Single-molecule Sensors Research Articles

Triplexed Tracking Labile Sulfur-Containing Species on a Single-Molecule "Nezha" Sensor.

Sulfur-containing species (SCS), especially sulfur dioxide-relevant species, play an essential role in ecological balance. Owing to the intrinsically labile and mobile characteristics of SCS, it is still considered to be an insurmountable challenge for multiplexed tracking dynamics of SCS with distinct molecular structure, valence state, and condensed state. To address this key problem, we proposed herein alternative versatile single-molecule sensors (VSMs) that intramolecularly integrate high affinity target-guided multiple recognition units into a single sensory molecule, clarified as molecular Nezha available in triplexed responses to gaseous sulfur dioxide, liquid sulfur trioxide, and aqueous bisulfite through ubiquitous charge transfer and nucleophilic addition. High-performance molecular Nezha remarkably facilitated promising applications in a quantitative visualization of SCS on lab-on-paper and tracking the dynamics transformation of SCS as well comprehensive evaluation of multiphase adsorption science of SCS on an advanced Zeolitic imidazolate framework-8 (ZIF-8).

Facile and Highly Selective Ratiometric Fluorescence Probe Based on Benzo[5]helicene for the Detection of Hypochlorous Acid

In physiological processes, hypochlorous acid can regulate in vitro signaling molecules as one kind of reactive oxygen species (ROS). Serious diseases, such as cardiovascular disorders, neurodegenerative diseases, Alzheimer’s disease, and cancers are usually concerned with the abnormal levels of hypochlorous acid in human bodies. Herein, we report a new probe DPH-BP for HClO, which consists of a benzo[5]helicene-pyridine fluorophore and benzyl-benzeneboronic acid pinacol ester as HClO reaction sites. The structural motifs combined with chromogenic media and fluorescence become a single-molecule sensor response in aqueous solutions. In the presence of HClO, this probe shows a remarkable blue shift of fluorescence from 536 to 452 nm in an aqueous solution and obvious fluorescence color change from yellow to blue. In the same conditions, almost no response can be recorded with the other common ROS/RNS, such as H2O2, TBHP, •OH, t-BuO•, ONOO–, and O2•–. As we have designed, the oxidation of phenylboronic ester by HClO induces the cleavage of the benzyl in DPH-BP, which has been proven by 1H NMR spectra and density functional theory calculations. To the best of our knowledge, this is the first report of the analysis of HClO using the oxidation of benzyl-benzeneboronic acid pinacol ester.

Quantum Interference Enhanced Chemical Responsivity in Single-Molecule Dithienoborepin Junctions.

Providing a chemical control over charge transport through molecular junctions is vital to developing sensing applications at the single-molecule scale. Quantum-interference effects that affect the charge transport through molecules offer a unique chance to enhance the chemical control. Here, we investigate how interference effects can be harnessed to optimize the response of single molecule dithienoborepin (DTB) junctions to the specific coordination of a fluoride ion in solution. The single-molecule conductance of two DTB isomers is measured using scanning tunneling microscopy break-junction (STM-BJ) before and after fluoride ion exposure. We find a significant change of conductance before and after the capture of a fluoride ion, the magnitude of which depends on the position of the boron atom in the molecular structure. This single-molecule sensor exhibits switching ratios of up to four orders of magnitudes, suggesting that the boron-fluoride coordination can lead to quantum-interference effects. This is confirmed by a quantum chemical characterization, pointing toward a cross-conjugated path through the molecular structure as the origin of the effect.

Free-Standing Lipid Bilayers Based on Nanopore Array and Ion Channel Formation.

