Detection of Biomolecules Using Solid-State Nanopores Fabricated by Controlled Dielectric Breakdown

Nanopore sensor technology is widely used in biomolecular detection due to its advantages of low cost and easy operation. In a variety of nanopore manufacturing methods, controlled dielectric breakdown has the advantages of a simple manufacturing process and low cost under the premise of ensuring detection performance. In this paper, we have made enhancements to the applied pulses in controlled dielectric breakdown and utilized the improved dielectric breakdown technique to fabricate silicon nitride nanopores with diameters of 5 to 15 nm. Our improved fabrication method offers the advantage of precise control over the nanopore diameter (±0.4 nm) and enhances the symmetry of the nanopore. After fabrication, we performed electrical characterization on the nanopores, and the IV characteristics exhibited high linearity. Subsequently, we conducted detection experiments for DNA and protein using the prepared nanopores to assess the detection performance of the nanopores fabricated using our method. In addition, we also give a physical model of molecule translocation through the nanopores to give a reasonable explanation of the data processing results.

Surface Roughness Effects on Confined Nanoscale Transport of Ions and Biomolecules

Biological channels, especially membrane proteins, play a crucial role in metabolism, facilitating the transport of nutrients and other materials across cell membranes in a bio-electrolyte environment. Artificial nanopores are employed to study ion and biomolecule transport behavior inside. While the non-specific interaction between the nanopore surface and transport targets has garnered significant attention, the impact of surface roughness is overlooked. In this study, Nanopores with different levels of inner surface roughness is created by adjusting the FIB (Focus Ion Beam) fabrication parameters. Experiments and molecular dynamics (MD) simulations are employed to demonstrate that greater roughness results from larger FIB beam currents and shorter processing times. Lower roughness increases the capture rate of biomolecules, while greater roughness enhances the normalized blockade current (ΔI/I0 ). The phenomenon of rougher nanopores are attributed to a barrier-dominated capture mechanism and more likely to induce DNA folding. This transport barrier exists in rough nanopores by utilizing steer molecular dynamics (SMD) simulations to investigate the force profile of a dA10 DNA molecule during translocation is demonstrated. This work illustrates how surface roughness influences the ionic current features and the translocation of biomolecules, paving a new way for tunning the molecule transport in nanopores.

CRISPR-based diagnostics of different biomolecules from nucleic acids, proteins, and small molecules to exosomes

CRISPR-based detection technologies have been widely explored for molecular diagnostics. However, the challenge lies in converting the signal of different biomolecules, such as nucleic acids, proteins, small molecules, exosomes, and ions, into a CRISPR-based nucleic acid detection signal. Understanding the detection of different biomolecules using CRISPR technology can aid in the development of practical and promising detection approaches. Unfortunately, existing reviews rarely provide an overview of CRISPR-based molecular diagnostics from the perspective of different biomolecules. Herein, we first introduce the principles and characteristics of various CRISPR nucleases for molecular diagnostics. Then, we focus on summarizing and evaluating the latest advancements in CRISPR-based detection of different biomolecules. Through a comparison of different methods of amplification and signal readout, we discuss how general detection methods can be integrated with CRISPR. Finally, we conclude by identifying opportunities for the improvement of CRISPR in quantitative, amplification-free, multiplex, all-in-one, and point-of-care testing (POCT) purposes.

Electrokinetic Active Particles for Motion-Based Biomolecule Detection

Detection of biomolecules is essential for patient diagnosis, disease management, and numerous other applications. Recently, nano- and microparticle-based detection has been explored for improving traditional assays by reducing required sample volumes and assay times as well as enhancing tunability. Among these approaches, active particle-based assays that couple particle motion to biomolecule concentration expand assay accessibility through simplified signal outputs. However, most of these approaches require secondary labeling, which complicates workflows and introduces additional points of error. Here, we show a proof-of-concept for a label-free, motion-based biomolecule detection system using electrokinetic active particles. We prepare induced-charge electrophoretic microsensors (ICEMs) for the capture of two model biomolecules, streptavidin and ovalbumin, and show that the specific capture of the biomolecules leads to direct signal transduction through ICEM speed suppression at concentrations as low as 0.1 nM. This work lays the foundation for a new paradigm of rapid, simple, and label-free biomolecule detection using active particles.

