Trapping of a single DNA molecule using nanoplasmonic structures for biosensor applications

Mirror-Enhanced Plasmonic Nanoaperture for Ultrahigh Optical Force Generation with Minimal Heat Generation

Double Nanohole Plasmonic Tweezers (DNH) have emerged as a powerful approach for confining light to sub-wavelength volume, enabling the trapping of nanoscale particles much smaller than the wavelength of light. However, to circumvent plasmonic heating effects, DNH tweezers are typically operated off-resonance, resulting in reduced optical forces and field enhancements. In this study, we introduce a novel DNH design with a reflector layer, enabling on-resonance illumination while minimizing plasmonic heating. This design efficiently dissipates heat and redistributes the electromagnetic hotspots, making them more accessible for trapping nanoscale particles and enhancing light-matter interactions. We also demonstrate low-power trapping and release of small extracellular vesicles. Our work opens new possibilities for trapping-assisted Surface Enhanced Raman Spectroscopy (SERS), plasmon-enhanced imaging, and single photon emission applications that demand strong light-matter interactions.

Nanoscale Optical Trapping by Means of Dielectric Bowtie

Plasmonic and dielectric tweezers represent a common paradigm for an innovative and efficient optical trapping at the micro/nanoscale. Plasmonic configurations provide subwavelength mode confinement, resulting in very high optical forces, at the expense of a higher thermal effect, that could undermine the biological sample under test. On the contrary, dielectric configurations show limited optical forces values but overcome the thermal challenge. Achieving efficient optical trapping without affecting the sample temperature is still demanding. Here, we propose the design of a silicon (Si)-based dielectric nanobowtie dimer, made by two tip-to-tip triangle semiconductor elements. The combination of the conservation of the normal component of the electric displacement and the tangential component of the electric field, with a consequent large energy field confinement in the trapping site, ensures optical forces of about 27 fN with a power of 6 mW/µm2. The trapping of a virus with a diameter of 100 nm is demonstrated with numerical simulations, calculating a stability S = 1, and a stiffness k = 0.33 fN/nm, within a footprint of 0.96 µm2, preserving the temperature of the sample (temperature variation of 0.3 K).

DNA sequencing: an overview of solid-state and biological nanopore-based methods

The field of sequencing is a topic of significant interest since its emergence and has become increasingly important over time. Impressive achievements have been obtained in this field, especially in relations to DNA and RNA sequencing. Since the first achievements by Sanger and colleagues in the 1950s, many sequencing techniques have been developed, while others have disappeared. DNA sequencing has undergone three generations of major evolution. Each generation has its own specifications that are mentioned briefly. Among these generations, nanopore sequencing has its own exciting characteristics that have been given more attention here. Among pioneer technologies being used by the third-generation techniques, nanopores, either biological or solid-state, have been experimentally or theoretically extensively studied. All sequencing technologies have their own advantages and disadvantages, so nanopores are not free from this general rule. It is also generally pointed out what research has been done to overcome the obstacles. In this review, biological and solid-state nanopores are elaborated on, and applications of them are also discussed briefly.

Plasmonic Biosensors for Single-Molecule Biomedical Analysis

The rapid spread of epidemic diseases (i.e., coronavirus disease 2019 (COVID-19)) has contributed to focus global attention on the diagnosis of medical conditions by ultrasensitive detection methods. To overcome this challenge, increasing efforts have been driven towards the development of single-molecule analytical platforms. In this context, recent progress in plasmonic biosensing has enabled the design of novel detection strategies capable of targeting individual molecules while evaluating their binding affinity and biological interactions. This review compiles the latest advances in plasmonic technologies for monitoring clinically relevant biomarkers at the single-molecule level. Functional applications are discussed according to plasmonic sensing modes based on either nanoapertures or nanoparticle approaches. A special focus was devoted to new analytical developments involving a wide variety of analytes (e.g., proteins, living cells, nucleic acids and viruses). The utility of plasmonic-based single-molecule analysis for personalized medicine, considering technological limitations and future prospects, is also overviewed.