Integrated nanopores are novel and versatile single-molecule sensors for individual label-free biopolymer detection and characterization. However, their studies and application requires a stable lipid bilayer to maintain protein function. Herein, we describe a method for producing lipid bilayers across a nanopore array on a silicon nitride substrate. We used a painting technique commonly used with Teflon films to embed α-hemolysin (α-HL) into bilayer lipid membranes (BLMs) to form an ion channel. This was carried out in nanofluid developed in our lab. The membrane formation process, stability of BLMs and ion channel recordings were monitored by patch clamp in real-time. BLM formation was demonstrated by electrical recording (<10 pS conductance) of suspended lipid bilayers spanning a nanopore in the range of ±100 mV. Membrane resistance (Rm) and capacitance (Cm) of the device with the bilayer were assessed by membrane test as above 1.0 GΩ and ~20±2 pF, respectively. The silicon nitride surface and aperture edge were smooth at the nanometer lever leading to remarkable membrane stability. The membrane lifetime was 5-24 h. A single α-HL channel inserted in 30-60 min applied a potential of +100 mV. The α-HL channel currents were recorded at ~100±10 pA. Such integrated nanopores enable analysis of channel functions under various solution conditions from the same BLM. This will open up a variety of applications for ion channels including high-throughput medical screening and diagnosis.

Chemical-Labeling-Assisted Detection of Nucleobase Modifications by Quantum-Tunneling-Based Single-Molecule Sensing.

Quantum-tunneling-based DNA sensing is a single-molecule technique that promises direct mapping of nucleobase modifications. However, its applicability is seriously limited because of the small difference in conductivity between modified and unmodified nucleobases. Herein, a chemical labeling strategy is presented that facilitates the detection of modified nucleotides by quantum tunneling. We used 5-Formyl-2'-deoxyuridine as a model compound and demonstrated that chemical labeling dramatically alters its molecular conductance compared with that of canonical nucleotides; thus, facilitating statistical discrimination, which is impeded in the unlabeled state. This work introduces a chemical strategy that overcomes the intrinsic difficulty in quantum-tunneling-based modification analysis-the similarity of the molecular conductance of the nucleobases of interest.

Controllable and reversible proton transfer for inorganic cyanide visual sensing based on the deprotonation of azo-phenolic hydroxyl group

ABSTRACTMethods for optical detection of inorganic cyanide based on the single molecule sensor with high selectivity and sensitivity have attracted increasing interest recently due to the high toxicity of cyanide ions. In this work, a visual sensor (S1) containing both imidazole NH and azo-phenolic OH was synthesised and characterised. The spectral experimental data indicated that protic aqueous solution facilitated enhancing the selectivity of cyanide ions with the nanomolar-level detection limit in semi-aqueous solution. The visual sensing mechanism arising from the deprotonation of azo-phenolic OH and the enhancement of intramolecular charge transfer could be clearly demonstrated by titration experiments of 1H NMR, HR MS and energy changes between the HOMO−LUMO band gaps. Furthermore, the reversibility and reusability of S1 upon alternating addition of CN− and H+ were studied.

Photonic nanojet beam shaping by illumination polarization engineering

Photonic Nanojets (PNJs) have attracted considerable research attention in the fields of super-resolution optical microscopy, nano-photolithography, and single molecule sensors because of their sub-wavelength near-field focusing properties. In this paper, we thoroughly studied how the polarizations and amplitude profiles of the incident beams affect the shape, size, and location of the PNJs generated from the illuminated microspheres. Numerical results showed that the PNJs generated by microspheres were strongly modulated by the polarizations and amplitude profiles of the illumination beams. Therefore, PNJs can be engineered according to the requirements of a specific application by designing the polarizations and amplitude profiles of the illumination light. Various fascinating properties of the PNJs generated with different illumination schemes were demonstrated and their implications for potential applications were discussed as well.

Nanopore-Based Single-Biomolecule Interfaces: From Information to Knowledge.

