Computation-Assisted Nanopore Detection of Thorium Ions

Probe-assisted detection of Fe3+ ions in a multi-functionalized nanopore

Iron is an essential element that plays critical roles in many biological/metabolic processes, ranging from oxygen transport, mitochondrial respiration, to host defense and cell signaling. Maintaining an appropriate iron level in the body is vital to the human health. Iron deficiency or overload can cause life-threatening conditions. Thus, developing a new, rapid, cost-effective, and easy to use method for iron detection is significant not only for environmental monitoring but also for disease prevention. In this study, we report an innovative Fe3+ detection strategy by using both a ligand probe and an engineered nanopore with two binding sites. In our design, one binding site of the nanopore has a strong interaction with the ligand probe, while the other is more selective toward interfering species. Based on the difference in the number of ligand DTPMPA events in the absence and presence of ferric ions, micromolar concentrations of Fe3+ could be detected within minutes. Our method is selective: micromolar concentrations of Mg2+, Ca2+, Cd2+, Zn2+, Ni2+, Co2+, Mn2+, and Cu2+ would not interfere with the detection of ferric ions. Furthermore, Cu2+, Ni2+, Co2+, Zn2+, and Mn2+ produced current blockage events with quite different signatures from each other, enabling their simultaneous detection. In addition, simulated water and serum samples were successfully analyzed. The nanopore sensing strategy developed in this work should find useful application in the development of stochastic sensors for other substances, especially in situations where multi-analyte concurrent detection is desired.

Ultrafast Removal of Thorium and Uranium from Radioactive Waste and Groundwater Using Highly Efficient and Radiation-Resistant Functionalized Triptycene-Based Porous Organic Polymers

Thorium (Th) and uranium (U) are important strategic resources in nuclear energy-based heavy industries such as energy and defense sectors that also generate significant radioactive waste in the process. The management of nuclear waste is therefore of paramount importance. Contamination of groundwater/surface water by Th/U is increasing at an alarming rate in certain geographical locations. This necessitates the development of strategic adsorbent materials with improved performance for capturing Th/U species from radioactive waste and groundwater. This report describes the design of a unique, robust, and radiation-resistant porous organic polymer (POP: TP-POP-SO3NH4), which demonstrates ultrafast removal of Th(IV) (<30 s)/U(VI) (<60 s) species present in simulated radioactive wastewater/groundwater samples. Thermal, chemical, and radiation stabilities of these POPs were studied in detail. The synthesized ammoniated POP revealed exceptional capture efficiency for trace-level Th (<4 ppb) and U (<3 ppb) metal ions through the cation-exchange mechanism. TP-POP-SO3NH4 shows a significant sorption capacity [Th (787 mg/g) and U (854 mg/g)] with an exceptionally high distribution coefficient (Kd) of 107 mL/g for Th. This work also demonstrates a facile protocol to convert a nonperforming POP, by simple chemical modifications, into a superfast adsorbent for efficient uptake/removal of U/Th.

Advances of nanopore-based sensing techniques for contaminants evaluation of food and agricultural products

Food safety assurance systems are becoming more stringent in response to the growing food safety problems. Rapid, sensitive, and reliable detection technology is a prerequisite for the establishment of food safety assurance systems. Nanopore technology has been taken as one of the emerging technology capable of dealing with the detection of harmful contaminants as efficiently as possible due to the advantage of label-free, high-throughput, amplification-free, and rapid detection features. Start with the history of nanopore techniques, this review introduced the underlying knowledge of detection mechanism of nanopore-based sensing techniques. Meanwhile, sensing interfaces for the construction of nanopore sensors are comprehensively summarized. Moreover, this review covers the current advances of nanopore techniques in the application of food safety screening. Currently, the establishment of nanopore sensing devices is mainly based on the blocking current phenomenon. Sensing interfaces including biological nanopores, solid-state nanopores, DNA origami, and de novo designed nanopores can be used in the manufacture of sensing devices. Food harmful substances, including heavy metals, veterinary drugs, pesticide residues, food toxins, and other harmful substances can be quickly determined by nanopore-based sensors. Moreover, the combination of nanopore techniques with advanced materials has become one of the most effective methods to improve sensing properties.

