Single Molecule DNA Analysis Based on Atomic-Controllable Nanopores in Covalent Organic Frameworks

Sequence-Dependent Single-Molecule DNA Sensing Using Covalent Organic Framework Nanopores

Enzyme-free single-molecule sequencing has the potential to significantly expand the application of nanopore technology to DNA, proteins, and saccharides. Despite their advantages over biological nanopores and natural suitability for enzyme-free single-molecule sequencing, conventional solid-state nanopores have not yet achieved single-molecule DNA sequencing. The biggest challenge for the accuracy of single-molecule sequencing using solid-state nanopores lies in the precise control of the pore size and conformity. In this study, we fabricated nanopore devices by covering the tip of a quartz nanopipette with ultrathin two-dimensional (2D) covalent organic framework (COF) nanosheets (pore size ≈ 1.1 nm). The size of the periodically arranged nanopores in COF is comparable to that of protein nanopores, and the structure of each COF nanopore is consistent at the atomic scale. The COF nanopore device could roughly distinguish dAMP, dCMP, dGMP, and dTMP. Furthermore, a certain percentage of the current blockades originating from 150 nucleotides model DNA molecules (13.5% for dA50dC50dA50 and 11.1% for dC50dA50dC50) show distinct DNA sequence-specific concave and convex resistive current patterns. The finite element simulation confirmed that the current blockade pattern of a DNA molecule passing through a COF nanopore is dependent on the relative location of the nanopore with respect to the wall of the nanopipette. Our study is a significant step toward single-molecule DNA sequencing by solid-state nanopores.

A covalent organic framework nanosheet-nanochannel composite with signal amplification strategy for electrochemical enantioselective recognition

Recognition and separation of chiral isomers are of great importance in both industrial and biological applications. However, owing to identical molecular formulas and chemical properties of enantiomers, signal transduction and amplification are still two major challenges in chiral sensing. In this study, we developed an enantioselective device by integrating chiral covalent organic framework nanosheets (CONs) with nanochannels for sensitive identification and quantification of enantiomers. Using 3,4-dihydroxyphenylalanine (DOPA) as the model analyte, the as-prepared chiral nanofluidic device exhibits a remarkable chiral recognition ability to l-DOPA than d-DOPA. More importantly, due to the chelation of DOPA with Fe3+ ions, it can efficiently block the ion transport through channel and shield the channel surface charge, which will amplify the difference in the electrochemical response of l-DOPA and d-DOPA. Therefore, a sensitive chiral recognition can be achieved using the present nanofluidic device coupled using electrochemical amplification strategy. Notably, using this method, an ultra-low concentration of l-DOPA (as low as 0.21 pM) can be facilely and successfully detected with a linear range of 1 pM-10 μM. This study provides a reliable and sensitive approach for achieving highly selective detection of chiral molecules.

Research Progress on Saccharide Molecule Detection Based on Nanopores

Saccharides, being one of the fundamental molecules of life, play essential roles in the physiological and pathological functions of cells. However, their intricate structures pose challenges for detection. Nanopore technology, with its high sensitivity and capability for single-molecule-level analysis, has revolutionized the identification and structural analysis of saccharide molecules. This review focuses on recent advancements in nanopore technology for carbohydrate detection, presenting an array of methods that leverage the molecular complexity of saccharides. Biological nanopore techniques utilize specific protein binding or pore modifications to trigger typical resistive pulses, enabling the high-sensitivity detection of monosaccharides and oligosaccharides. In solid-state nanopore sensing, boronic acid modification and pH gating mechanisms are employed for the specific recognition and quantitative analysis of polysaccharides. The integration of artificial intelligence algorithms can further enhance the accuracy and reliability of analyses. Serving as a crucial tool in carbohydrate detection, we foresee significant potential in the application of nanopore technology for the detection of carbohydrate molecules in disease diagnosis, drug screening, and biosensing, fostering innovative progress in related research domains.