Single-molecule measurements have greatly enhanced our understanding of living systems. Biological systems offer nanopores, a sub-class of membrane proteins, the well-defined confined space for accommodating a single molecule. The biological nanopore acts as a single-biomolecule interface for capturing and identifying a single molecule of interest, and thus it can be used as a single-molecule sensor. In this Perspective, we focus on biological nanopore-based single-biomolecule interfaces for single-biomolecule detection. First, we outline the design of the nanopore-based single-biomolecule interface, which provides rich stochastic information regarding each biomolecule. Next, we highlight future research directions beyond DNA sequencing, including detection of rare species, identification of hidden intermediates, spectral analysis of covalent/noncovalent interactions, and tracing of the dynamic pathways of single-biopolymer behaviors. The concept of a "single-molecule ionic spectrum" is discussed, which may allow mapping of noncovalent interactions at an atomic level in the future. We also discuss the challenges and goals for the future to make this measurement possible for addressing entirely new types of biological questions, which would be an exciting area of future research.

Single-Step FRET-Based Detection of Femtomoles DNA.

Sensitive detection of nucleic acids and identification of single nucleotide polymorphism (SNP) is crucial in diagnosis of genetic diseases. Many strategies have been developed for detection and analysis of DNA, including fluorescence, electrical, optical, and mechanical methods. Recent advances in fluorescence resonance energy transfer (FRET)-based sensing have provided a new avenue for sensitive and quantitative detection of various types of biomolecules in simple, rapid, and recyclable platforms. Here, we report single-step FRET-based DNA sensors designed to work via a toehold-mediated strand displacement (TMSD) process, leading to a distinct change in the FRET efficiency upon target binding. Using single-molecule FRET (smFRET), we show that these sensors can be regenerated in situ, and they allow detection of femtomoles DNA without the need for target amplification while still using a dramatically small sample size (fewer than three orders of magnitude compared to the typical sample size of bulk fluorescence). In addition, these single-molecule sensors exhibit a dynamic range of approximately two orders of magnitude. Using one of the sensors, we demonstrate that the single-base mismatch sequence can be discriminated from a fully matched DNA target, showing a high specificity of the method. These sensors with simple and recyclable design, sensitive detection of DNA, and the ability to discriminate single-base mismatch sequences may find applications in quantitative analysis of nucleic acid biomarkers.

Precise Construction and Tuning of an Aerolysin Single-Biomolecule Interface for Single-Molecule Sensing

Precise Construction and Tuning of an Aerolysin Single-Biomolecule Interface for Single-Molecule Sensing

Single Molecule Identification and Quantification of Glycosaminoglycans Using Solid-State Nanopores.

Glycosaminoglycans (GAGs) are a class of polysaccharides with potent biological activities. Due to their complex and heterogeneous composition, varied charge, polydispersity, and presence of isobaric stereoisomers, the analysis of GAG samples poses considerable challenges to current analytical techniques. In the present study, we combined solid-state nanopores-a single molecule sensorwith a support vector machine (SVM)-a machine learning algorithm for the analysis of GAGs. Our results indicate that the nanopore/SVM technique could distinguish between monodisperse fragments of heparin and chondroitin sulfate with high accuracy (>90%), allowing as low as 0.8% (w/w) of chondroitin sulfate impurities in a heparin sample to be detected. In addition, the nanopore/SVM technique distinguished between unfractionated heparin (UFH) and enoxaparin (low molecular weight heparin) with an accuracy of ∼94% on average. With a reference sample for calibration, a nanopore could achieve nanomolar sensitivity and a5-Log dynamic range. We were able to quantify heparin with reasonable accuracy using multiple nanopores. Our studies demonstrate the potential of the nanopore/SVM technique to quantify and identify GAGs.

Probing and imaging spin interactions with a magnetic single-molecule sensor.

