Optical analysis of Hg2+ ions by oligonucleotide-gold-nanoparticle hybrids and DNA-based machines

Advances in colorimetric aptasensors for heavy metal ion detection utilizing nanomaterials: a comprehensive review

Heavy metal ion contamination poses significant environmental and health risks, necessitating rapid and efficient detection methods. In the last decade, colorimetric aptasensors have emerged as powerful tools for heavy metal ion detection, owing to their notable attributes such as high specificity, facile synthesis, adaptability to modifications, long-term stability, and heightened sensitivity. This comprehensive overview summarizes the key developments in this field over the past ten years. It discusses the principles, design strategies, and innovative techniques employed in colorimetric aptasensors using nanomaterials. Recent advancements in enhancing sensitivity, selectivity, and on-site applicability are highlighted. The review also presents application studies of successful heavy metal ion detection using colorimetric aptasensors, underlining their potential for environmental monitoring and health protection. Finally, future directions and challenges in the continued evolution of these aptasensors are outlined.

Dynamic DNA Networks-Guided Directional and Orthogonal Transient Biocatalytic Cascades

DNA frameworks, consisting of constitutional dynamic networks (CDNs) undergoing fuel-driven reconfiguration, are coupled to a dissipative reaction module that triggers the reconfigured CDNs into a transient intermediate CDNs recovering the parent CDN state. Biocatalytic cascades consisting of the glucose oxidase (GOx)/horseradish peroxidase (HRP) couple or the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD+) couple are tethered to the constituents of two different CDNs, allowing the CDNs-guided operation of the spatially confined GOx/HRP or LDH/NAD+ biocatalytic cascades. By applying two different fuel triggers, the directional transient CDN-guided upregulation/downregulation of the two biocatalytic cascades are demonstrated. By mixing the GOx/HRP-biocatalyst-modified CDN with the LDH/NAD+-biocatalyst-functionalized CDN, a composite CDN is assembled. Triggering the composite CDN with two different fuel strands results in orthogonal transient upregulation of the GOx/HRP cascade and transient downregulation of the LDH/NAD+ cascade or vice versa. The transient CDNs-guided biocatalytic cascades are computationally simulated by kinetic models, and the computational analyses allow the prediction of the performance of transient biocatalytic cascades under different auxiliary conditions. The concept of orthogonally triggered temporal, transient, biocatalytic cascades by means of CDN frameworks is applied to design an orthogonally operating CDN for the temporal upregulated or downregulated transient thrombin-induced coagulation of fibrinogen to fibrin.

Heavy Metal Ions Trigger a Fluorescent Quenching in DNA–Organic Semiconductor Hybrid Assemblies

The significance of DNA is no longer limited to its role as a biological information carrier; as a natural polymer, it also become in the field of materials. Single-stranded DNA (ssDNA) molecules with specific sequences can form a G-quadruplex or hairpin-shaped conformation with specific heavy metal ions through coordination bonds. In this study, ssDNA molecules of the four sequences were prepared into hybrid assemblies with one of the famous display materials, the tris-(8-hydroxyquinoline)aluminum (Alq₃) semiconductor. Based on these hybrid assemblies, heavy metal ions, namely Pb²⁺, Hg²⁺, Cd²⁺ and As³⁺, were detected individually at the ppb level. Apart from this, in practical application, many samples containing heavy metal ions are digested with acid. By introducing MES buffer solution, the influence of acidity on the fluorescent signal of Alq₃ was excluded. This strategy showed promising results in the practical application of detecting heavy metal ions in shrub branches and leaves.

Self-Powered Active Sensing Based on Triboelectric Generators

The demand for portable and wearable chemical or biosensors and their expeditious development in recent years has created a scientific challenge in terms of their continuous powering. As a result, mechanical energy harvesters such as piezoelectric and triboelectric generators (TEGs) have been explored recently either as sensors or harvesters to store charge in small, but long-life, energy-storage devices to power the sensors. The use of energy harvesters as sensors is particularly interesting, as with such multifunctional operations it is possible to reduce the number devices needed in a system, which also helps overcome the integration complexities. In this regard, TEGs are promising, particularly for energy autonomous chemical and biological sensors, as they can be developed with a wide variety of materials, and their mechanical energy to electricity conversion can be modulated by various analytes. This review focuses on this interesting dimension of TEGs and presents various self-powered active chemical and biological sensors. A brief discussion about the development of TEG-based physical, magnetic, and optical sensors is also included. The influence of environmental factors, various figures of merit, and the significance of TEG design are explained in context with the active sensing. Finally, the key applications, challenges, and future perspective of chemical and biological detection via TEGs are discussed with a view to drive further advances in the field of self-powered sensors.

