efficient relaxation gateway. Instead, the relaxation is mediated by exchanging energy quanta matching the energy gap between the dark states and lower polariton into vibrational modes (vibrationally assisted scattering). To understand better how the fluorescing state of a molecule that is not strongly coupled to the cavity can transfer its excitation energy to the lower polariton in the radiative pumping mechanism, we performed multi-scale molecular dynamics simulations. The results of these simulations suggest that non-adiabatic couplings between uncoupled molecules and the polaritons are the driving force for this energy transfer process.

Optimizing geometry of low-Q all-metal Fabry-Pérot microcavity for fluorescence spectroscopy

Fluorescence spectroscopy is commonly employed to study the excited-state photophysics of organic molecules. Planar Fabry-Pérot microcavities play an essential role in such studies and a strategic cavity design is necessary to attain an enhanced light-matter interaction. In this work, we computationally study different geometries for a planar metallic Fabry-Pérot microcavity tuned for the absorption of Sulforhodamine 101, a typical dye for fluorescence spectroscopy. The cavity consists of a polymer layer enclosed between two silver mirrors, where the thicknesses of all the three layers are varied to optimize the cavity. Our transfer-matrix and finite-difference time-domain simulations suggest that a cavity with 30 nm thin top mirror and 200 nm fully reflective thick bottom mirror, thus having only reflection and absorption and no transmission, is an optimal design for maximizing the Purcell factor and spectral overlap between the cavity and molecule, while still sustaining an efficient measurability of the fluorescence.

Polariton response in the presence of Brownian dissipation from molecular vibrations

We study the elastic response of a stationarily driven system of a cavity field strongly coupled with molecular excitons, taking into account the main dissipation channels due to the finite cavity linewidth and molecular vibrations. We show that the frequently used coupled oscillator model fails in describing this response especially due to the non-Lorentzian dissipation of the molecules to their vibrations. Signatures of this failure are the temperature dependent minimum point of the polariton peak splitting, the uneven polariton peak height at the minimum splitting, and the asymmetric shape of the polariton peaks even at the experimentally accessed "zero-detuning" point. Using a rather generic yet representative model of molecular vibrations, we predict the polariton response in various conditions, depending on the temperature, molecular Stokes shift and vibration frequencies, and the size of the Rabi splitting. Our results can be used as a sanity check of the experiments trying to "prove" results originating from strong coupling, such as vacuum-enhanced chemical reaction rate.

Influence of Fano resonance on SERS enhancement in Fano-plasmonic oligomers

Plasmonic oligomers can provide profound Fano resonance in their scattering responses. The sub-radiant mode of Fano resonance can result in significant near-field enhancement due to its light trapping capability into the so-called hotspots. Appearance of these highly localized hotspots at the excitation and/or Stokes wavelengths of the analytes makes such oligomers promising SERS active substrates. In this work, we numerically and experimentally investigate optical properties of two disk-type gold oligomers, which have different strength and origin of Fano resonance. Raman analysis of rhodamine 6G and adenine with the presence of the fabricated oligomers clearly indicates that an increment in the strength of Fano resonance can improve the Raman enhancement of an oligomer significantly. Therefore, by suitable engineering of Fano lineshape, one can achieve efficient SERS active substrates with spatially localized hotspots.

DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications

Structural DNA nanotechnology provides a viable route for building from the bottom-up using DNA as construction material. The most common DNA nanofabrication technique is called DNA origami, and it allows high-throughput synthesis of accurate and highly versatile structures with nanometer-level precision. Here, it is shown how the spatial information of DNA origami can be transferred to metallic nanostructures by combining the bottom-up DNA origami with the conventionally used top-down lithography approaches. This allows fabrication of billions of tiny nanostructures in one step onto selected substrates. The method is demonstrated using bowtie DNA origami to create metallic bowtie-shaped antenna structures on silicon nitride or sapphire substrates. The method relies on the selective growth of a silicon oxide layer on top of the origami deposition substrate, thus resulting in a patterning mask for following lithographic steps. These nanostructure-equipped surfaces can be further used as molecular sensors (e.g., surface-enhanced Raman spectroscopy (SERS)) and in various other optical applications at the visible wavelength range owing to the small feature sizes (sub-10 nm). The technique can be extended to other materials through methodological modifications; therefore, the resulting optically active surfaces may find use in development of metamaterials and metasurfaces.