Chemistry solutions to facilitate nanopore detection and analysis

Characteristic ionic current modulations will be produced in a single molecule manner during the communication of individual molecules with a nanopore. Hence, the information regarding the length, composition, and structure of a molecule can be extracted from deciphering the electrical message. However, until now, achieving a satisfactory resolution for observation and quantification of a target analyte in a complex system remains a nontrivial task. In this review, we summarize the progress and especially the recent advance in utilizing chemistry solutions to facilitate nanopore detection and analysis. The discussed chemistry solutions are classified into several major categories, including covalent/non-covalent chemistry, redox chemistry, displacement chemistry, back titration chemistry, chelation chemistry, hydrolysis-chemistry, and click chemistry. Considering the significant success of using chemical reaction-assisted nanopore sensing strategies to improve sensor sensitivity & selectivity and to study various topics, other non-chemistry based methodologies can undoubtedly be employed by nanopore sensors to explore new applications in the interdisciplinary area of chemistry, biology, materials, and nanotechnology.

Hydrophobic core formation and secondary structure elements in uranyl(VI)-binding peptides

Cyclic peptides as well as a modified EF-hand motif of calmodulin have been newly designed to achieve high affinity towards uranyl(VI). Cyclic peptides may be engineered to bind uranyl(VI) to its backbone under acidic conditions, which may enhance its selectivity. For the modified EF-hand motif of calmodulin, strong electrostatic interactions between uranyl(VI) and negatively charged side chains play an important role in achieving high affinity; however, it is also essential to have a secondary structure element and formation of hydrophobic cores in the metal-bound state of the peptide.

Phenanthridine based rapid "turn-on" fluorescent sensor for selective detection of Th4+ ion and its real-time application

A new and highly sensitive and selective phenanthridine based sensor, 9-(7,8,13,14-tetrahydrodibenzo[a,i]phenanthridin-5-yl)benzo[h]quinolin-10-ol (PHBQ), was developed for the fluorescent ''turn-on'' detection of Th⁴⁺ ion in acetonitrile: water (8:2) medium. The fluorescence intensity of PHBQ diminished in the region of pH 1 to 3 and could be recovered by adjusting the pH to above 4. The sensor PHBQ showed distinct spectral changes in response to Th⁴⁺ ion over other competitive metal ions. The fluorescence displayed good linearity with the Th⁴⁺ concentration in the equivalence of 0-0.5 equivalents. The detection limit was calculated to be as low as 99 nM, which was less than that of previously reported sensors. The recognizing mechanism of PHBQ towards Th⁴⁺ was investigated in detail using HR-MS, NMR, and IR spectroscopy. The economically viable Whatman filter paper was fabricated with PHBQ to develop a paper-based fluorescence kit to detect the Th⁴⁺ in an aqueous medium efficiently. Furthermore, the application of sensor ligand in fluorescence imaging was studied in E-coli cells due to its minimal cytotoxicity and good optical properties. The obtained data suggest that the ligand PHBQ can be used as a fluorescent sensor for tracking Th⁴⁺ in multiple applications.

Nanoparticle-assisted detection of nucleic acids in a polymeric nanopore with a large pore size

Rapid and accurate detection of nucleic acids is of paramount importance in many fields, including medical diagnosis, gene therapy and virus identification. In this work, by taking advantage of two DNA hybridization probes, one of which was immobilized on the surface of gold nanoparticles, while the other was free in solution, detection of short length nucleic acids was successfully achieved using a large size (20 nm tip diameter) polyethylene terephythalate (PET) nanopore. The sensor was sensitive and selective: DNA samples with concentrations at as low as 0.5 nM could be detected within minutes and the number of mismatches can be discerned from the translocation frequency. Furthermore, the nanopore can be repeatedly used many times. Our developed large-size nanopore sensing platform offers the potential for fieldable/point-of-care diagnostic applications.

Nanopore sensing: A physical-chemical approach

Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.

Nanopore Technology for the Application of Protein Detection

Protein is an important component of all the cells and tissues of the human body and is the material basis of life. Its content, sequence, and spatial structure have a great impact on proteomics and human biology. It can reflect the important information of normal or pathophysiological processes and promote the development of new diagnoses and treatment methods. However, the current techniques of proteomics for protein analysis are limited by chemical modifications, large sample sizes, or cumbersome operations. Solving this problem requires overcoming huge challenges. Nanopore single molecule detection technology overcomes this shortcoming. As a new sensing technology, it has the advantages of no labeling, high sensitivity, fast detection speed, real-time monitoring, and simple operation. It is widely used in gene sequencing, detection of peptides and proteins, markers and microorganisms, and other biomolecules and metal ions. Therefore, based on the advantages of novel nanopore single-molecule detection technology, its application to protein sequence detection and structure recognition has also been proposed and developed. In this paper, the application of nanopore single-molecule detection technology in protein detection in recent years is reviewed, and its development prospect is investigated.