Bio-inspired Track-Etched Polymeric Nanochannels: Steady-State Biosensors for Detection of Analytes

Bio-inspired polymeric nanochannel (also referred as nanopore)-based biosensors have attracted considerable attention on account of their controllable channel size and shape, multi-functional surface chemistry, unique ionic transport properties, and good robustness for applications. There are already very informative reviews on the latest developments in solid-state artificial nanochannel-based biosensors, however, which concentrated on the resistive-pulse sensing-based sensors for practical applications. The steady-state sensing-based nanochannel biosensors, in principle, have significant advantages over their counterparts in term of high sensitivity, fast response, target analytes with no size limit, and extensive suitable range. Furthermore, among the diverse materials, nanochannels based on polymeric materials perform outstandingly, due to flexible fabrication and wide application. This compressive Review summarizes the recent advances in bio-inspired polymeric nanochannels as sensing platforms for detection of important analytes in living organisms, to meet the high demand for high-performance biosensors for analysis of target analytes, and the potential for development of smart sensing devices. In the future, research efforts can be focused on transport mechanisms in the field of steady-state or resistive-pulse nanochannel-based sensors and on developing precisely size-controlled, robust, miniature and reusable, multi-functional, and high-throughput biosensors for practical applications. Future efforts should aim at a deeper understanding of the principles at the molecular level and incorporating these diverse pore architectures into homogeneous and defect-free multi-channel membrane systems. With the rapid advancement of nanoscience and biotechnology, we believe that many more achievements in nanochannel-based biosensors could be achieved in the near future, serving people in a better way.

Manipulating the Assembly of DNA Nanostructures and Their Enzymatic Properties by Incorporating a 5'-5' Polarity of Inversion Site in the G-Tract

Supramolecular DNA complexes consisting of both DNA duplexes and tetrameric G-quadruplexes are fabricated successfully by utilizing a single short DNA strand that contains one 5'-5' polarity of inversion site in the middle of G-tract. The resulting DNA supramolecules exhibit significantly high peroxidase activities after interaction with hemin due to the presence of various G-quadruplex-duplex (G4-duplex) interfaces. Significantly, we find that the addition of a C-rich fragment to the designed sequence not only allows the self-assembly of two-dimensional porous DNA nanostructures via the formation of dimeric i-motif structures but also could act as a control element to facilitate the generation of pH-sensitive G4-based DNAzymes. The enhanced catalytic activity obtained from specific sequence modifications as well as the controllable feature of these DNA nanostructures can significantly benefit further applications of DNA functional materials in complex biological systems.

Transient Dissipative Optical Properties of Aggregated Au Nanoparticles, CdSe/ZnS Quantum Dots, and Supramolecular Nucleic Acid-Stabilized Ag Nanoclusters

Transient, dissipative, aggregation and deaggregation of Au nanoparticles (NPs) or semiconductor quantum dots (QDs) leading to control over their transient optical properties are introduced. The systems consist of nucleic acid-modified pairs of Au NPs or pairs of CdSe/ZnS QDs, an auxiliary duplex L₁/T₁, and the nicking enzyme Nt.BbvCI as functional modules yielding transient aggregation/deaggregation of the NPs and dynamically controlling over their optical properties. In the presence of a fuel strand L₁', the duplex L₁/T₁ is separated, leading to the release of T₁ and the formation of duplex L₁/L₁'. The released T₁ leads to aggregation of the Au NPs or to the T₁-induced G-quadruplex bridged aggregated CdSe/ZnS QDs. Biocatalytic nicking of the L₁/L₁' duplex fragments L₁' and the released L₁ displaces T₁ bridging the aggregated NPs or QDs, resulting in the dynamic recovery of the original NPs or QDs modules. The dynamic aggregation/deaggregation of the Au NPs is followed by the transient interparticle plasmon coupling spectral changes. The dynamic aggregation/deaggregation of the CdSe/ZnS QDs is probed by following the transient chemiluminescence generated by the hemin/G-quadruplexes bridging the QDs and by the accompanying transient chemiluminescence resonance energy transfer proceeding in the dynamically formed QDs aggregates. A third system demonstrating transient, dissipative, luminescence properties of a reaction module consisting of nucleic acid-stabilized Ag nanoclusters (NCs) is introduced. Transient dynamic formation and depletion of the supramolecular luminescent Ag NCs system via strand displacement accompanied by a nicking process are demonstrated.

