Glypican-3-targeted precision diagnosis of hepatocellular carcinoma on clinical sections with a supramolecular 2D imaging probe

The ability of chemical tools to effectively detect malignancy in frozen sections removed from patients during surgery is important for the timely determination of the subsequent surgical program. However, current clinical methods for tissue imaging rely on dye-based staining or antibody-based techniques, which are sluggish and complicated. Methods: Here, we have developed a 2D material-based supramolecular imaging probe for the simple, rapid yet precise diagnosis of hepatocellular carcinoma (HCC). The 2D probe is constructed through supramolecular self-assembly between a water soluble, fluorescent peptide ligand that selectively targets glypican-3 (GPC-3, a specific cell-surface biomarker for HCC) and 2D molybdenum disulfide that acts as a fluorescence quencher as well as imaging enhancer. Results: We show that the 2D imaging probe developed with minimal background fluorescence can sensitively and selectively image cells overexpressing GPC-3 over a range of control cells expressing other membrane proteins. Importantly, we demonstrate that the 2D probe is capable of rapidly (signal became readable within 1 min) imaging HCC tissues over para-carcinoma regions in frozen sections derived from HCC patients; the results are in accordance with those obtained using traditional clinical staining methods. Conclusion: Compared to conventional staining methods, which are laborious (e.g., over 30 min is needed for antibody-based immunosorbent assays) and complex (e.g., diagnosis is based on discrimination of the nucleus morphology of cancer cells from that of normal cells), our probe, with its simplicity and quickness, might become a promising candidate for tumor-section staining as well as fluorescence imaging-guided surgery.

Electrocatalytic Oxidation of Tris(2-carboxyethyl)phosphine at Pyrroloquinoline Quinone Modified Carbon Nanotube through Single Nanoparticle Collision

Inspired by the addition-elimination catalytic mechanism of natural pyrroloquinoline quinone (PQQ) containing proteins, PQQ-modified hybrid nanomaterials have been increasingly developed recently as biomimetic heterogeneous electrocatalysts. However, up until now, no existing electrochemical approach was able to assess the intrinsic catalytic activity of PQQ sites, impeding the design of efficient PQQ-based electrocatalysts. Herein, in this work, we introduced a new method to calculate the turnover frequency (TOF) of any individual PQQ functional group for electrocatalytic oxidation of tris(2-carboxyethyl)phosphine (TCEP), through the study of single PQQ-decorated carbon nanotube (CNT) collisions at a carbon fiber ultramicroelectrode by chronoamperometry. The core advantage of this approach is being able to resolve the number of PQQ catalytic sites grafted on each individual CNT, so that the charge of any CNT collision event can be accurately translated into the intrinsic activity of the respective PQQ functional groups. The resulting collision-induced current responses clearly showed that the functionalization of CNTs with PQQ could indeed enhance its catalytic performance by 3 times, reaching a TOF value of 133 s^-1 at 1.0 V vs Ag/AgCl. Such a single CNT collision technique, which is proposed for the first time in this work, can open up a new avenue for studying the intrinsic (electro)catalytic performance at a molecular level.

A General Strategy of Aerolysin Nanopore Detection for Oligonucleotides with the Secondary Structure

An aerolysin nanopore is employed as a sensitive tool for single-molecule analysis of short oligonucleotides (≤10 nucleotides), poly(ethylene glycol) (PEGs), peptides, and proteins. However, the direct analysis of long oligonucleotides with the secondary structure (e.g., G-quadruplex topology) remains a challenge, which impedes the further practical applications of the aerolysin nanopore. Here, a simple and applicable method of aerolysin nanopore is presented to achieve a direct analysis of structured oligonucleotides that are extended to 30 nucleotides long by a cation-regulation mechanism. By regulating the cation type in electrolyte solution, the structured oligonucleotides are unfolded into linear form which ensures the successive translocation. The results show that each model oligonucleotide of 5'-(TTAGGG)_n -3' can produce a well-resolved current blockade in its unfolded solution of MgCl₂ . The length between 6 and 30 nucleotides long of model oligonucleotides is proportional to the duration time, showing a translocation velocity as low as 0.70-0.13 ms nt^-1 at +140 mV. This method exhibits an excellent sensitivity and a sufficient temporal resolution, provides insight into the aerolysin nanopore methodology for genetic and epigenetic biosensing, making aerolysin applicable in practical diagnosing with long and structured nucleic acids.