Template-Assisted Plasmonic Nanogap Shells for Highly Enhanced Detection of Cancer Biomarkers

We present a template-assisted method for synthesizing nanogap shell structures for biomolecular detections based on surface-enhanced Raman scattering. The interior nanogap-containing a silver shell structure, referred to as a silver nanogap shell (Ag NGS), was fabricated on silver nanoparticles (Ag NPs)-coated silica, by adsorbing small aromatic thiol molecules on the Ag NPs. The Ag NGSs showed a high enhancement factor and good signal uniformity, using 785-nm excitation. We performed in vitro immunoassays using a prostate-specific antigen as a model cancer biomarker with a detection limit of 2 pg/mL. To demonstrate the versatility of Ag NGS nanoprobes, extracellular duplex surface-enhanced Raman scattering (SERS) imaging was also performed to evaluate the co-expression of cancer biomarkers, human epidermal growth factor-2 (HER2) and epidermal growth factor receptor (EGFR), in a non-small cell lung cancer cell line (H522). Developing highly sensitive Ag NGS nanoprobes that enable multiplex biomolecular detection and imaging can open up new possibilities for point-of-care diagnostics and provide appropriate treatment options and prognosis.

Photonic Crystal Nanobeam Cavities for Nanoscale Optical Sensing: A Review

The ability to detect nanoscale objects is particular crucial for a wide range of applications, such as environmental protection, early-stage disease diagnosis and drug discovery. Photonic crystal nanobeam cavity (PCNC) sensors have attracted great attention due to high-quality factors and small-mode volumes (Q/V) and good on-chip integrability with optical waveguides/circuits. In this review, we focus on nanoscale optical sensing based on PCNC sensors, including ultrahigh figure of merit (FOM) sensing, single nanoparticle trapping, label-free molecule detection and an integrated sensor array for multiplexed sensing. We believe that the PCNC sensors featuring ultracompact footprint, high monolithic integration capability, fast response and ultrahigh sensitivity sensing ability, etc., will provide a promising platform for further developing lab-on-a-chip devices for biosensing and other functionalities.

Direct growth of few-layer graphene on AlN-based resonators for high-sensitivity gravimetric biosensors

We present the successful growth of few-layer graphene on top of AlN-based solidly mounted resonators (SMR) using a low-temperature chemical vapour deposition (CVD) process assisted by Ni catalysts, and its effective bio-functionalization with antibodies. The SMRs are manufactured on top of fully insulating AlN/SiO2 acoustic mirrors able to withstand the temperatures reached during the CVD growth of graphene (up to 650 °C). The active AlN films, purposely grown with the c-axis tilted, effectively excite shear modes displaying excellent in-liquid performance, with electromechanical coupling and quality factors of around 3% and 150, respectively, which barely vary after graphene integration. Raman spectra reveal that the as-grown graphene is composed of less than five weakly coupled layers with a low density of defects. Two functionalization protocols of the graphene are proposed. The first one, based on a covalent binding approach, starts with a low-damage O2 plasma treatment that introduces a controlled density of defects in graphene, including carboxylic groups. After that, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride/N-hydroxysuccinimide (EDC/NHS) chemistry is used to covalently bind streptavidin molecules to the surface of the sensors. The second functionalization protocol is based on the non-covalent bonding of streptavidin on hydrophobic graphene surfaces. The two protocols end with the effective bonding of biotinylated anti-IgG antibodies to the streptavidin, which leaves the surface of the devices ready for possible IgG detection.