Nanopore detection of metal ions: Current status and future directions

In this review, we highlight recent research efforts that aimed at developing nanopore sensors for detection of metal ions, which play a crucial role in environmental safety and human health. Protein pores use three stochastic sensing-based strategies for metal ion detection. The first strategy is to construct engineered nanopores with metal ion binding sites, so that the interaction between the target analytes and the nanopore can slow the movement of metal ions in the nano-channel. Second, large molecules such as nucleic acids and especially peptides could be utilized as external selective molecular probes to detect metal ions based on the conformational change of the ligand molecules induced by the metal ion-ligand chelation / coordination interaction. Third, enzymatic reactions can also be used as an alternative to the molecule probe strategy in the situation that a sensitive and selective probe molecule for the target analyte is difficult to obtain. On the other hand, by taking advantage of steady-state analysis, synthetic nanopores mainly use two strategies (modification and modification-free) to detect metals. Given the advantages of high sensitivity & selectivity, and label-free detection, nanopore-based metal ion sensors should find useful application in many fields, including environmental monitoring, medical diagnosis, and so on.

Analysis with biological nanopore: On-pore, off-pore strategies and application in biological fluids

Inspired from ion channels in biology, nanopores have been developed as promising analytical tools. In principle, nanopores provide crucial information from the observation and analysis of ionic current modulations caused by the interaction between target analytes and fluidic pores. In this respect, the biological, chemical and physical parameters of the nanopore regime need to be well-understood and regulated for intermolecular interaction. Because of well-defined molecular structures, biological nanopores consequently are of a focal point, allowing precise interaction analysis at single-molecule level. In this overview, two analytical strategies are summarized and discussed accordingly, upon the challenges arising in case-dependent analysis using biological nanopores. One kind of strategies relies on modification, functionalization and engineering on nanopore confined interface to improve molecular recognition sites (on-pore strategies); The other kind of highlighted strategies concerns to measurement of various chemistry/biochemistry based interactions triggered by employed molecular agents or probes (off-pore strategies). In particularly, a few recent paradigms using these strategies for practical application of accurate analysis of biomarkers in biological fluids are illustrated. To end, the challenging and future outlook of using analytical tools by means of biological nanopores are depicted.

DNA nanotechnology assisted nanopore-based analysis

Nanopore technology is a promising label-free detection method. However, challenges exist for its further application in sequencing, clinical diagnostics and ultra-sensitive single molecule detection. The development of DNA nanotechnology nonetheless provides possible solutions to current obstacles hindering nanopore sensing technologies. In this review, we summarize recent relevant research contributing to efforts for developing nanopore methods associated with DNA nanotechnology. For example, DNA carriers can capture specific targets at pre-designed sites and escort them from nanopores at suitable speeds, thereby greatly enhancing capability and resolution for the detection of specific target molecules. In addition, DNA origami structures can be constructed to fulfill various design specifications and one-pot assembly reactions, thus serving as functional nanopores. Moreover, based on DNA strand displacement, nanopores can also be utilized to characterize the outputs of DNA computing and to develop programmable smart diagnostic nanodevices. In summary, DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis.

Enzymatic reaction-based nanopore detection of zinc ions

We report a label-free nanopore sensor for the detection of Zn2+ ions. By taking advantage of the cleavage of a substrate peptide by zinc-dependent enzymes, nanomolar concentrations of Zn2+ ions could be detected within minutes. Furthermore, structurally similar transition metals such as Ni2+, Co2+, Hg2+, Cu2+, and Cd2+ did not interfere with their detection. The enzymatic reaction-based nanopore sensing strategy developed in this work may find potential applications in environmental monitoring and medical diagnosis.