Magnetic single atoms and molecules are receiving intensifying research focus because of their potential as the smallest possible memory, spintronic, and qubit elements. Scanning probe microscopes used to study these systems have benefited greatly from new techniques that use molecule-functionalized tips to enhance spatial and spectroscopic resolutions and enable new sensing capabilities. We demonstrate a microscopy technique that uses a magnetic molecule, Ni(cyclopentadienyl)2, adsorbed at the apex of a scanning probe tip, to sense exchange interactions with another molecule adsorbed on a Ag(110) surface in a continuously tunable fashion in all three spatial directions. We further used the probe to image contours of exchange interaction strength, revealing angstrom-scale regions where the quantum states of two magnetic molecules strongly mix. Our results pave the way for new nanoscale imaging capabilities based on magnetic single-molecule sensors.

Charge Transport and Thermoelectric Properties of Carbon Sulfide Nanobelts in Single-Molecule Sensors

The design, synthesis, and operation of single-molecule sensor devices are outstanding challenges in the field of molecular electronics. These devices are of significant interest as they could report the presence of harmful substances in different environments. Motivated by this, by means of non-equilibrium Green’s function density functional theory, we investigate the properties of pristine single-molecule junctions comprised of single-walled heterocyclic nanobelts terminated with sulfur in contact with gold electrodes. These nanobelts are single slices of nanotubes, resulting in a molecular belt of fused aromatic rings, which have the shortest possible length of a nanotube; thus, fundamental studies of transport properties can be performed because of their finite size. We probe the charge transport and thermoelectric properties as a function of voltage bias and temperature. We find the radius of the nanobelt, and thus the number of Au–S contacts, has a strong impact on their electronic properties. With ...

Microscopic Imaging of Restriction Engineered Biological Nanopores for Highly Specific Spotting of Epigenetic Markers

Biological nanopores, which originate from ion channel proteins, are capable of sequencing genomic DNAs but with a limited throughput even in a commercialized form. By digitally encoding fluorescence from Ca2+ fluxes through individual nanopores, an array of single molecule sensors (>10∧4) could be visually monitored in parallel within a finger-tip sized device. Nanopore sensors have long been restricted to either natural ion channel proteins or fabricated solid state apertures, which have limited spatial resolution for identifying a single nucleotide without any interference from its neighbour bases. Our recent investigation unveils that precise engineering within the pore restriction could be performed with an enhanced sensing performance by signal amplification. The demonstrated progress in the measurement throughput and the spatial resolution for a nanopore sensor could benefit fundamental biophysical studies in single molecule and practical precision medicine applications such as epigenetic marker spotting, which is to be demonstrated in our talk.

Single-Molecule Analysis with Solid-State Nanopores

Solid-state nanopores and nanopipettes are an exciting class of single-molecule sensors that has grown enormously over the last two decades. They offer a platform for testing fundamental concepts of stochasticity and transport at the nanoscale, for studying single-molecule biophysics and, increasingly, also for new analytical applications and in biomedical sensing. This review covers some fundamental aspects underpinning sensor operation and transport and, at the same time, it aims to put these into context as an analytical technique. It highlights new and recent developments and discusses some of the challenges lying ahead.

Quantum Dots in Biomedical Applications

Semiconducting nanocrystals, more commonly known as quantum dots, possess unique size and shape dependent optoelectronic properties. In recent years, these unique properties have attracted much attention in the biomedical field to enable real-time tissue imaging (bioimaging), diagnostics, single molecule sensors, and drug delivery, among many other areas. The optical properties of quantum dots can be tuned by size and composition, and their small size and high surface area make them excellent candidates for intracellular tracking, diagnostics, in vivo imaging, and therapeutic delivery. We discuss recent advances and challenges in the molecular design of quantum dots are discussed, along with applications of quantum dots as drug delivery vehicles, theranostic agents, single molecule sensors, and real-time in vivo deep tissue imaging agents. We present a detailed discussion of the biodistribution and toxicity of quantum dots, and highlight recent advances to improve long-term stability in biological buffers, increase quantum yield following bioconjugation, and improve clearance from the body. Last, we present an outlook on future challenges and strategies to further advance translation to clinical application.