Nanomotors for Nucleic Acid, Proteins, Pollutants and Cells Detection

The development of nanomachines able to operate at the nanoscale, performing complex tasks such as drug delivery, precision surgery, or cell detection, constitutes one of the most important challenges in nanotechnology. The principles that rule the nanoscale are completely different from the ones which govern the macroscopic world and, therefore, the collaboration of scientists with expertise in different fields is required for the effective fabrication of these tiny machines. In this review, the most recent advances carried out in the synthesis and application of nanomachines for diagnosis applications will be presented in order to provide a picture of their potential in the detection of important biomolecules or pathogens in a selective and controlled manner.

Fabrication and Optimization of Bilayered Nanoporous Anodic Alumina Structures as Multi-Point Interferometric Sensing Platform

Herein, we present an innovative strategy for optimizing hierarchical structures of nanoporous anodic alumina (NAA) to advance their optical sensing performance toward multi-analyte biosensing. This approach is based on the fabrication of multilayered NAA and the formation of differential effective medium of their structure by controlling three fabrication parameters (i.e., anodization steps, anodization time, and pore widening time). The rationale of the proposed concept is that interferometric bilayered NAA (BL-NAA), which features two layers of different pore diameters, can provide distinct reflectometric interference spectroscopy (RIfS) signatures for each layer within the NAA structure and can therefore potentially be used for multi-point biosensing. This paper presents the structural fabrication of layered NAA structures, and the optimization and evaluation of their RIfS optical sensing performance through changes in the effective optical thickness (EOT) using quercetin as a model molecule. The bilayered or funnel-like NAA structures were designed with the aim of characterizing the sensitivity of both layers of quercetin molecules using RIfS and exploring the potential of these photonic structures, featuring different pore diameters, for simultaneous size-exclusion and multi-analyte optical biosensing. The sensing performance of the prepared NAA platforms was examined by real-time screening of binding reactions between human serum albumin (HSA)-modified NAA (i.e., sensing element) and quercetin (i.e., analyte). BL-NAAs display a complex optical interference spectrum, which can be resolved by fast Fourier transform (FFT) to monitor the EOT changes, where three distinctive peaks were revealed corresponding to the top, bottom, and total layer within the BL-NAA structures. The spectral shifts of these three characteristic peaks were used as sensing signals to monitor the binding events in each NAA pore in real-time upon exposure to different concentrations of quercetin. The multi-point sensing performance of BL-NAAs was determined for each pore layer, with an average sensitivity and low limit of detection of 600 nm (mg mL⁻¹)⁻¹ and 0.14 mg mL⁻¹, respectively. BL-NAAs photonic structures have the capability to be used as platforms for multi-point RIfS sensing of biomolecules that can be further extended for simultaneous size-exclusion separation and multi-analyte sensing using these bilayered nanostructures.

Surface-Enhanced Raman Scattering (SERS) Active Gold Nanoparticles Decorated on a Porous Polymer Filter

In this work, we designed a process to assemble gold nanoparticles onto a three-dimensional (3D) polymer surface, which can then be monitored using surface-enhanced Raman scattering (SERS). This work is the first demonstration of the assembly of gold nanoparticles on a filter film and in situ measurement with Raman spectroscopy. Herein, a polyhexamethylene adipamide (Nylon66) film embedded in the organic filter film was used as a template to fabricate a tunable SERS-active substrate. A "hotspot"-rich gold-nanoparticle-decorated polymer substrate for SERS was prepared; this substrate exhibited high sensitivity in trace detection of targets. The study was conducted using 4-mercaptobenzoic acid as a probe molecule with the aim of comparing the scattering efficiency and the homogeneity of the Raman signal on selected substrates. In addition, we used the gold-decorated polymer film to detect a biotin-avidin complex. The most powerful advantage of the proposed microanalytical device is the in situ SERS application. The 3D nanoporous structures described in this work hold strong potential for use in various applications such as environmental monitoring and biomolecule detection.

