Theoretical analysis of divalent cation effects on aptamer recognition of neurotransmitter targets.

Aptamer-based sensing of small molecules such as dopamine and serotonin in the brain, requires characterization of the specific aptamer sequences in solutions mimicking the in vivo environment with physiological ionic concentrations. In particular, divalent cations (Mg2+ and Ca2+) present in brain fluid, have been shown to affect the conformational dynamics of aptamers upon target recognition. Thus, for biosensors that transduce aptamer structure switching as the signal response, it is critical to interrogate the influence of divalent cations on each unique aptamer sequence. Herein, we demonstrate the potential of molecular dynamics (MD) simulations to predict the behaviour of dopamine and serotonin aptamers on sensor surfaces. The simulations enable molecular-level visualization of aptamer conformational changes that, in some cases, are significantly influenced by divalent cations. The correlations of theoretical simulations with experimental findings validate the potential for MD simulations to predict aptamer-specific behaviors on biosensors.

Swarm of lightsail nanosatellites for Solar System exploration.

This paper presents a study for the realization of a space mission which employs nanosatellites driven by an external laser source impinging on an optimized lightsail, as a valuable technology to launch swarms of spacecrafts into the Solar System. Nanosatellites propelled by laser can be useful for heliosphere exploration and for planetary observation, if suitably equipped with sensors, or be adopted for the establishment of network systems when placed into specific orbits. By varying the area-to-mass ratio (i.e. the ratio between the sail area and the payload weight) and the laser power, it is possible to insert nanosatellites into different hyperbolic orbits with respect to Earth, thus reaching the target by means of controlled trajectories in a relatively short amount of time. A mission involving nanosatellites of the order of 1 kg of mass is envisioned, by describing all the on-board subsystems and satisfying all the requirements in terms of power and mass budget. Particular attention is paid to the telecommunication subsystem, which must offer all the necessary functionalities. To fabricate the lightsail, the thin films technology has been considered, by verifying the sail's thermal stability during the thrust phase. Moreover, the problem of mechanical stability of the lightsail has been tackled, showing that the distance between the ligthsail structure and the payload plays a pivotal role. Some potential applications of the proposed technology are discussed, such as the mapping of the heliospheric environment.

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores.

Aptamers that undergo conformational changes upon small-molecule recognition have been shown to gate the ionic flux through nanopores by rearranging the charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces is limited. To understand the fundamental mechanisms that facilitate the detection of small-molecule analytes inside structure-switching aptamer-modified nanopores, we correlated experimental observations to theoretical models. We developed a dopamine aptamer-functionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with that of a serotonin sensor fabricated with the same methodology. When these two neurotransmitters with comparable mass and equal charge were detected, the sensors showed an opposite electronic behavior. This distinctive phenomenon was extensively studied using complementary experimental techniques such as quartz crystal microbalance with dissipation monitoring, in combination with theoretical assessment by the finite element method and molecular dynamic simulations. Taken together, our studies demonstrate that the sensing behavior of aptamer-modified nanopores in detecting specific small-molecule analytes correlates with the structure-switching mechanisms of individual aptamers. We believe that such investigations not only improve our understanding of the complex interactions occurring in confined nanoscale environments but will also drive further innovations in biomimetic nanopore technologies.

Transformable Plasmonic Helix with Swinging Gold Nanoparticles.

Control over multiple optical elements that can be dynamically rearranged to yield substantial three-dimensional structural transformations is of great importance to realize reconfigurable plasmonic nanoarchitectures with sensitive and distinct optical feedback. In this work, we demonstrate a transformable plasmonic helix system, in which multiple gold nanoparticles (AuNPs) can be directly transported by DNA swingarms to target positions without undergoing consecutive stepwise movements. The swingarms allow for programmable AuNP translocations in large leaps within plasmonic nanoarchitectures, giving rise to tailored circular dichroism spectra. Our work provides an instructive bottom-up solution to building complex dynamic plasmonic systems, which can exhibit prominent optical responses through cooperative rearrangements of the constituent optical elements with high fidelity and programmability.

Emerging Approaches to DNA Data Storage: Challenges and Prospects.

With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 1014 GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 103 GB/mm3. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies.

Smart Approach for the Design of Highly Selective Aptamer-Based Biosensors.