Single-Digit Nanobubble Sensing via Nanopore Technology

Nanobubbles play an important role in diverse fields, including engineering, medicine, and agriculture. Understanding the characteristics of individual nanobubbles is essential for comprehending fluid dynamics behaviors and advancing nanoscale science across various fields. Here, we report a strategy based on nanopore sensors for characterizing single-digit nanobubbles. We investigated the sizes and diffusion coefficients of nanobubbles at different voltages. Additionally, the finite element simulation and molecular dynamics simulation were introduced to account for counterion concentration variation around nanobubbles in the nanopore. In particular, the differences in stability and surface charge density of nanobubbles under various solution environments have been studied by the ion-stabilized model and the DLVO theory. Additionally, a straightforward method to mitigate nanobubble generation in the bulk for reducing current noise in nanopore sensing was suggested. The results hold significant implications for enhancing the understanding of individual nanobubble characterizations, especially in the nanofluid field.

The combination of DNA nanostructures and materials for highly sensitive electrochemical detection

Due to the wide range of electrochemical devices available, DNA nanostructures and material-based technologies have been greatly broadened. They have been actively used to create a variety of beautiful nanostructures owing to their unmatched programmability. Currently, a variety of electrochemical devices have been used for rapid sensing of biomolecules and other diagnostic applications. Here, we provide a brief overview of recent advances in DNA-based biomolecular assays. Biosensing platform such as electrochemical biosensor, nanopore biosensor, and field-effect transistor biosensors (FET), which are equipped with aptamer, DNA walker, DNAzyme, DNA origami, and nanomaterials, has been developed for amplification detection. Under the optimal conditions, the proposed biosensor has good amplification detection performance. Further, we discussed the challenges of detection strategies in clinical applications and offered the prospect of this field.

Ionic Current Saturation Enabled by Cation Gating Effect in Metal-Organic-Framework Membranes

Ion transport through nanoporous two-dimensional (2D) membranes is predicted to be tunable by controlling the charging status of the membranes' planar surfaces, the behavior of which though remains to be assessed experimentally. Here we investigate ion transport through intrinsically porous membranes made of 2D metal-organic-framework layers. In the presence of certain cations, we observe a linear-to-nonlinear transition of the ionic current in response to the applied electric field, the behavior of which is analogous to the cation gating effect in the biological ion channels. Specifically, the ionic currents saturate at transmembrane voltages exceeding a few hundreds of millivolts, depending on the concentration of the gating cations. This is attributed to the binding of cations at the membranes' surfaces, tuning the charging states there and affecting the entry/exit process of translocating ions. Our work also provides 2D membranes as candidates for building nanofluidic devices with tunable transport properties.

Determination of Acetylamantadine by γ-Cyclodextrin-Assisted α-HL Nanopore for Potential Cancer Prediagnosis

The high expression of Spermidine/spermine N1-acetyltransferase (SSAT-1) is an important indicator in early cancer diagnosis. Here, we developed a nanopore-based methodology with γ-cyclodextrin as an adaptor to detect and quantify acetylamantadine, the specific SSAT-1-catalyzed product from amantadine, to accordingly reflect the activity of SSAT-1. We employ γ-cyclodextrin and report that amantadine cannot cause any secondary signals in γ-cyclodextrin-assisted α-HL nanopore, while its acetylation product, acetylamantadine, does. This allows γ-cyclodextrin to practically detect acetylamantadine in the interference of excessive amantadine, superior to the previously reported β-cyclodextrin. The quantification of acetylamantadine was not interfered with even a 50-fold amantadine and displayed no interference in artificial urine sample analysis, which indicates the good feasibility of this nanopore-based methodology in painless cancer prediagnosis. In addition, the discrimination mechanism is also explored by 2-D nuclear magnetic resonance (NMR) and nanopore experiments with a series of adamantane derivatives with different hydrophilic and hydrophobic groups. We found that both the hydrophobic region matching effect and hydrophilic interactions play a synergistic effect in forming a host-guest complex to further generate the characteristic signals, which may provide insights for the subsequent design and study of drug-cyclodextrin complexes.

Single-Molecule Discrimination of Saccharides Using Carbon Nitride Nanopores

Structural complexity brings a huge challenge to the analysis of sugar chains. As a single-molecule sensor, nanopores have the potential to provide fingerprint information on saccharides. Traditionally, direct single-molecule saccharide detection with nanopores is hampered by their small size and weak affinity. Here, a carbon nitride nanopore device is developed to discern two types of trisaccharide molecules (LeApN and SLeCpN) with minor structural differences. The resolution of LeApN and SLeCpN in the mixture reaches 0.98, which has never been achieved in solid-state nanopores so far. Monosaccharide (GlcNAcpN) and disaccharide (LacNAcpN) can also be discriminated using this system, indicating that the versatile carbon nitride nanopores possess a monosaccharide-level resolution. This study demonstrates that the carbon nitride nanopores have the potential for conducting structure analysis on single-molecule saccharides.