LSPR-based colorimetric biosensing for food quality and safety

Ensuring consistently high quality and safety is paramount to food producers and consumers alike. Wet chemistry and microbiological methods provide accurate results, but those methods are not conducive to rapid, onsite testing needs. Hence, many efforts have focused on rapid testing for food quality and safety, including the development of various biosensors. Herein, we focus on a group of biosensors, which provide visually recognizable colorimetric signals within minutes and can be used onsite. Although there are different ways to achieve visual color-change signals, we restrict our focus on sensors that exploit the localized surface plasmon resonance (LSPR) phenomenon of metal nanoparticles, primarily gold and silver nanoparticles. The typical approach in the design of LSPR biosensors is to conjugate biorecognition ligands on the surface of metal nanoparticles and allow the ligands to specifically recognize and bind the target analyte. This ligand-target binding reaction leads to a change in color of the test sample and a concomitant shift in the ultraviolet-visual absorption peak. Various designs applying this and other signal generation schemes are reviewed with an emphasis on those applied for evaluating factors that compromise the quality and safety of food and agricultural products. The LSPR-based colorimetric biosensing platform is a promising technology for enhancing food quality and safety. Aided by the advances in nanotechnology, this sensing technique lends itself easily for further development on field-deployable platforms such as smartphones for onsite and end-user applications.

DNAzyme- and light-induced dissipative and gated DNA networks

Nucleic acid-based dissipative, out-of-equilibrium systems are introduced as functional assemblies emulating transient dissipative biological transformations. One system involves a Pb²⁺-ion-dependent DNAzyme fuel strand-driven network leading to the transient cleavage of the fuel strand to “waste” products. Applying the Pb²⁺-ion-dependent DNAzyme to two competitive fuel strand-driven systems yields two parallel operating networks. Blocking the competitively operating networks with selective inhibitors leads, however, to gated transient operation of dictated networks, yielding gated catalytic operations. A second system introduces a “non-waste” generating out-of-equilibrium, dissipative network driven by light. The system consists of a trans-azobenzene-functionalized photoactive module that is reconfigured by light to an intermediary state consisting of cis-azobenzene units that are thermally recovered to the original trans-azobenzene-modified module. The cyclic transient photoinduced operation of the device is demonstrated. The kinetic simulation of the systems allows the prediction of the transient behavior of the networks under different auxiliary conditions.

Functional DNA modules are triggered in the presence of appropriate inhibitors to yield transient gated catalytic functions, and a photoresponsive DNA module leads to “waste-free” operation of transient, dissipative dynamic transitions.

Gated Dissipative Dynamic Artificial Photosynthetic Model Systems

Gated dissipative artificial photosynthetic systems modeling dynamically modulated environmental effects on the photosynthetic apparatus are presented. Two photochemical systems composed of a supramolecular duplex scaffold, a photosensitizer-functionalized strand (photosensitizer is Zn(II)protoporphyrin IX, Zn(II)PPIX, or pyrene), an electron acceptor bipyridinium (V²⁺)-modified strand, and a nicking enzyme (Nt.BbvCI) act as functional assemblies driving transient photosynthetic-like processes. In the presence of a fuel strand, the transient electron transfer quenching of the photosensitizers, in each of the photochemical systems, is activated. In the presence of a sacrificial electron donor (mercaptoethanol) and continuous irradiation, the resulting electron transfer process in the Zn(II)PPIX/V²⁺ photochemical module leads to the transient accumulation and depletion of the bipyridinium radical-cation (V·⁺) product, and in the presence of ferredoxin-NADP⁺ reductase and NADP⁺, to the kinetically modulated photosynthesis of NADPH. By subjecting the mixture of two photochemical modules to one of two inhibitors, the gated transient photoinduced electron transfer in the two modules is demonstrated. Such gated dissipative process highlights its potential as an important pathway to protect artificial photosynthetic module against overdose of irradiance and to minimize photodamage.