Tracking Polariton Relaxation with Multiscale Molecular Dynamics Simulations

When photoactive molecules interact strongly with confined light modes in optical cavities, new hybrid light-matter states form. They are known as polaritons and correspond to coherent superpositions of excitations of the molecules and of the cavity photon. The polariton energies and thus potential energy surfaces are changed with respect to the bare molecules, such that polariton formation is considered a promising paradigm for controlling photochemical reactions. To effectively manipulate photochemistry with confined light, the molecules need to remain in the polaritonic state long enough for the reaction on the modified potential energy surface to take place. To understand what determines this lifetime, we have performed atomistic molecular dynamics simulations of room-temperature ensembles of rhodamine chromophores strongly coupled to a single confined light mode with a 15 fs lifetime. We investigated three popular experimental scenarios and followed the relaxation after optically pumping (i) the lower polariton, (ii) the upper polariton, or (iii) uncoupled molecular states. The results of the simulations suggest that the lifetimes of the optically accessible lower and upper polaritons are limited by (i) ultrafast photoemission due to the low cavity lifetime and (ii) reversible population transfer into the "dark" state manifold. Dark states are superpositions of molecular excitations but with much smaller contributions from the cavity photon, decreasing their emission rates and hence increasing their lifetimes. We find that population transfer between polaritonic modes and dark states is determined by the overlap between the polaritonic and molecular absorption spectra. Importantly, excitation can also be transferred "upward" from the lower polariton into the dark-state reservoir due to the broad absorption spectra of the chromophores, contrary to the common conception of these processes as a "one-way" relaxation from the dark states down to the lower polariton. Our results thus suggest that polaritonic chemistry relying on modified dynamics taking place within the lower polariton manifold requires cavities with sufficiently long lifetimes and, at the same time, strong light-matter coupling strengths to prevent the back-transfer of excitation into the dark states.

Identifying yeasts using surface enhanced Raman spectroscopy

The molecular fingerprints of yeasts Saccharomyces cerevisiae, Dekkera bruxellensis, and Wickerhamomyces anomalus (former name Pichia anomala) have been examined using surface-enhanced Raman spectroscopy (SERS) and helium ion microscopy (HIM). The SERS spectra obtained from cell cultures (lysate and non-treated cells) distinguish between these very closely related fungal species. Highly SERS active silver nano-particles suitable for detecting complex biomolecules were fabricated using a simple synthesis route. The yeast samples mixed with aggregated Ag nanoparticles yielded highly enhanced and reproducible Raman signal owing to the high density of the hot spots at the junctions of two or more Ag nanoparticles and enabled to differentiate the three species based on their unique features (spectral fingerprint). We also collected SERS spectra of the three yeast species in beer medium to demonstrate the potential of the method for industrial application. These findings demonstrate the great potential of SERS for detection and identification of fungi species based on the biochemical compositions, even in a chemically complex sample.

Plasmonic Nanosensor Array for Multiplexed DNA-based Pathogen Detection

In this research we introduce a plasmonic nanoparticle based optical biosensor for monitoring of molecular binding events. The sensor utilizes spotted gold nanoparticle arrays as sensing platform. The nanoparticle spots are functionalized with capture DNA sequences complementary to the analyte (target) DNA. Upon incubation with the target sequence, it will bind on the respectively complementary functionalized particle spot. This binding changes the local refractive index, which is detected spectroscopically as the resulting changes of the localized surface plasmon resonance (LSPR) peak wavelength. In order to increase the signal, a small gold nanoparticle label is introduced. The binding can be reversed using chemical means (10 mM HCl). It is demonstrated that multiplexed detection and identification of several fungal pathogen DNA sequences subsequently on one sensor array are possible by this approach.

