Universal Click-Chemistry Approach for the DNA Functionalization of Nanoparticles.

Nanotechnology has revolutionized the fabrication of hybrid species with tailored functionalities. A milestone in this field is the deoxyribonucleic acid (DNA) conjugation of nanoparticles, introduced almost 30 years ago, which typically exploits the affinity between thiol groups and metallic surfaces. Over the last decades, developments in colloidal research have enabled the synthesis of an assortment of nonmetallic structures, such as high-index dielectric nanoparticles, with unique properties not previously accessible with traditional metallic nanoparticles. However, to stabilize, integrate, and provide further functionality to nonmetallic nanoparticles, reliable techniques for their functionalization with DNA will be crucial. Here, we combine well-established dibenzylcyclooctyne-azide click-chemistry with a simple freeze-thaw method to achieve the functionalization of silica and silicon nanoparticles, which form exceptionally stable colloids with a high DNA surface density of ∼0.2 molecules/nm2. Furthermore, we demonstrate that these functionalized colloids can be self-assembled into high-index dielectric dimers with a yield of over 50% via the use of DNA origami. Finally, we extend this method to functionalize other important nanomaterials, including oxides, polymers, core-shell, and metal nanostructures. Our results indicate that the method presented herein serves as a crucial complement to conventional thiol functionalization chemistry and thus greatly expands the toolbox of DNA-functionalized nanoparticles currently available.

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.

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.

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.

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.

Plasmonic Nanopores for Single-Molecule Detection and Manipulation: Toward Sequencing Applications.

Solid-state nanopore-based sensors are promising platforms for next-generation sequencing technologies, featuring label-free single-molecule sensitivity, rapid detection, and low-cost manufacturing. In recent years, solid-state nanopores have been explored due to their miscellaneous fabrication methods and their use in a wide range of sensing applications. Here, we highlight a novel family of solid-state nanopores which have recently appeared, namely plasmonic nanopores. The use of plasmonic nanopores to engineer electromagnetic fields around a nanopore sensor allows for enhanced optical spectroscopies, local control over temperature, thermophoresis of molecules and ions to/from the sensor, and trapping of entities. This Mini Review offers a comprehensive understanding of the current state-of-the-art plasmonic nanopores for single-molecule detection and biomolecular sequencing applications and discusses the latest advances and future perspectives on plasmonic nanopore-based technologies.

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.

3D nanoporous antennas as a platform for high sensitivity IR plasmonic sensing.

Nanoporous gold can be exploited as plasmonic material for enhanced spectroscopy both in the visible and in the near-infrared spectral regions. In particular, the peculiar morphology of such a substrate leads to a higher field confinement with respect to conventional plasmonic materials. This property can be exploited to achieve extremely high sensitivity to the changes in environmental conditions, making it an interesting tool for the development of sensors and biosensors. Here, we compared the sensitivity of a plasmonic resonator made of nanoporous gold with a similar structure made of homogeneous gold. To assess the enhanced sensitivity the same stoichiometric quantity of dielectric material was deposited via Atomic Layer Deposition onto the two considered structures. Experimental results proved the higher sensitivity was achievable using nanoporous gold. In particular, such 3D nanoporous structures can be proposed as a promising sensing platform in the near-infrared with a sensitivity over 4.000 nm/RIU.

Beaming of Helical Light from Plasmonic Vortices via Adiabatically Tapered Nanotip.

We demonstrate the generation of far-field propagating optical beams with a desired orbital angular momentum by using a smooth optical-mode transformation between a plasmonic vortex and free-space Laguerre-Gaussian modes. This is obtained by means of an adiabatically tapered gold tip surrounded by a spiral slit. The proposed physical model, backed up by the numerical study, brings about an optimized structure that is fabricated by using a highly reproducible secondary electron lithography technique. Optical measurements of the structure excellently agree with the theoretically predicted far-field distributions. This architecture provides a unique platform for a localized excitation of plasmonic vortices followed by its beaming.

Sub-wavelength confinement of the orbital angular momentum of light probed by plasmonic nanorods resonances.

We discuss how the topological charge of an OAM-carrying plasmon (Plasmonic Vortex) can be probed by monitoring the near-field response of plasmonic nanostructures suitably arranged inside a Plasmonic Vortex Lens. The turning "on" or "off" of four gold nanorods, detected by a Scanning Near field Optical Microscope (SNOM), acts as a fingerprint of the OAM state of the PV at the nanoscale. Different configurations are studied numerically, the integrated structure is fabricated and near field characterization is performed for a particularly meaningful case.

Bilayer holey plasmonic vortex lenses for the far field transmission of pure orbital angular momentum light states.

We report the design of a holey plasmonic vortex lens (PVL) structure able to couple circularly polarized impinging light to a plasmonic vortex in the form of the fundamental TM mode of a metal-insulator-metal plasmonic waveguide. The field transmitted through the hole milled at the center of the second metal layer of the structure is characterized by a well-defined spiral harmonic, entirely determined by the spin of impinging light and by the chirality of the PVL structure. Scattering finite elements simulations are presented for single layer standard PVLs and for bilayer ones, comparing the spiral spectra of the transmitted field and the efficiencies of the architectures.

Gate-All-Around Nanopore Osmotic Power Generators.

Nanofluidic channels in a membrane represent a promising avenue for harnessing blue energy from salinity gradients, relying on permselectivity as a pivotal characteristic crucial for inducing electricity through diffusive ion transport. Surface charge emerges as a central player in the osmotic energy conversion process, emphasizing the critical significance of a judicious selection of membrane materials to achieve optimal ion permeability and selectivity within specific channel dimensions. Alternatively, here we report a field-effect approach for in situ manipulation of the ion selectivity in a nanopore. Application of voltage to a surround-gate electrode allows precise adjustment of the surface charge density at the pore wall. Leveraging the gating control, we demonstrate permselectivity turnover to enhanced cation selective transport in multipore membranes, resulting in a 6-fold increase in the energy conversion efficiency with a power density of 15 W/m2 under a salinity gradient. These findings not only advance our fundamental understanding of ion transport in nanochannels but also provide a scalable and efficient strategy for nanoporous membrane osmotic power generation.

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.

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.

Focusing dynamics on circular distributed tapered metallic waveguides by means of plasmonic vortex lenses.

We investigate the focusing effect on circularly distributed planar tapered plasmonic waveguides by means of three-dimensional (3D) finite elements simulations. The proposed configuration allows nanofocusing on four faced planar nanotips, showing efficient condensation of surface plasmons polaritons (SPPs) at the silver/air interface toward the endpoint of the tips. By means of a plasmonic vortex lens it is possible to illuminate the tips with SPP waves carrying orbital angular momentum (OAM), namely plasmonic vortices. Our 3D simulations show that by acting on the topological charge of the plasmonic vortex the electric field charge distribution at the tips apex can be controlled accordingly to the input electric field phase distribution. The results for three particular OAM values are shown, along with a generalization for arbitrary plasmonic vortex angular momentum values.

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.

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.

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.