Nanoconfined Electrokinetic Chromatography (NEC): Gradient Separation and Sensing of Short DNA Fragments at the Single-Molecule Level

Glass nanopipets have been demonstrated to be a powerful tool for the sensing and discrimination of biomolecules, such as DNA strands with different lengths or configurations. Despite progress made in nanopipet-based sensors, it remains challenging to develop effective strategies that separate and sense in one operation. In this study, we demonstrate an agarose gel-filled nanopipet that enables hyphenated length-dependent separation and electrochemical sensing of short DNA fragments based on the electrokinetic flow of DNA molecules in the nanoconfined channel at the tip of the nanopipet. This nanoconfined electrokinetic chromatography (NEC) method is used to distinguish the mixture of DNA strands without labels, and the ionic current signals measured in real time show that the mixed DNA strands pass through the tip hole in order according to the molecular weight. With NEC, gradient separation and electrochemical measurement of biomolecules can be achieved simultaneously at the single-molecule level, which is further applied for programmable gene delivery into single living cells. Overall, NEC provides a multipurpose platform integrating separation, sensing, single-cell delivery, and manipulation, which may bring new insights into advanced bioapplication.

Dynamic and Asymmetrical Ion Concentration Polarization in Dual Nanopipettes

Dual nanopipettes with two channels have been receiving great attention due to the convenient experimental setup and multiple measuring channels in sensing applications at nanoscale, while the involved dynamic and asymmetrical ion transport processes have not been fully elucidated. In this paper, both experimental and simulation methods are used to investigate the dynamic mass transport processes inside dual nanopipettes with two well-separated channels. The results present that the ion transport resistance through the two channels (R12) is always the add-up of the individual ones (R13 + R23) with respect to the bulk solutions, at various ionic strengths and scan rates. A constant zero-current potential is obtained when loading an asymmetrical electrolyte concentration in the two channels, and the zero-potential current displays a good linear relationship with the bulk concentration outside the pipet. Besides revealing the dynamic and asymmetrical concentration polarization in the dual nanopipettes, these results would also further promote the better usage of dual nanopipettes in electrochemical sensing and imaging applications.

Solid-State Nanopore Distinguishes Ferritin and Apo-Ferritin with Identical Exteriors through Amplified Flexibility at Single-Molecule Level

Protein identification and discrimination at the single-molecule level are big challenges. Solid-state nanopores as a sensitive biosensor have been used for protein analysis, although it is difficult to discriminate proteins with similar structures in the traditional discrimination method based on the current blockage fraction. Here, we select ferritin and apo-ferritin as the model proteins that exhibit identical exterior and different interior structures and verify the practicability of their discrimination with flexibility features by the strategy of gradually decreasing the nanopore size. We show that the larger nanopore (relative to the protein size) has no obvious effect on discriminating two proteins. Then, the comparable-sized nanopore plays a key role in discriminating two proteins based on the dwell time and fraction distribution, and the conformational changes of both proteins are also studied with this nanopore. Finally, in the smaller nanopore, the protein molecules are trapped rather than translocated, where two proteins are obviously discriminated through the current fluctuation caused by the vibration of proteins. This strategy has potential in the discrimination of other important similar proteins.

Thermoelectric Nanofluidics Probing Thermal Heterogeneity inside Single Cells

Accurate temperature measurement in one living cell is of great significance for understanding biological functions and regulation. Here, a nanopipet electric thermometer (NET) is established for real-time intracellular temperature measurement. Based on the temperature-controlled ion migration, the temperature change in solution results in altered ion mobilities and ion distributions, which can be converted to the thermoelectric responses of NET in a galvanostatic configuration. The exponential relationship between the voltage and the temperature promises highly sensitive thermoelectric responses up to 11.1 mV K-1, which is over an order of magnitude higher than previous thermoelectric thermometry. Moreover, the NET exhibits superior thermal resolution of 25 mK and spatiotemporal resolution of 100 nm and 0.9 ms as well as excellent stability and reproducibility. Benefiting from these unique features, both thermal fluctuations in steady-state cells and heat generation and dissipation upon drug administration can be successfully monitored, which are hardly achieved by current methods. By using NET, thermal heterogeneities of single cancer cells during immunotherapy were reported first in this work, in which the increased intracellular temperature was demonstrated to be associated with the survival benefit and resistance of cancer cells in immunotherapy. This work not only provides a reliable method for microscopic temperature monitoring but also gains new insights to elucidate the mechanism of immune evasion and therapeutic resistance.