Rationally Designed Sensing Selectivity and Sensitivity of an Aerolysin Nanopore via Site-Directed Mutagenesis

Selectivity and sensitivity are two key parameters utilized to describe the performance of a sensor. In order to investigate selectivity and sensitivity of the aerolysin nanosensor, we manipulated its surface charge at different locations via single site-directed mutagenesis. To study the selectivity, we replaced the positively charged R220 at the entrance of the pore with negatively charged glutamic acid, resulting in barely no current blockages for sensing negatively charged oligonucleotides. For the sensitivity, we substituted the positively charged lumen-exposed amino acid K238 located at trans-ward third of the β-barrel stem with glutamic acid. This leads to a surprisingly longer duration time at +140 mV, which is about 20 times slower in translocation speed for Poly(dA)₄ compared to that of wild-type aerolysin, indicating the stronger pore-analyte interactions and enhanced sensitivity. Therefore, it is both feasible and understandable to rationally design confined biological nanosensors for single molecule detection with high selectivity and sensitivity.

Asymmetric Nanopore Electrode-Based Amplification for Electron Transfer Imaging in Live Cells

Capturing real-time electron transfer, enzyme activity, molecular dynamics, and biochemical messengers in living cells is essential for understanding the signaling pathways and cellular communications. However, there is no generalizable method for characterizing a broad range of redox-active species in a single living cell at the resolution of cellular compartments. Although nanoelectrodes have been applied in the intracellular detection of redox-active species, the fabrication of nanoelectrodes to maximize the signal-to-noise ratio of the probe remains challenging because of the stringent requirements of 3D fabrication. Here, we report an asymmetric nanopore electrode-based amplification mechanism for the real-time monitoring of NADH in a living cell. We used a two-step 3D fabrication process to develop a modified asymmetric nanopore electrode with a diameter down to 90 nm, which allowed for the detection of redox metabolism in living cells. Taking advantage of the asymmetric geometry, the above 90% potential drop at the two terminals of the nanopore electrode converts the faradaic current response into an easily distinguishable bubble-induced transient ionic current pattern. Therefore, the current signal was amplified by at least 3 orders of magnitude, which was dynamically linked to the presence of trace redox-active species. Compared to traditional wire electrodes, this wireless asymmetric nanopore electrode exhibits a high signal-to-noise ratio by increasing the current resolution from nanoamperes to picoamperes. The asymmetric nanopore electrode achieves the highly sensitive and selective probing of NADH concentrations as low as 1 pM. Moreover, it enables the real-time nanopore monitoring of the respiration chain (i.e., NADH) in a living cell and the evaluation of the effects of anticancer drugs in an MCF-7 cell. We believe that this integrated wireless asymmetric nanopore electrode provides promising building blocks for the future imaging of electron transfer dynamics in live cells.

Single Ag Nanoparticle Electro-oxidation: Potential-Dependent Current Traces and Potential-Independent Electron Transfer Kinetic

Potential-dependent current traces were first observed for the same sized nanoparticles (NPs) during the dynamic electro-oxidation process of single AgNPs. In this work, we demonstrated that the motion trajectories of NPs, coupled with electrochemical kinetics parameters, qualitatively predicted from the series of the experimentally observed current traces obtained single AgNPs collision behaviors. Based on the Poisson-Boltzmann equation for a general electrochemical reaction, a rate constant of Ag oxidation could be further estimated to be 1 × 10^-6 mol·cm^-2·s^-1 for electron transfer between AgNPs and the Au electrode by comparing the experimental results. Our method provided a meaningful attempt to test electron transfer kinetics and motion behaviors of single NPs using the high-resolution electrochemical signal.

Real-Time and Accurate Identification of Single Oligonucleotide Photoisomers via an Aerolysin Nanopore

Identification of the configuration for the photoresponsive oligonucleotide plays an important role in the ingenious design of DNA nanomolecules and nanodevices. Due to the limited resolution and sensitivity of present methods, it remains a challenge to determine the accurate configuration of photoresponsive oligonucleotides, much less a precise description of their photoconversion process. Here, we used an aerolysin (AeL) nanopore-based confined space for real-time determination and quantification of the absolute cis/ trans configuration of each azobenzene-modified oligonucleotide (Azo-ODN) with a single molecule resolution. The two completely separated current distributions with narrow peak widths at half height (<0.62 pA) are assigned to cis/ trans-Azo-ODN isomers, respectively. Due to the high current sensitivity, each isomer of Azo-ODN could be undoubtedly identified, which gives the accurate photostationary conversion values of 82.7% for trans-to- cis under UV irradiation and 82.5% for cis-to- trans under vis irradiation. Further real-time kinetic evaluation reveals that the photoresponsive rate constants of Azo-ODN from trans-to- cis and cis-to -trans are 0.43 and 0.20 min^-1, respectively. This study will promote the sophisticated design of photoresponsive ODN to achieve an efficient and applicable photocontrollable process.