Nanopore-Based Strategy for Sensing of Copper(II) Ion and Real-Time Monitoring of a Click Reaction

A straightforward yet efficient, nanopore-based strategy that enables the sensitive detection of copper(II) ion (Cu²⁺) and real-time monitoring of a click reaction is provided. Two single-stranded DNAs (ssDNAs) are designed to act as the preprobes, one being modified with an azide and the other an alkyne. The presence of Cu²⁺ induces the ligation of two ssDNAs via click reaction, leading to the formation of a forked DNA which can quantitatively generate characteristic current signatures when interacts with α-hemolysin (α-HL) nanopore. The assay facilitates a highly selective and sensitive measurement of Cu²⁺ without the need for labels or signal amplification. More importantly, this nanopore platform exhibits excellent performance in real-time monitoring of a copper(I) ion (Cu⁺)-catalyzed click reaction at the single-molecule level, by recording the current signals of the forked DNA generated by click chemistry. The proposed strategy is believed to play an important role in both nanopore sensing and characterization of chemistry reactions, especially coupling reactions.

Salt-Mediated Nanopore Detection of ADAM-17

ADAM-17 (a disintegrin and metalloproteinase 17) plays an important role in various physiological and pathophysiological processes. Overexpression/underexpression of ADAM-17 could lead to various diseases. In this work, by taking advantage of ionic strength and salt gradient, and monitoring the cleavage of a substrate peptide by ADAM-17 in a nanopore, we developed a label-free sensor for the rapid detection of ADAM-17. The sensor was highly sensitive and selective: picomolar concentrations of ADAM-17 could be detected within minutes, while structure similar proteases such as ADAM-9 and MMP-9 did not interfere with its detection. Our developed nanopore sensing strategy should find useful applications in the development of nanopore sensors for other proteases of biological, pharmaceutical, and medical importance.

Displacement chemistry-based nanopore analysis of nucleic acids in complicated matrices

To overcome the effect of other components of complicated biological samples on nanopore stochastic sensing, displacement chemical reaction was utilized to selectively extract the target nucleic acid from whole blood. Given its simplicity and high sensitivity for detecting nucleic acids, our developed displacement chemistry-based nanopore sensing strategy offers the potential for fieldable/point-of-care diagnostic applications.

Metal-Ion Displacement Approach for Optical Recognition of Thorium: Application of a Molybdenum(VI) Complex for Nanomolar Determination and Enrichment of Th(IV)

An azine-based molybdenum (Mo(VI)) complex (M1) is exploited for selective detection of thorium (Th(IV)) ions through a metal-ion displacement protocol. Th(IV) displaces Mo(VI) from M1 instantly leading to the formation of the Th(IV) complex, having orange-red emission. Consequently, a red shift of the emission wavelength along with 41-fold fluorescence enhancement is observed. This unique method allows detection of Th(IV) as low as 1.5 × 10^-9 M. The displacement of Mo(VI) from M1 by Th(IV) is established by spectroscopic studies and kinetically followed by the stopped-flow technique. The displacement binding constant for Th(IV) is notably strong, 4.59 × 10⁶ M^-1. Extraction of Th(IV) from aqueous solution to the ethyl acetate medium using M1 has been achieved. The silica-immobilized M1 efficiently enriches Th(IV) from its reservoir through solid-phase extraction. Computational studies (density functional theory) support experimental findings.

A highly selective pH switchable colorimetric fluorescent rhodamine functionalized azo-phenol derivative for thorium recognition up to nano molar level in semi-aqueous media: Implication towards multiple logic gates

A new rhodamine functionalized Schiff base (3',6'-bis(diethylamino)-2-((Z)-(5-((E)-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)diazenyl)-2,4-dihydroxybenzylidene) amino)spiro[isoindoline-1,9'-xanthen]-3-one (1) has been synthesized and was characterized spectroscopically. The optical properties of the schiff base have been studied using UV-vis and fluorescence spectra. Schiff base 1 displayed a selective behaviour towards Th⁴⁺ ions, as evidenced by UV-vis and fluorescence spectra. It shows visible colour change from orangish-yellow to red upon addition of Th⁴⁺ ions. A strong new emission band at 586 nm and about 24-fold enhancement in fluorescence intensity was observed upon binding with Th⁴⁺ which could be quenched by subsequent addition of oxalate and chromate ions. Probe 1 also acts as a reversible pH sensor in the highly acidic region (pH < 4, pK_{a =} 2.01) via the photophysical response to pH as well as visible detectable colour change from orangish-yellow to red to pink. The absorbance and emission intensities of 1 diminished in the pH region from 4 to 11.5 and could be recovered by adding acid to adjust the pH < 4. Probe 1 exhibited high binding constant (8.595 × 10⁶ M^-1) and low limit of detection (1.122 × 10^-9) compared to most previously reported sensors for Th⁴⁺ ions. Furthermore, two multiple logic gates i.e. 3 and 5 input, have been constructed.