Noble metal nanoparticles in biosensors: recent studies and applications

The aim of this review is to cover advances in noble metal nanoparticle (MNP)-based biosensors and to outline the principles and main functions of MNPs in different classes of biosensors according to the transduction methods employed. The important biorecognition elements are enzymes, antibodies, aptamers, DNA sequences, and whole cells. The main readouts are electrochemical (amperometric and voltametric), optical (surface plasmon resonance, colorimetric, chemiluminescence, photoelectrochemical, etc.) and piezoelectric. MNPs have received attention for applications in biosensing due to their fascinating properties. These properties include a large surface area that enhances biorecognizers and receptor immobilization, good ability for reaction catalysis and electron transfer, and good biocompatibility. MNPs can be used alone and in combination with other classes of nanostructures. MNP-based sensors can lead to significant signal amplification, higher sensitivity, and great improvements in the detection and quantification of biomolecules and different ions. Some recent examples of biomolecular sensors using MNPs are given, and the effects of structure, shape, and other physical properties of noble MNPs and nanohybrids in biosensor performance are discussed.

Three-Dimensional Clustered Nanostructures for Microfluidic Surface-Enhanced Raman Detection

A materials fabrication concept based on a fluid-construction strategy to create three-dimensional (3D) ZnO@ZnS-Ag active nanostructures at arbitrary position within confined microchannels to form an integrated microfluidic surface-enhanced Raman spectroscopy (SERS) system is presented. The fluid-construction process allowed facile construction of the nanostructured substrates, which were shown to possess a substantial number of integrated hot spots that support SERS activity. Finite-difference time-domain (FDTD) analysis suggested that the 3D clustered geometry facilitated hot spot formation. High sensitivity and good recycle performance were demonstrated using 4-mercaptobenzoic acid (4-MBA) and a mixture of Rhodamine 6G (R6G) and 4-MBA as target organic pollutants to evaluate the SERS microfluidic device performance. The 3D clustered nanostructures were also effective in the detection of a representative nerve agent and biomolecule. The results of this investigation provide a materials and process approach to the fabrication of requisite nanostructures for the online detection of organic pollutants, devices for real-time observation of environmental hazards, and personal-health monitoring.

Electrically Excited Plasmonic Nanoruler for Biomolecule Detection

Plasmon-based sensors are excellent tools for a label-free detection of small biomolecules. An interesting group of such sensors are plasmonic nanorulers that rely on the plasmon hybridization upon modification of their morphology to sense nanoscale distances. Sensor geometries based on the interaction of plasmons in a flat metallic layer together with metal nanoparticles inherit unique advantages but need a special optical excitation configuration that is not easy to miniaturize. Herein, we introduce the concept of nanoruler excitation by direct, electrically induced generation of surface plasmons based on the quantum shot noise of tunneling currents. An electron tunneling junction consisting of a metal-dielectric-semiconductor heterostructure is directly incorporated into the nanoruler basic geometry. With the application of voltage on this modified nanoruler, the plasmon modes are directly excited without any additional optical component as a light source. We demonstrate via several experiments that this electrically driven nanoruler possesses similar properties as an optically exited one and confirm its sensing capabilities by the detection of the binding of small biomolecules such as antibodies. This new sensing principle could open the way to a new platform of highly miniaturized, integrated plasmonic sensors compatible with monolithic integrated circuits.

Thermally stable plasmonic nanocermets grown on microengineered surfaces as versatile surface enhanced Raman spectroscopy sensors for multianalyte detection

Noble metal nanoparticle-based plasmonic sensors, fabricated by top-down and colloidal routes, are widely used for high sensitivity detection of diverse analyte molecules using surface enhanced Raman spectroscopy (SERS). However, most of these sensors do not show stability under harsh environments, which limits their use as versatile SERS substrates. In this work, we report the first use of plasmonic nanocermets, grown on microengineered Si surfaces, as potential candidates for a highly robust SERS sensor. The robustness of the sensor is attributed to the anchoring of the nanoparticles in the nanocermet, which is an important factor for exploiting its reusability. The fairly uniform distribution of nanoparticles in the sensor led to high enhancement factors (10(6)-10(7)) and enabled the detection of low concentrations of a wide range of analytes, including differently charged biomolecules, which is extremely difficult for other SERS sensors. With more precise control over the particle geometry and distribution, plasmonic nanocermets may play an important role in ultrasensitive SERS measurements in adverse conditions such as high temperature.