Analysis of the electron transfer properties of carbon quantum dots on gold nanorod surfaces via plasmonic resonance scattering spectroscopy

Carbon quantum dot wrapped gold nanorods were fabricated on an ITO electrode surface via electrostatic interactions. The electron transfer properties of carbon quantum dots on gold nanorod surfaces were systematically investigated by plasmonic resonance scattering spectroscopy.

Dehydrogenative homocoupling of tetrafluorobenzene on Pd(111) via para-selective C-H activation

Aryl homocoupling reactions via meta- and ortho-selective C-H activation have been achieved on surfaces, but the highly important para-selective C-H activation has not been reported yet. Combined with scanning tunneling microscopy, time-of-flight secondary ion mass spectrometry and density functional theory, here we describe dehydrogenative homocoupling of tetrafluorobenzene on Pd(111) via para-selective C-H activation to form perfluorinated oligo(p-phenylene)s.

Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis

Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis, we develop an integrated current measurement system and an accurate data processing method for nanopore sensing. The unique geometric structure of a biological nanopore offers a distinct advantage as a nanosensor for single-molecule sensing. The construction of the pore entrance is responsible for capturing the target molecule, while the lumen region determines the translocation process of the single molecule. Since the capture of the target molecule is predominantly diffusion-limited, it is expected that the capture ability of the nanopore toward the target analyte could be effectively enhanced by site-directed mutations of key amino acids with desirable groups. Additionally, changing the side chains inside the wall of the biological nanopore could optimize the geometry of the pore and realize an optimal interaction between the single-molecule interface and the analyte. These improvements would allow for high spatial and current resolution of nanopore sensors, which would ensure the possibility of dynamic study of single biomolecules, including their metastable conformations, charge distributions, and interactions. In the future, data analysis with powerful algorithms will make it possible to automatically and statistically extract detailed information while an analyte translocates through the pore. We conclude that these improvements could have tremendous potential applications for nanopore sensing in the near future.

Measuring a frequency spectrum for single-molecule interactions with a confined nanopore

The time-domain nanopore signal is preciously converted into energy–frequency–time spectra with high frequency resolution and high time resolution using the Hilbert–Huang transform for revealing the detail behaviours of single-molecule weak interactions.

Spectroelectrochemical study of the AMP-Ag+and ATP-Ag+complexes using silver mesh electrodes

In this study, electrochemical reaction mechanism of adenosine monophosphate (AMP) and adenosine triphosphate (ATP) on a silver mesh was investigated in acetate buffer using spectroelectrochemical technique.

In situ and real-time ToF-SIMS analysis of light-induced chemical changes in perovskite CH3NH3PbI3

A hybrid light/ToF-SIMS system was used to analyze the dynamic chemical changes of perovskite CH₃NH₃PbI₃ materials under light illumination.

A thumb-size electrochemical system for portable sensors

A thumb-size and precise electrochemical system is designed for sensors in size and cost sensitive applications.

Reversible redox inter-conversion of biologically active NAD+/NADH derivatives bound to a gold electrode: ToF-SIMS evidence

The electrochemical reversible redox of NAD⁺/NADH is realized, which is confirmed by time-of-flight secondary ion mass spectrometry.

Direct Readout of Single Nucleobase Variations in an Oligonucleotide

Direct, low-cost, label-free, and enzyme-free identification of single nucleobase is a great challenge for genomic studies. Here, this study reports that wild-type aerolysin can directly identify the difference of four types of single nucleobase (adenine, thymine, cytosine, and guanine) in a free DNA oligomer while avoiding the operations of additional DNA immobilization, adapter incorporation, and the use of the processing enzyme. The nanoconfined space of aerolysin enables DNA molecules to be limited in the narrow pore. Moreover, aerolysin exhibits an unexpected capability of detecting DNA oligomers at the femtomolar concentration. In the future, by virtue of the high sensitivity of aerolysin and its high capture ability for DNA oligomers, aerolysin will play an important role in the studies of single nucleobase variations and open up new avenues for a broad range of nucleic-acid-based sensing and disease diagnosis.