Nanopore-Based Confined Spaces for Single-Molecular Analysis

The field of nanopore sensing at the single-molecular level is in a "boom" period. Such nanopores, which are either composed of biological materials or are fabricated from solid-state substrates, offer a unique confined space that is compatible with the single-molecular scale. Under the influence of an electrical field, such single-biomolecular interfaces can read single-molecular information and, if appropriately fine-tuned, each molecule plays its individual ionic rhythm to compose a "molecular symphony". Over the past few decades, many research groups have worked on nanopore-based single-molecular sensors for a range of thrilling chemical and clinical applications. Furthermore, for the past decade, we have also focused on nanopore-based sensors. In this Minireview, we summarize the recent developments in fundamental research and applications in this area, along with data algorithms and advances in hardware, which act as infrastructure for the electrochemical analysis.

Real-time monitoring of electrochemical reactions on single nanoparticles by dark-field and Raman microscopy

Dark-field and Raman microscopy to probe the single NP electrochemistry in real time.

Direct Sensing of Single Native RNA with a Single-Biomolecule Interface of Aerolysin Nanopore

RNA sensing is of vital significance to advance our comprehension of gene expression and to further benefit medical diagnostics. Taking advantage of the excellent sensing capability of the aerolysin nanopore as a single-biomolecule interface, we for the first time achieved the direct characterization of single native RNA of Poly(A)₄ and Poly(U)₄. Poly(A)₄ induces ∼10% larger blockade current amplitude than Poly(U)₄. The statistical duration of Poly(A)₄ is 18.83 ± 1.08 ms, which is 100 times longer than that of Poly(U)₄. Our results demonstrated that the capture of RNA homopolymers is restricted by the biased diffusion. The translocation of RNA needs to overcome a lower free-energy barrier than that of DNA. Moreover, the strong RNA-aerolysin interaction is attributed to the hydroxyl in pentose, which prolongs the translocation time. This study opens an avenue for aerolysin nanopores to directly achieve RNA sensing, including discrimination of RNA epigenetic modification and selective detection of miRNA.

Manipulating and visualizing the dynamic aggregation-induced emission within a confined quartz nanopore

Aggregation-induced emission (AIE) as a unique photophysical process has been intensively explored for their features in fields from optical sensing, bioimaging to optoelectronic devices. However, all AIE luminogens (AIEgens) hardly recover into the initial dispersed state after illuminating at the ultimate aggregated state, which limits AIEgens to achieve reversible sensing and reproducible devices. To real-time manipulate the emission of AIEgen, here we take the advantage of confined space in the quartz nanopore to achieve a nanopore-size-dependent restriction of AIEgens for reversible conversions of “on-to-off” and “off-to-on” emission. By electrochemically manipulating 26 fL AIEgen solution inside nanopore confinement, AIE illuminates while moves along nanopore from the constricted tip to inside cavity at a velocity of 1.4–2.2 μm s⁻¹, and vice versa. We further apply this dynamic manipulation for a target delivery of AIEgen into single cells, which opens up new possibility to design powerful and practical AIE applications.

The difficulty in recovering the aggregation-induced emission fluorogens (AIEgens) to the initial dispersed state upon illuminating has limited their applications. Here, the authors employ the confined space in the quartz nanopore to achieve a nanopore-size dependent restriction of AIEgens.

Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore

Docking of a protein-DNA complex onto a nanopore can provide ample observation time, and has enabled collection of analytic applications of biological nanopores, including DNA sequencing. However, the application of the same principle to solid-state nanopores is tempered by poor understanding of the docking process. Here, we elucidate the behavior of individual protein-DNA complexes docked onto a solid-state nanopore by monitoring the nanopore ionic current. Repeat docking of monovalent streptavidin-DNA complexes is found to produce ionic current blockades that fluctuate between discrete levels. We elucidate the roles of the protein plug and the DNA tether in the docking process, finding the docking configurations to determine the multitude of the current blockade levels, whereas the frequency of the current level switching is determined by the interactions between the molecules and the solid-state membrane. Finally, we prove the feasibility of using the nanopore docking principle for single-molecule sensing using solid-state nanopores by detecting conformational changes of a tethered DNA molecule from a random coil to an i-motif state.

Investigation of the Ionization Mechanism of NAD+/NADH-Modified Gold Electrodes in ToF-SIMS Analysis

Analysis of nicotinamide adenine dinucleotide (NAD⁺/NADH)-modified electrodes is important for in vitro monitoring of key biological processes. In this work, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to analyze NAD⁺/NADH-modified gold electrodes. Interestingly, no obvious characteristic peaks of nicotinamide fragment could be observed in the mass spectra of NAD⁺/NADH in their neutral sodium pyrophosphate form. However, after acidification, the characteristic peaks for both NAD⁺ and NADH were detected. This was due to the suppression effect of inner pyrophosphoric salts in both neutral molecules. Besides, it was proved that the suppression by inner salt was intramolecular. No obvious suppression was found between neighboring molecules. These results demonstrated the suppression effect of inner salts in ToF-SIMS analysis, providing useful evidence for the study of ToF-SIMS ionization mechanism of organic molecule-modified electrodes. Graphical Abstract ᅟ.

Exploring a naturally tailored small molecule for stretchable, self-healing, and adhesive supramolecular polymers

Polymeric materials with integrated functionalities are required to match their ever-expanding practical applications, but there is always a trade-off between complex material performances and synthetic simplification. A simple and effective synthesis route is reported to transform a small molecule of biological origin, thioctic acid, into a high-performance supramolecular polymeric material, which combines processability, ultrahigh stretchability, rapid self-healing ability, and reusable adhesivity to surfaces. The proposed one-step preparation process of this material involves the mixing of three commercially available feedstocks at mild temperature without any external solvent and a subsequent cooling process that resulted in a dynamic, high-density, and dry supramolecular polymeric network cross-linked by three different types of dynamic chemical bonds, whose cooperative effects in the network enable high performance of this supramolecular polymeric material.

Identification of Essential Sensitive Regions of the Aerolysin Nanopore for Single Oligonucleotide Analysis

The aerolysin nanopore channel is one of the confined spaces for single molecule analysis which displays high spatial and temporal resolution for the discrimination of single nucleotides, identification of DNA base modification, and analyzing the structural transition of DNAs. However, to overcome the challenge of achieving the ultimate goal of the widespread real analytical application, it is urgent to probe the sensing regions of the aerolysin to further improve the sensitivity. In this paper, we explore the sensing regions of the aerolysin nanopore by a series of well-designed mutant nanopore experiments combined with molecular dynamics simulations-based electrostatic analysis. The positively charged lumen-exposed Lys-238, identified as one of the key sensing sites due to the presence of a deep valley in the electrostatic potentials, was replaced by different charged and sized amino acids. The results show that the translocation time of oligonucleotides through the nanopore can be readily modulated by the choice of the target amino acid at the 238 site. In particular, a 7-fold slower translocation at a voltage bias of +120 mV is observed with respect to the wild-type aerolysin, which provides a high resolution for methylated cytosine discrimination. We further determine that both the electrostatic properties and geometrical structure of the aerolysin nanopore are crucial to its sensing ability. These insights open ways for rationally designing the sensing mechanism of the aerolysin nanopore, thus providing a novel paradigm for nanopore sensing.

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.