DNA Assembly-Based Stimuli-Responsive Systems

Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.

Crystallographic Structure of Novel Types of AgI -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids

Metal-mediated base pairs have widespread applications, such as in DNA-metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non-canonical DNA/DNA duplex containing 2'-O,4'-C-methylene bridged nucleic acid in the presence of Ag^I ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of Ag^I -mediated base pair between the N1 positions of anti-conformation of adenines in the duplex was observed. In the central non-canonical region, a hexad nucleobase structure containing Ag^I -mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of Ag^I -mediated base pairs in the central region. The bent duplex structure induced by the addition of Ag^I ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.

Thymine-Functionalized Gold Nanoparticles (Au NPs) for a Highly Sensitive Fiber-Optic Surface Plasmon Resonance Mercury Ion Nanosensor

Mercury ion (Hg²⁺) is considered to be one of the most toxic heavy metal ions. Once the content of Hg²⁺ exceeds the quality standard in drinking water, the living environment and health of human beings will be threatened and destroyed. Therefore, the establishment of simple and efficient methods for Hg²⁺ ion detection has important practical significance. In this paper, we present a highly sensitive and selective fiber-optic surface plasmon resonance (SPR) Hg²⁺ ion chemical nanosensor by designing thymine (T)-modified gold nanoparticles (Au NPs/T) as the signal amplification tags. Thymine-1-acetic acid (T-COOH) was covalently coupled to the surface of 2-aminoethanethiol (AET)-modified Au NPs and Au film by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride/N-Hydroxysuccinimide (EDC/NHS) activation effect, respectively. In the presence of Hg²⁺ ions, the immobilized thymine combines specifically with Hg²⁺ ions, and forms an Au/thymine-Hg²⁺-thymine/Au (Au/T-Hg²⁺-T/Au) complex structure, leading to a shift in SPR wavelength due to the strong electromagnetic couple between Au NPs and Au film. Under optimal conditions, the proposed sensor was found to be highly sensitive to Hg²⁺ in the range of 80 nM–20 µM and the limit of detection (LOD) for Hg²⁺ was as low as 9.98 nM. This fiber-optic SPR sensor afforded excellent selectivity for Hg²⁺ ions against other heavy metal ions such as Fe³⁺, Cu²⁺, Ni²⁺, Ba²⁺, K⁺, Na⁺, Pb²⁺, Co²⁺, and Zn²⁺. In addition, the proposed sensor was successfully applied to Hg²⁺ assay in real environmental samples with excellent recovery. Accordingly, considering its simple advantages, this novel strategy provides a potential platform for on-site determination of Hg²⁺ ions by SPR sensor.

Fluorescence resonance energy transfer between carbon quantum dots and silver nanoparticles: Application to mercuric ion sensing

Fluorescence resonance energy transfer (FRET) process as a practical and competitive sensing strategy was utilized between carbon quantum dots (C-dots) and silver nanoparticles (Ag NPs) for the determination of mercuric ions. The novel synthesized C-dots with the quantum yield of 84% acted as the donor and Ag NPs operated as the acceptor in the FRET process leading to the fluorescence quenching of the C-dots. In the presence of Hg(II) ions, the FRET-quenched fluorescence emission of the C-dots-Ag NPs system was recovered owing to oxidation of Ag NPs by Hg(II) ions, so that the turn-on fluorescence intensity was directly proportional to the Hg(II) ion concentration. Accordingly, combination of the FRET system with the redox reaction was firstly utilized to construct an innovative turn-off/on fluorescent sensor for the quantification of Hg(II) ion. The calibration plot was linear in the concentration range 0.5-500.0 nmol L^-1 with a determination coefficient (R²) of 0.9965. The limit of detection and limit of quantification were 0.10 and 0.35 nmol L^-1, respectively, according to the IUPAC definition. The method was applied for the determination of Hg(II) ion in lake water, wastewater and tea samples, and the proper relative recoveries (98.0-104.0%) were obtained for the spiked samples. The method has high potential to diagnose trace values of mercuric ions in real samples with high sensitivity and repeatability.