Aptamers are chemically synthesized single-stranded DNA or RNA oligonucleotides widely used nowadays in sensors and nanoscale devices as highly sensitive biorecognition elements. With proper design, aptamers are able to bind to a specific target molecule with high selectivity. To date, the systematic evolution of ligands by exponential enrichment (SELEX) process is employed to isolate aptamers. Nevertheless, this method requires complex and time-consuming procedures. In silico methods comprising machine learning models have been recently proposed to reduce the time and cost of aptamer design. In this work, we present a new in silico approach allowing the generation of highly sensitive and selective RNA aptamers towards a specific target, here represented by ammonium dissolved in water. By using machine learning and bioinformatics tools, a rational design of aptamers is demonstrated. This "smart" SELEX method is experimentally proved by choosing the best five aptamer candidates obtained from the design process and applying them as functional elements in an electrochemical sensor to detect, as the target molecule, ammonium at different concentrations. We observed that the use of five different aptamers leads to a significant difference in the sensor's response. This can be explained by considering the aptamers' conformational change due to their interaction with the target molecule. We studied these conformational changes using a molecular dynamics simulation and suggested a possible explanation of the experimental observations. Finally, electrochemical measurements exposing the same sensors to different molecules were used to confirm the high selectivity of the designed aptamers. The proposed in silico SELEX approach can potentially reduce the cost and the time needed to identify the aptamers and potentially be applied to any target molecule.

Detection of small-sized DNA fragments in a glassy nanopore by utilization of CRISPR-Cas12a as a converter system.

The fabrication of nanopores with a matched pore size, and the existence of multiple interferents make the reproducible detection of small-sized molecules by means of solid-state nanopores still challenging. A useful method to solve these problems is based on the detection of large DNA nanostructures related to the existence of small-sized targets. In particular, a DNA tetrahedron with a well-defined 3D nanostructure is the ideal candidate for use as a signal transducer. Here, we demonstrate the detection of an L1-encoding gene of HPV18 as a test DNA target sequence in a reaction buffer solution, where long single-stranded DNA linking DNA tetrahedra onto the surface of the magnetic beads is cleaved by a target DNA-activated CRISPR-cas12 system. The DNA tetrahedra are subsequently released and can be detected by the current pulse in a glassy nanopore. This approach has several advantages: (1) one signal transducer can be used to detect different targets; (2) a glassy nanopore with a pore size much larger than the target DNA fragment can boost the tolerance of the contaminants and interferents which often degrade the performance of a nanopore sensor.

Photonic Cavity Effects for Enhanced Efficiency in Layered Perovskite-Based Light-Emitting Diodes.

Layered architectures for light-emitting diodes (LEDs) are the standard approach for solution-processable materials such as metal-halide perovskites. Upon designing the composition and thicknesses of the layers forming the LED, the primary focus is typically on the optimization of charge injection and balance. However, this approach only considers the process until electrons and holes recombine to generate photons, while for achieving optimized LED performance, the generated light must also be efficiently outcoupled. Our work focuses on the latter aspect. We assume efficient photon generation and analyze the effects of the geometrical configuration together with the dipole orientation, mimicking the light emission, on the main characteristics defining the LED, such as the Purcell effect and the outcoupling efficiency. We find that in-plane dipoles result in significantly increased outcoupling efficiency. Furthermore, the mismatch in refractive index among the layers and their different thicknesses can be tuned to maximize the Purcell effect and minimize internal losses. The combined optimization of dipole orientation and layer thicknesses can improve the efficiency of the LED up to a factor 10, hence highlighting the importance of considering also the photonic properties of the LED structures if the objective is to maximize the LED performance.

Directional Plasmonic Excitation by Helical Nanotips.

The phenomenon of coupling between light and surface plasmon polaritons requires specific momentum matching conditions. In the case of a single scattering object on a metallic surface, such as a nanoparticle or a nanohole, the coupling between a broadband effect, i.e., scattering, and a discrete one, such as surface plasmon excitation, leads to Fano-like resonance lineshapes. The necessary phase matching requirements can be used to engineer the light-plasmon coupling and to achieve a directional plasmonic excitation. Here, we investigate this effect by using a chiral nanotip to excite surface plasmons with a strong spin-dependent azimuthal variation. This effect can be described by a Fano-like interference with a complex coupling factor that can be modified thanks to a symmetry breaking of the nanostructure.

Nanoporous Metals: From Plasmonic Properties to Applications in Enhanced Spectroscopy and Photocatalysis.