Plasmonic tweezers: for nanoscale optical trapping and beyond

Optical tweezers and associated manipulation tools in the far field have had a major impact on scientific and engineering research by offering precise manipulation of small objects. More recently, the possibility of performing manipulation with surface plasmons has opened opportunities not feasible with conventional far-field optical methods. The use of surface plasmon techniques enables excitation of hotspots much smaller than the free-space wavelength; with this confinement, the plasmonic field facilitates trapping of various nanostructures and materials with higher precision. The successful manipulation of small particles has fostered numerous and expanding applications. In this paper, we review the principles of and developments in plasmonic tweezers techniques, including both nanostructure-assisted platforms and structureless systems. Construction methods and evaluation criteria of the techniques are presented, aiming to provide a guide for the design and optimization of the systems. The most common novel applications of plasmonic tweezers, namely, sorting and transport, sensing and imaging, and especially those in a biological context, are critically discussed. Finally, we consider the future of the development and new potential applications of this technique and discuss prospects for its impact on science.

Label-free plasmonic assisted optical trapping of single DNA molecules

DNA molecules are hard to catch using traditional optical trapping due to the nanometer width of their chains. Here we experimentally demonstrate a label-free optical trapping of a single micrometer λ-DNA in solution by the aid of plasmonic gold nanoparticles (GNPs), where a double-laser trap induces strong optical interparticle forces for the tweezer. We examine such sub-resolved interparticle forces by tracking the GNP dynamics in solution. Moreover, surface-enhanced Raman scattering signals of trapped λ-DNA have also been measured simultaneously in the same setup. In comparison with prior works, ours benefit from the excitation in a dynamic configuration without fabrication. This technique opens a new avenue for all-optical manipulation of biomolecules, as well as ultra-sensitive bio-medical sensing applications.

Controlling DNA Translocation Through Solid-state Nanopores

Compared with the status of bio-nanopores, there are still several challenges that need to be overcome before solid-state nanopores can be applied in commercial DNA sequencing. Low spatial and low temporal resolution are the two major challenges. Owing to restrictions on nanopore length and the solid-state nanopores' surface properties, there is still room for improving the spatial resolution. Meanwhile, DNA translocation is too fast under an electrical force, which results in the acquisition of few valid data points. The temporal resolution of solid-state nanopores could thus be enhanced if the DNA translocation speed is well controlled. In this mini-review, we briefly summarize the methods of improving spatial resolution and concentrate on controllable methods to promote the resolution of nanopore detection. In addition, we provide a perspective on the development of DNA sequencing by nanopores.

Overcoming Diffusion-Limited Trapping in Nanoaperture Tweezers Using Opto-Thermal-Induced Flow

Nanoaperture-based plasmonic tweezers have shown tremendous potential in trapping, sensing, and spectroscopic analysis of nano-objects with single-molecule sensitivity. However, the trapping process is often diffusion-limited and therefore suffers from low-throughput. Here, we present bubble- and convection-assisted trapping techniques, which use opto-thermally generated Marangoni and Rayleigh-Bénard convection flow to rapidly deliver particles from large distances to the nanoaperture instead of relying on normal diffusion, enabling a reduction of 1-2 orders of magnitude in particle-trapping time (i.e., time before a particle is trapped). At a concentration of 2 × 107 particles/mL, average particle-trapping times in bubble- and convection-assisted trapping were 7 and 18 s, respectively, compared with more than 300 s in the diffusion-limited trapping. Trapping of a single particle at an ultralow concentration of 2 × 106 particles/mL was achieved within 2-3 min, which would otherwise take several hours in the diffusion-limited trapping. With their quick delivery and local concentrating of analytes at the functional surfaces, our convection- and bubble-assisted trapping could lead to enhanced sensitivity and throughput of nanoaperture-based plasmonic sensors.

Plasmonic Tweezers towards Biomolecular and Biomedical Applications

With the capability of confining light into subwavelength scale, plasmonic tweezers have been used to trap and manipulate nanoscale particles. It has huge potential to be utilized in biomolecular research and practical biomedical applications. In this short review, plasmonic tweezers based on nano-aperture designs are discussed. A few challenges should be overcome for these plasmonic tweezers to reach a similar level of significance as the conventional optical tweezers.