Surface Characteristics Control the Attachment and Functionality of (Chimeric) Avidin

The physical adsorption (physisorption) of proteins to surfaces is an important but incompletely understood factor in many biological processes and is of increasing significance in bionanotechnology as well. Avidin is an important protein because of strong avidin-biotin binding, which has been exploited in numerous applications. We have undertaken thorough experimentation on the physisorption of avidin, to chemically different flat surfaces of Si and graphite and also to the curved version of the latter, on multiwalled carbon nanotubes (MWNTs) of different diameters. The difference in the behavior of avidin on Si versus graphite is drastic; on Si, avidin deposits as single globular tetrameric units and maintains functionality, whereas on graphite, it forms irregular networks of two-layer thick filaments, where the first layer has lost its biological activity. On MWNTs, avidin also deposits as one-dimensional formations, or stripes, but these appear to order in a perpendicular arrangement to the MWNT axis. A better understanding of protein-surface interactions is essential for the development of robust and reliable methods for biofunctionalization of materials. This work also provides insights into the importance of the nanoscale surface architecture.

A DNA-nanoparticle actuator enabling optical monitoring of nanoscale movements induced by an electric field

Merging biological and non-biological matter to fabricate nanoscale assemblies with controllable motion and function is of great interest due to its potential application, for example, in diagnostics and biosensing. Here, we have constructed a DNA-based bionanoactuator that interfaces with biological and non-biological matter via an electric field in a reversibly controllable fashion. The read-out of the actuator is based on motion-induced changes in the plasmon resonance of a gold nanoparticle immobilized to a gold surface by single stranded DNA. The motion of the gold nanoparticle and thus the conformational changes of the DNA under varying electric field were analyzed by dark field spectroscopy. After this basic characterization, another actuator was built utilizing hairpin-DNA coated gold nanoparticles, where the hairpin-DNA induced discrete transitions between two specific open-loop and folded-loop states. These two states and the transition dynamics between them were clearly visible in the actuator behavior. The demonstrated nanoactuator concept could be readily extended to inspection of conformational changes of other biomolecules as well. Besides, this concept enables other possibilities in applications like surface-enhanced Raman spectroscopy and fluorescence enhancement, since the specific wavelength of the plasmon resonance of the actuator can be tuned by the external voltage.

Coherent Light Harvesting through Strong Coupling to Confined Light

When photoactive molecules interact strongly with confined light modes, new hybrid light-matter states may form: the polaritons. These polaritons are coherent superpositions of excitations of the molecules and of the cavity photon. Recently, polaritons were shown to mediate energy transfer between chromophores at distances beyond the Förster limit. Here we explore the potential of strong coupling for light-harvesting applications by means of atomistic molecular dynamics simulations of mixtures of photoreactive and non-photo-reactive molecules strongly coupled to a single confined light mode. These molecules are spatially separated and present at different concentrations. Our simulations suggest that while the excitation is initially fully delocalized over all molecules and the confined light mode, it very rapidly localizes onto one of the photoreactive molecules, which then undergoes the reaction.

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.

Toward Single Electron Nanoelectronics Using Self-Assembled DNA Structure

DNA based structures offer an adaptable and robust way to develop customized nanostructures for various purposes in bionanotechnology. One main aim in this field is to develop a DNA nanobreadboard for a controllable attachment of nanoparticles or biomolecules to form specific nanoelectronic devices. Here we conjugate three gold nanoparticles on a defined size TX-tile assembly into a linear pattern to form nanometer scale isolated islands that could be utilized in a room temperature single electron transistor. To demonstrate this, conjugated structures were trapped using dielectrophoresis for current-voltage characterization. After trapping only high resistance behavior was observed. However, after extending the islands by chemical growth of gold, several structures exhibited Coulomb blockade behavior from 4.2 K up to room temperature, which gives a good indication that self-assembled DNA structures could be used for nanoelectronic patterning and single electron devices.

Core-Shell Nanorod Columnar Array Combined with Gold Nanoplate-Nanosphere Assemblies Enable Powerful In Situ SERS Detection of Bacteria

Development of a label-free ultrasensitive nanosensor for detection of bacteria is presented. Sensitive assay for Gram-positive bacteria was achieved via electrostatic attraction-guided plasmonic bifacial superstructure/bacteria/columnar array assembled in one step. Dynamic optical hotspots were formed in the hybridized nanoassembly under wet-dry critical state amplifying efficiently the weak vibrational modes of three representative food-borne Gram-positive bacteria, that is, Staphylococcus xylosus, Listeria monocytogenes, and Enterococcus faecium. These three bacteria with highly analogous Raman spectra can be effectively differentiated through droplet wet-dry critical SERS approach combined with 3D PCA statistical analysis so that highly sensitive discrimination of bacterial species and samples containing mixtures of bacteria can be achieved.