The field of plasmonics is capable of enabling interesting applications in different wavelength ranges, spanning from the ultraviolet up to the infrared. The choice of plasmonic material and how the material is nanostructured has significant implications for ultimate performance of any plasmonic device. Artificially designed nanoporous metals (NPMs) have interesting material properties including large specific surface area, distinctive optical properties, high electrical conductivity, and reduced stiffness, implying their potentials for many applications. This paper reviews the wide range of available nanoporous metals (such as Au, Ag, Cu, Al, Mg, and Pt), mainly focusing on their properties as plasmonic materials. While extensive reports on the use and characterization of NPMs exist, a detailed discussion on their connection with surface plasmons and enhanced spectroscopies as well as photocatalysis is missing. Here, we report on different metals investigated, from the most used nanoporous gold to mixed metal compounds, and discuss each of these plasmonic materials' suitability for a range of structural design and applications. Finally, we discuss the potentials and limitations of the traditional and alternative plasmonic materials for applications in enhanced spectroscopy and photocatalysis.

Metal-Modified Montmorillonite as Plasmonic Microstructure for Direct Protein Detection.

Thanks to its negative surface charge and high swelling behavior, montmorillonite (MMT) has been widely used to design hybrid materials for applications in metal ion adsorption, drug delivery, or antibacterial substrates. The changes in photophysical and photochemical properties observed when fluorophores interact with MMT make these hybrid materials attractive for designing novel optical sensors. Sensor technology is making huge strides forward, achieving high sensitivity and selectivity, but the fabrication of the sensing platform is often time-consuming and requires expensive chemicals and facilities. Here, we synthesized metal-modified MMT particles suitable for the bio-sensing of self-fluorescent biomolecules. The fluorescent enhancement achieved by combining clay minerals and plasmonic effect was exploited to improve the sensitivity of the fluorescence-based detection mechanism. As proof of concept, we showed that the signal of fluorescein isothiocyanate can be harvested by a factor of 60 using silver-modified MMT, while bovine serum albumin was successfully detected at 1.9 µg/mL. Furthermore, we demonstrated the versatility of the proposed hybrid materials by exploiting their plasmonic properties to develop liquid label-free detection systems. Our results on the signal enhancement achieved using metal-modified MMT will allow the development of highly sensitive, easily fabricated, and cost-efficient fluorescent- and plasmonic-based detection methods for biomolecules.

Detecting COVID-19 from Breath: A Game Changer for a Big Challenge.

Coronavirus disease 2019 (COVID-19) is probably the most commonly heard word of the last 12 months. The outbreak of this virus (SARS-CoV-2) is strongly compromising worldwide healthcare systems, social behavior, and everyone's lives. The early diagnosis of COVID-19 and isolation of positive cases has proven to be fundamental in containing the spread of the infection. Even though the polymerase chain reaction (PCR) based methods remain the gold standard for SARS-CoV-2 detection, the urgent demand for rapid and wide-scale diagnosis precipitated the development of alternative diagnostic approaches. The millions of tests performed every day worldwide are still insufficient to achieve the desired goal, that of screening the population during daily life. Probably the most appealing approach to consistently monitor COVID-19 spread is the direct detection of SARS-CoV-2 from exhaled breath. For instance, the challenging incorporation of reliable, highly sensitive, and cost-efficient detection methods in masks could represent a breakthrough in the development of portable and noninvasive point-of-care diagnosis for COVID-19. In this perspective paper, we discuss the critical technical aspects related to the application of breath analysis in the diagnosis of viral infection. We believe that, if achieved, it could represent a game-changer in containing the pandemic spread.

Dependence of the damage in optical metal/dielectric coatings on the energy of ions in irradiation experiments for space qualification.

Terrestrial accelerator facilities can generate ion beams which enable the testing of the resistance of materials and thin film coatings to be used in the space environment. In this work, a [Formula: see text]/Al bi-layer coating has been irradiated with a [Formula: see text] beam at three different energies. The same flux and dose have been used in order to investigate the damage dependence on the energy. The energies were selected to be in the range 4-100 keV, in order to consider those associated to the quiet solar wind and to the particles present in the near-Earth space environment. The optical, morphological and structural modifications have been investigated by using various techniques. Surprisingly, the most damaged sample is the one irradiated at the intermediate energy, which, on the other hand, corresponds to the case in which the interface between the two layers is more stressed. Results demonstrate that ion energies for irradiation tests must be carefully selected to properly qualify space components.

Recent advances in plasmonic nanocavities for single-molecule spectroscopy.

Plasmonic nanocavities are able to engineer and confine electromagnetic fields to subwavelength volumes. In the past decade, they have enabled a large set of applications, in particular for sensing, optical trapping, and the investigation of physical and chemical phenomena at a few or single-molecule levels. This extreme sensitivity is possible thanks to the highly confined local field intensity enhancement, which depends on the geometry of plasmonic nanocavities. Indeed, suitably designed structures providing engineered local optical fields lead to enhanced optical sensing based on different phenomena such as surface enhanced Raman scattering, fluorescence, and Förster resonance energy transfer. In this mini-review, we illustrate the most recent results on plasmonic nanocavities, with specific emphasis on the detection of single molecules.