Ion transport based structural description for in situ synthesized SBA-15 nanochannels in a sub-micropipette

Construction of nanoporous arrays can greatly facilitate their development in the fields of sensing, energy conversion, and nanofluidic devices. It is important to characterize the structure and understand the ion transport behaviour of a nanoporous array, especially those prepared by in situ synthesis, which are difficult to be characterized by conventional methods. Herein, an inorganic and non-crystalline mesoporous silica SBA-15 is selected as a template, where a combination (GP-SBA-15) of a sub-micropipette and SBA-15 is constructed by in situ synthesis, and the multichannel array structure of GP-SBA-15 is illustrated by its ion transport properties from current-voltage responses. Experiments of linear scan voltammetry and chronoamperometry show a rapid accumulation and slow redistribution of ions in the surface-charged nanochannels, and the high/low currents originate from the accumulation/depletion of ions in the channels. The finite element simulation is introduced to calculate the effects of surface charge and pore size on ion rectification and ion concentration distribution. In addition, the short straight channels and long bending channels present in GP-SBA-15 are demonstrated by the voltage-independent resistance pulse signals in the translocation of BSA. This study shows that electrochemical means effectively provide insight into ion transport, achieve structural description and reveal the sensing potential of GP-SBA-15.

Nanoporous Crystalline Materials for the Recognition and Applications of Nucleic Acids

Nucleic acid plays a crucial role in countless biological processes. Hence, there is great interest in its detection and analysis in various fields from chemistry, biology, to medicine. Nanoporous crystalline materials exhibit enormous potential as an effective platform for nucleic acid recognition and application. These materials have highly ordered and uniform pore structures, as well as adjustable surface chemistry and pore size, making them good carriers for nucleic acid extraction, detection, and delivery. In this review, the latest developments in nanoporous crystalline materials, including metal organic frameworks (MOFs), covalent organic frameworks (COFs), and supramolecular organic frameworks (SOFs) for nucleic acid recognition and applications are discussed. Different strategies for functionalizing these materials are explored to specifically identify nucleic acid targets. Their applications in selective separation and detection of nucleic acids are highlighted. They can also be used as DNA/RNA sensors, gene delivery agents, host DNAzymes, and in DNA-based computing. Other applications include catalysis, data storage, and biomimetics. The development of novel nanoporous crystalline materials with enhanced biocompatibility has opened up new avenues in the fields of nucleic acid analysis and therapy, paving the way for the development of sensitive, selective, and cost-effective diagnostic and therapeutic tools with widespread applications.

The Modification and Applications of Nanopipettes in Electrochemical Analysis

Nanopipette, which is fabricated by glasses and possesses a nanoscale pore in the tip, has been proven to be immensely useful in electrochemical analysis. Numerous nanopipette-based sensors have emerged with improved sensitivity, selectivity, ease of use, and miniaturization. In this minireview, we provide an overview of the recent developments of nanopipette-based electrochemical sensors based on different types of nanopipettes, including single-nanopipettes, self-referenced nanopipettes, dual-nanopipettes, and double-barrel nanopipettes. Several important modification materials for nanopipette functionalization are highlighted, such as conductive materials, macromolecular materials, and functional molecules. These materials can improve the sensing performance and targeting specificities of nanopipettes. We also discuss examples of related applications and the future development of nanopipette-based strategies.