DNA-Based Enzyme Reactors and Systems

During recent years, the possibility to create custom biocompatible nanoshapes using DNA as a building material has rapidly emerged. Further, these rationally designed DNA structures could be exploited in positioning pivotal molecules, such as enzymes, with nanometer-level precision. This feature could be used in the fabrication of artificial biochemical machinery that is able to mimic the complex reactions found in living cells. Currently, DNA-enzyme hybrids can be used to control (multi-enzyme) cascade reactions and to regulate the enzyme functions and the reaction pathways. Moreover, sophisticated DNA structures can be utilized in encapsulating active enzymes and delivering the molecular cargo into cells. In this review, we focus on the latest enzyme systems based on novel DNA nanostructures: enzyme reactors, regulatory devices and carriers that can find uses in various biotechnological and nanomedical applications.

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

DNA origami nanostructures have tremendous potential to serve as versatile platforms in self-assembly -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/mm(2). 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.

Custom-shaped metal nanostructures based on DNA origami silhouettes

The DNA origami technique provides an intriguing possibility to develop customized nanostructures for various bionanotechnological purposes. One target is to create tailored bottom-up-based plasmonic devices and metamaterials based on DNA metallization or controlled attachment of nanoparticles to the DNA designs. In this article, we demonstrate an alternative approach: DNA origami nanoshapes can be utilized in creating accurate, uniform and entirely metallic (e.g. gold, silver and copper) nanostructures on silicon substrates. The technique is based on developing silhouettes of the origamis in the grown silicon dioxide layer, and subsequently using this layer as a mask for further patterning. The proposed method has a high spatial resolution, and the fabrication yields can approach 90%. The approach allows a cost-effective, parallel, large-scale patterning on a chip with fully tailored metallic nanostructures; the DNA origami shape and the applied metal can be specifically chosen for each conceivable implementation.

Plasmonic coupling and long-range transfer of an excitation along a DNA nanowire

We demonstrate an excitation transfer along a fluorescently labeled dsDNA nanowire over a length of several micrometers. Launching of the excitation is done by exciting a localized surface plasmon mode of a 40 nm silver nanoparticle by 800 nm femtosecond laser pulses via two-photon absorption. The plasmonic mode is subsequently coupled or transformed to excitation in the nanowire in contact with the particle and propagated along it, inducing bleaching of the dyes on its way. In situ as well as ex situ fluorescence microscopy is utilized to observe the phenomenon. In addition, transfer of the excitation along the nanowire to another nanoparticle over a separation of 5.7 μm was clearly observed. The nature of the excitation coupling and transfer could not be fully resolved here, but injection of an electron into the DNA from the excited nanoparticle and subsequent coupled transfer of charge (Dexter) and delocalized exciton (Frenkel) is the most probable mechanism. However, a direct plasmonic or optical coupling and energy transfer along the nanowire cannot be totally ruled out either. By further studies the observed phenomenon could be utilized in novel molecular systems, providing a long-needed communication method between molecular devices.

Direct optical measurement of light coupling into planar waveguide by plasmonic nanoparticles

Coupling of light into a thin layer of high refractive index material by plasmonic nanoparticles has been widely studied for application in photovoltaic devices, such as thin-film solar cells. In numerous studies this coupling has been investigated through measurement of e.g. quantum efficiency or photocurrent enhancement. Here we present a direct optical measurement of light coupling into a waveguide by plasmonic nanoparticles. We investigate the coupling efficiency into the guided modes within the waveguide by illuminating the surface of a sample, consisting of a glass slide coated with a high refractive index planar waveguide and plasmonic nanoparticles, while directly measuring the intensity of the light emitted out of the waveguide edge. These experiments were complemented by transmittance and reflectance measurements. We show that the light coupling is strongly affected by thin-film interference, localized surface plasmon resonances of the nanoparticles and the illumination direction (front or rear).

Growth of immobilized DNA by polymerase: bridging nanoelectrodes with individual dsDNA molecules

We present a method for controlled connection of gold electrodes with dsDNA molecules (locally on a chip) by utilizing polymerase to elongate single-stranded DNA primers attached to the electrodes. Thiol-modified oligonucleotides are directed and immobilized to nanoscale electrodes by means of dielectrophoretic trapping, and extended in a procedure mimicking PCR, finally forming a complete dsDNA molecule bridging the gap between the electrodes. The technique opens up opportunities for building from the bottom-up, for detection and sensing applications, and also for molecular electronics.