Multiplexed Discrimination of Single Amino Acid Residues in Polypeptides in a Single SERS Hot Spot.

The SERS-based detection of protein sequences with single-residue sensitivity suffers from signal dominance of aromatic amino acid residues and backbones, impeding detection of non-aromatic amino acid residues. Herein, we trap a gold nanoparticle in a plasmonic nanohole to generate a single SERS hot spot for single-molecule detection of 2 similar polypeptides (vasopressin and oxytocin) and 10 distinct amino acids that constitute the 2 polypeptides. Significantly, both aromatic and non-aromatic amino acids are detected and discriminated at the single-molecule level either at individual amino acid molecules or within the polypeptide chains. Correlated with molecular dynamics simulations, our results suggest that the signal dominance due to large spatial occupancy of aromatic rings of the polypeptide sidechains on gold surfaces can be overcome by the high localization of the single hot spot. The superior spectral and spatial discriminative power of our approach can be applied to single-protein analysis, fingerprinting, and sequencing.

Two-state switchable plasmonic tweezers for dynamic manipulation of nano-objects.

In this work, we present a plasmonic platform capable of trapping nano-objects in two different spatial configurations. The switch between the two trapping states, localized on the tip and on the outer wall of a vertical gold nanochannel, can be activated by varying the focusing position of the excitation laser along the main axis of the nanotube. We show that the switching of the trapping site is induced by changes in the distribution of the electromagnetic field and of the trapping force. The "inner" and "outer" trapping states are characterized by a static and a dynamic behavior respectively, and their stiffness is measured by analyzing the positions of the trapped specimens as a function of time. In addition, we demonstrate that the stiffness of the static state is high enough to trap particles with diameter as small as 40 nm. These results show a simple, controllable way to generate a switchable two-state trapping regime, which could be used as a model for the study of dynamic trapping or as a mechanism for the development of nanofluidic devices.

Particle trapping and beaming using a 3D nanotip excited with a plasmonic vortex.

Recent advances in nanotechnology have prompted the need for tools to accurately and noninvasively manipulate individual nano-objects. Among the possible strategies, optical forces have been widely used to enable nano-optical tweezers capable of trapping or moving a specimen with unprecedented accuracy. Here, we propose an architecture consisting of a nanotip excited with a plasmonic vortex enabling effective dynamic control of nanoparticles in three dimensions. The structure illuminated by a beam with angular momentum can generate an optical field that can be used to manipulate single dielectric nanoparticles. We demonstrate that it is possible to stably trap or push the particle from specific points, thus enabling a new, to the best of our knowledge, platform for nanoparticle manipulation.

Galvanic Replacement Reaction as a Route to Prepare Nanoporous Aluminum for UV Plasmonics.

There is a growing interest in extending plasmonics applications into the ultraviolet region of the electromagnetic spectrum. Noble metals are commonly used in plasmonic, but their intrinsic optical properties limit their use above 350 nm. Aluminum is probably the most suitable material for UV plasmonics, and in this work we fabricated substrates of nanoporous aluminum starting from an alloy of Al2Mg3. The porous metal is obtained by means of a galvanic replacement reaction. Such nanoporous metal can be exploited to achieve a plasmonic material suitable for enhanced UV Raman spectroscopy and fluorescence. Thanks to the large surface to volume ratio, this material represents a powerful platform for promoting interaction between plasmonic substrates and molecules in the UV.

SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping.

Surface-enhanced Raman spectroscopy (SERS) sensing of DNA bases by plasmonic nanopores could pave a way to novel methods for DNA analyses and new generation single-molecule sequencing platforms. The SERS discrimination of single DNA bases depends critically on the time that a DNA strand resides within the plasmonic hot spot. In fact, DNA molecules flow through the nanopores so rapidly that the SERS signals collected are not sufficient for single-molecule analysis. Here, we report an approach to control the residence time of molecules in the hot spot by an electro-plasmonic trapping effect. By directly adsorbing molecules onto a gold nanoparticle and then trapping the single nanoparticle in a plasmonic nanohole up to several minutes, we demonstrate single-molecule SERS detection of all four DNA bases as well as discrimination of single nucleobases in a single oligonucleotide. Our method can be extended easily to label-free sensing of single-molecule amino acids and proteins.