Blending Aryl Ketone in Covalent Organic Frameworks to Promote Photoinduced Electron Transfer

Aryl-ketone derivatives have been acknowledged as promising organic photocatalysts for photosynthesis. However, they are limited by their photostability and have been less explored for photoinduced electron transfer (PET) applications. Herein we demonstrate a novel strategy to cover the shortage of aryl-ketone photocatalysts and control the photoreactivity by implanting symmetric aryl ketones into the conjugated covalent organic frameworks (COFs). To prove the concept, three comparative materials with the same topology and varied electronic structures were built, adopting truxenone knot and functionalized terephthalaldehyde linkers. Spectroscopic investigation and excited carrier dynamics analysis disclosed improvements in the photostability and electronic transfer efficiency as well as the structure-performance relationships toward N-aryl tetrahydroisoquinoline oxidation. This system provides a robust rule of thumb for designing new-generation aryl-ketone photocatalysts.

Experimental study on single biomolecule sensing using MoS2-graphene heterostructure nanopores

Solid-state nanopores play an important role in sensing single-biomolecules such as DNA and proteins. However, an ultra-short translocation time hinders nanopores from acquiring more detailed information about biomolecules, and further applications such as sequencing and molecular structure analysis are limited. Related studies have shown that MoS₂ has no obvious impediment to biomolecule translocation while graphene may cause obstacles to this process. By combining these two-dimensional materials, nanopores might slow the biomolecule passage. Herein, we fabricated sub-10 nm ultra-thin MoS₂-graphene heterostructure nanopores with high stability and tested both dsDNA and native protein (BSA) at the single-molecule level in experiments for the first time. Some special signals with advanced order are observed, which may reflect the shape change of the BSA molecules during the slow translocation process. The results show that the translocation time of BSA is slowed down up to more than 100 ms and the signal length and form are determined by the extent of interaction between the BSA and the heterostructure nanopore. The weak interaction between the BSA and the MoS₂ layer increases the translocation probability, and meanwhile, the strong interaction of the graphene layer to BSA slows down the translocation and changes its structure. Therefore, our findings indicate the possibilities of slowing down the single-biomolecule translocation and the capability of acquiring more detailed information about biomolecules using MoS₂-graphene heterostructure nanopores.

Study on Ammonia Content and Distribution in the Microenvironment Based on Covalent Organic Framework Nanochannels

A crack-free micrometer-sized compact structure of 1,3,5-tris(4-aminophenyl)benzene-terephthaldehyde-covalent organic frameworks (TAPB-PDA-COFs) was constructed in situ at the tip of a theta micropipette (TMP). The COF-covered theta micropipette (CTP) then created a stable liquid-gas interface inside COF nanochannels, which was utilized to electrochemically analyze the content and distribution of ammonia gas in the microenvironments. The TMP-based electrochemical ammonia sensor (TEAS) shows a high sensing response, with current increasing linearly from 0 to 50,000 ppm ammonia, owing to the absorption of ammonia gas in the solvent meniscus that connects both barrels of the TEAS. The TEAS also exhibits a short response and recovery time of 5 ± 2 s and 6 ± 2 s, respectively. This response of the ammonia sensor is remarkably stable and repeatable, with a relative standard deviation of 6% for 500 ppm ammonia gas dispensing with humidity control. Due to its fast, reproducible, and stable response to ammonia gas, the TEAS was also utilized as a scanning electrochemical microscopy (SECM) probe for imaging the distribution of ammonia gas in a microspace. This study unlocks new possibilities for using a TMP in designing microscale probes for gas sensing and imaging.

High Spatial Resolution of Ultrathin Covalent Organic Framework Nanopores for Single-Molecule DNA Sensing

Ultrathin nanosheets of two-dimensional covalent organic frameworks covered a quartz nanopipette and then acted as a nanopore device for single-molecule DNA sensing. Our results showed that a single DNA homopolymer as short as 6 bases could be detected. The dwell times of 30-mer DNA homopolymers were obviously longer than the times of 10- or 6-mer ones. For different bases, poly(dA)₆ showed the slowest transport speed (∼595 μs/base) compared with cytosine (∼355 μs/base) in poly(dC)₆ and thymine (∼220 μs/base) in poly(dT)₆. Such translocation speeds are the slowest ever reported in two-dimensional material-based nanopores. Poly(dA)₆ also showed the biggest current blockade (94.74 pA) compared with poly(dC)₆ (79.54 pA) and poly(dT)₆ (71.41 pA). However, the present difference in blockade current was not big enough to distinguish the four DNA bases. Our study exhibits the shortest single DNA molecules that can be detected by COF nanopores at the present stage and lights the way for DNA sequencing based on solid-state nanopores.