Defined-size DNA triple crossover construct for molecular electronics: modification, positioning and conductance properties

We present a novel, defined-size, small and rigid DNA template, a so-called B-A-B complex, based on DNA triple crossover motifs (TX tiles), which can be utilized in molecular scale patterning for nanoelectronics, plasmonics and sensing applications. The feasibility of the designed construct is demonstrated by functionalizing the TX tiles with one biotin-triethylene glycol (TEG) and efficiently decorating them with streptavidin, and furthermore by positioning and anchoring single thiol-modified B-A-B complexes to certain locations on a chip via dielectrophoretic trapping. Finally, we characterize the conductance properties of the non-functionalized construct, first by measuring DC conductivity and second by utilizing AC impedance spectroscopy in order to describe the conductivity mechanism of a single B-A-B complex using a detailed equivalent circuit model. This analysis also reveals further information about the conductivity of DNA structures in general.

Trapping and immobilization of DNA molecules between nanoelectrodes

DNA is one of the most promising molecules for nanoscale bottom-up fabrication. For both scientific studies and fabrication of devices, it is desirable to be able to manipulate DNA molecules, or self--assembled DNA constructions, at the single unit level. Efficient methods are needed for precisely attaching the single unit to the external measurement setup or the device structure. So far, this has often been too cumbersome to achieve, and consequently most of the scientific studies are based on a statistical analysis or measurements done for a sample containing numerous molecules in liquid or in a dry state. Here, we explain a method for trapping and attaching nanoscale double-stranded DNA (dsDNA) molecules between nanoelectrodes. The method is based on dielectrophoresis and gives a high yield of trapping only single or a few molecules, which enables, for example, transport measurements at the single -molecule level. The method has been used to trap different dsDNA fragments, sizes varying from 27 to 8,416 bp, and also DNA origami constructions. We also explain how confocal microscopy can be used to determine and optimize the trapping parameters.

Vacuum Rabi splitting and strong-coupling dynamics for surface-plasmon polaritons and rhodamine 6G molecules

We report on strong coupling between surface-plasmon polaritons (SPP) and Rhodamine 6G (R6G) molecules, with double vacuum Rabi splitting energies up to 230 and 110 meV. In addition, we demonstrate the emission of all three energy branches of the strongly coupled SPP-exciton hybrid system, revealing features of system dynamics that are not visible in conventional reflectometry. Finally, in analogy to tunable-Q microcavities, we show that the Rabi splitting can be controlled by adjusting the interaction time between waveguided SPPs and R6G deposited on top of the waveguide. The interaction time can be controlled with sub-fs precision by adjusting the length of the R6G area with standard lithography methods.

Molecular coupling of light with plasmonic waveguides

We use molecules to couple light into and out of microscale plasmonic waveguides. Energy transfer, mediated by surface plasmons, from donor molecules to acceptor molecules over ten micrometer distances is demonstrated. Also surface plasmon coupled emission from the donor molecules is observed at similar distances away from the excitation spot. The lithographic fabrication method we use for positioning the dye molecules allows scaling to nanometer dimensions. The use of molecules as couplers between far-field and near-field light offers the advantages that no special excitation geometry is needed, any light source can be used to excite plasmons and the excitation can be localized below the diffraction limit. Moreover, the use of molecules has the potential for integration with molecular electronics and for the use of molecular self-assembly in fabrication. Our results constitute a proof-of-principle demonstration of a plasmonic waveguide where signal in- and outcoupling is done by molecules.

Carbon nanotubes as electrodes for dielectrophoresis of DNA

Dielectrophoresis can potentially be used as an efficient trapping tool in the fabrication of molecular devices. For nanoscale objects, however, the Brownian motion poses a challenge. We show that the use of carbon nanotube electrodes makes it possible to apply relatively low trapping voltages and still achieve high enough field gradients for trapping nanoscale objects, e.g., single molecules. We compare the efficiency and other characteristics of dielectrophoresis between carbon nanotube electrodes and lithographically fabricated metallic electrodes, in the case of trapping nanoscale DNA molecules. The results are analyzed using finite element method simulations and reveal information about the frequency-dependent polarizability of DNA.