Single-Molecule Protein Phosphorylation and Dephosphorylation by Nanopore Enzymology.

Reversible protein phosphorylation plays a crucial and ubiquitous role in the control of almost all cellular processes. The interplay of protein kinases and phosphatases acting in opposition ensures tight dynamic control of protein phosphorylation states within the cell. Previously, engineered α-hemolysin pores bearing kinase substrate peptides have been developed as single-molecule stochastic sensors for protein kinases. Here, we have used these pores to observe, label-free, the phosphorylation and dephosphorylation of a single substrate molecule. Further, we investigated the effect of Mg2+ and Mn2+ upon substrate and product binding and found that Mn2+ relaxes active-site specificity toward nucleotides and enhances product binding. In doing so, we demonstrate the power and versatility of nanopore enzymology to scrutinize a critical post-translational modification.

Label-Free Optical Detection of DNA Translocations through Plasmonic Nanopores.

Solid-state nanopores are single-molecule sensors that hold great potential for rapid protein and nucleic-acid analysis. Despite their many opportunities, the conventional ionic current detection scheme that is at the heart of the sensor suffers inherent limitations. This scheme intrinsically couples signal strength to the driving voltage, requires the use of high-concentration electrolytes, suffers from capacitive noise, and impairs high-density sensor integration. Here, we propose a fundamentally different detection scheme based on the enhanced light transmission through a plasmonic nanopore. We demonstrate that translocations of single DNA molecules can be optically detected, without the need of any labeling, in the transmitted light intensity through an inverted-bowtie plasmonic nanopore. Characterization and the cross-correlation of the optical signals with their electrical counterparts verify the plasmonic basis of the optical signal. We demonstrate DNA translocation event detection in a regime of driving voltages and buffer conditions where traditional ionic current sensing fails. This label-free optical detection scheme offers opportunities to probe native DNA–protein interactions at physiological conditions.

Challenges and Solutions in Developing Ultrasensitive Biosensors.

This Perspective focuses on the latest strategies and challenges for the development of bioanalytical sensors with sub-picomolar detection limits. Achieving sub-picomolar detection limits has three major challenges: (1) assay sensitivity, (2) response time, and (3) selectivity (including limiting background signals). Each of these challenges is discussed, along with how nanomaterials provide the solutions. One strategy to gain greater sensitivity involves confining the sensing volume to the nanoscale, as used in nanopore- or nanoparticle-based sensors, because nanoparticles are ubiquitous in amplification. Methods to improve response time typically focus on obtaining an intimate mixture between the sensor and the sample either by extending the length scale of nanoscale sensors using nanostructuring or by dispersing magnetic nanoparticles through the sample to capture the analyte. Loading nanoparticles with many biorecognition species is one solution to help address the challenge of selectivity. Many examples in this Perspective explore the detection of prostate-specific antigenwhich enables a comparison between strategies. Finally, exciting future opportunities in developing single-molecule sensors and the requirements to go even lower in concentration are explored.

Identification of Spherical and Nonspherical Proteins by a Solid-State Nanopore.

The three-dimensional structure of a protein plays an important role in protein dynamics in the biological system of human. By now, it remains a challenge to characterize and quantify the shape of a protein at the single-molecule level. The nanopores, as a novel single-molecule sensor, has been widely applied in many fields such as DNA sequencing and human diseases diagnosis. In this paper, we investigated the translocation of spherelike con.A and the prolate bovine serum albumin (BSA) under an electric field by a solid-state nanopore. By analyzing the ionic current, the con.A and the BSA could be characterized and differentiated due to their intrinsic shape difference. Because the prolate BSA will have the preferred orientations for a higher electric field, when it is residing inside the nanopore, multiple ionic current blockade levels will be observed. While for the spherical con.A, there is only one ionic current blockade level. The method presented here will be potentially applied to fingerprint a single protein as a new method having the features of low cost and high throughput in the near future.