Tunable optical forces enhanced by plasmonic modes hybridization in optical trapping of gold nanorods with plasmonic nanocavity

The optomechanical interaction between a plasmonic nanocavity and a gold nanorod through optical forces is demonstrated. It is revealed that strong localized plasmon resonance mode hybridization induced by a gold nanorod results in the resonance mode of the nanocavity splitting into two different plasmon resonance modes (bonding plasmon resonance mode and antibonding plasmon resonance mode). When the whole system (gold nanorod and gold nanocavity) is excited at the antibonding plasmon mode, the gold nanorod can receive an optical pushing force and be pushed away from the gold nanocavity. On the other hand, an optical pulling force acts on the gold nanorod and the gold nanorod can be trapped by the gold nanocavity when the plasmonic tweezers work at the bonding mode. The optical pulling force acting on the gold nanorod can be enhanced by two orders of magnitude larger than that of the same sized dielectric nanorod, which benefits from the strong resonant nearfield interaction between the gold nanorod and the gold nanocavity. More importantly, the shape and the position of the optical potential can be tuned by tailoring the wavelength of the laser used in the optical trapping, which can be used to manipulate the gold nanorod within a nanoscale region. Our findings have important implications for optical trapping, manipulation, sorting, and sieving of plasmonic nanoparticles with plasmonic tweezers.

Plasmonic Trapping and Release of Nanoparticles in a Monitoring Environment

Plasmonic tweezers use surface plasmon polaritons to confine polarizable nanoscale objects. Among the various designs of plasmonic tweezers, only a few can observe immobilized particles. Moreover, a limited number of studies have experimentally measured the exertable forces on the particles. The designs can be classified as the protruding nanodisk type or the suppressed nanohole type. For the latter, microscopic observation is extremely challenging. In this paper, a new plasmonic tweezer system is introduced to monitor particles, both in directions parallel and orthogonal to the symmetric axis of a plasmonic nanohole structure. This feature enables us to observe the movement of each particle near the rim of the nanohole. Furthermore, we can quantitatively estimate the maximal trapping forces using a new fluidic channel.

Photonic and Plasmonic Nanotweezing of Nano- and Microscale Particles

The ability to manipulate and sense biological molecules is important in many life science domains, such as single-molecule biophysics, the development of new drugs and cancer detection. Although the manipulation of biological matter at the nanoscale continues to be a challenge, several types of nanotweezers based on different technologies have recently been demonstrated to address this challenge. In particular, photonic and plasmonic nanotweezers are attracting a strong research effort especially because they are efficient and stable, they offer fast response time, and avoid any direct physical contact with the target object to be trapped, thus preventing its disruption or damage. In this paper, we critically review photonic and plasmonic resonant technologies for biomolecule trapping, manipulation, and sensing at the nanoscale, with a special emphasis on hybrid photonic/plasmonic nanodevices allowing a very strong light-matter interaction. The state-of-the-art of competing technologies, e.g., electronic, magnetic, acoustic and carbon nanotube-based nanotweezers, and a description of their applications are also included.

Dynamic motions of DNA molecules in an array of plasmonic traps

The dynamic motion of a DNA near a plasmonic nanohole.

A measurement of the maximal forces in plasmonic tweezers

Plasmonic tweezers that are designed to trap nanoscale objects create many new possibilities for single-molecule targeted studies. Numerous novel designs of plasmonic nanostructures are proposed in order to attain stronger forces and weaker laser intensity. Most experiments have consisted only of immobilization observations--that is, particles stick when the laser is turned on and fall away when the laser is turned off. Studies of the exertable forces were only theoretical. A few studies have experimentally measured trap stiffness. However, as far as we know, no studies have addressed maximal forces. In this paper, we present a new experimental design in which the motion of the trapped particle can be monitored in either parallel or orthogonal directions to the plasmonic structure's symmetric axis. We measured maximal trapping force through such monitoring. Although stiffness would be useful for force-calibration or immobilization purposes, for which most plasmonic tweezers are used, we believe that the maximal endurable force is significant and thus, this paper presents this aspect.

Separation of DNA by length in rotational flow: Lattice-Boltzmann-based simulations

We use a lattice-Boltzmann based Brownian dynamics simulation to investigate the separation of different lengths of DNA through the combination of a trapping force and the microflow created by counter-rotating vortices. We can separate most long DNA molecules from shorter chains that have lengths differing by as little as 30%. The sensitivity of this technique is determined by the flow rate, size of the trapping region, and the trapping strength. We expect that this technique can be used in microfluidic devices to separate long DNA fragments that result from techniques such as restriction enzyme digests of genomic DNA.

Label-free free-solution nanoaperture optical tweezers for single molecule protein studies

Recent advances in nanoaperture optical tweezers have enabled studies of single nanoparticles like proteins in label-free, free-solution environments.