Reusable, facile, and rapid aptasensor capable of online determination of trace mercury

Herein, we reported a homemade waveguide-based evanescent wave aptasensor for the facile online monitoring of mercury pollution. The aptasensor exploited the high selectivity of hairpin structure-based thymidine-Hg²⁺-thymidine coordination chemistry (T-T mismatch) for Hg²⁺ recognition and the stably regenerable capability of DNA-functionalized waveguide surfaces. The presence of Hg²⁺ caused the T-T mismatch of Cy5.5-labeled T-rich single-stranded DNA sequences. The formed hairpin structures blocked the further hybridization of T-rich single-stranded DNA sequences with the complementary DNA strands that are modified on the waveguide surface; this phenomenon was accompanied by the decrease in the fluorescent signals excited by the evanescent wave. The limit of detection in real water samples was determined to be 0.2 μg/L, which was comparable with that of 0.4 μg/L in an ultrapure water under controlled conditions. And the linear range was observed from 1.4 µg/L to 240.7 µg/L. The negligible environmental matrix effect on the performance ensured the reliability of the proposed aptasensor. Moreover, the cross reactivity of this method toward other investigated metal ions was negligible. Through the delicate surface modification with DNA molecules covalently, the chip was reused at least 31 times with a relative standard deviation (RSD) of less than 19%. A Hg²⁺ pollution accident was successfully detected within 30 min, shedding new light in pollution monitoring, environment restoration, and emergency treatment.

Organic Semiconductor-DNA Hybrid Assemblies

Organic semiconductors are photonic and electronic materials with high luminescence, quantum efficiency, color tunability, and size-dependent optoelectronic properties. The self-assembly of organic molecules enables the establishment of a fabrication technique for organic micro- and nano-architectures with well-defined shapes, tunable sizes, and defect-free structures. DNAs, a class of biomacromolecules, have recently been used as an engineering material capable of intricate nanoscale structuring while simultaneously storing biological genetic information. Here, the up-to-date research on hybrid materials made from organic semiconductors and DNAs is presented. The trends in photonic and electronic phenomena discovered in DNA-functionalized and DNA-driven organic semiconductor hybrids, comprising small molecules and polymers, are observed. Various hybrid forms of solutions, arrayed chips, nanowires, and crystalline particles are discussed, focusing on the role of DNA in the hybrids. Furthermore, the recent technical advances achieved in the integration of DNAs in light-emitting devices, transistors, waveguides, sensors, and biological assays are presented. DNAs not only serve as a recognizing element in organic-semiconductor-based sensors, but also as an active charge-control material in high-performance optoelectronic devices.

Dissecting the Effect of Salt for More Sensitive Label-Free Colorimetric Detection of DNA Using Gold Nanoparticles

Taking advantage of the protection effect of single-stranded DNA oligonucleotides, gold nanoparticles (AuNPs) remain dispersed and retain a red color with the addition of a low concentration of salt, while AuNPs would aggregate in the presence of double-stranded DNA. This difference has been used to design label-free colorimetric sensors for DNA detection. NaCl is the most commonly used salt to induce the aggregation of AuNPs. In this work, we aimed to test if other salts can provide even better sensor performance and to understand the effects of the cations and anions in salts. We first studied the effect of anions, including halides (NaF, NaCl, NaBr, and NaI), and other common salts (NaNO₃, NaClO₄, Na₂SO₄, Na₂S₂O₃, sodium phosphate, and sodium citrate). Among them, weakly adsorbing ones such as F^-, citrate, and phosphate appeared to yield better sensitivity than Cl^-. Anions can directly adsorb on the AuNPs and affect DNA adsorption. We then tested cations, and only group 1A metals (LiCl, NaCl, KCl, RbCl, and CsCl) can signal DNA adsorption, while divalent metals (MgCl₂, CaCl₂, MnCl_2, and NiCl₂) barely showed the effect of DNA. CsCl only works for strongly adsorbing DNA, such as A₁₅, but not weakly adsorbing T₁₅. Overall, NaF is a better salt than NaCl by having a 2.3-fold higher sensitivity, which was confirmed in a DNA sensing assay. This work has identified a better salt yielding higher sensitivity, and sensing work relying on the change of the aggregation state of AuNPs can benefit from this study.

Selective determination of Ag+ in the presence of Cd2+, Hg2+ and Cu2+ based on their different interactions with gold nanoclusters

In this work, a fluorescence method was developed for selective detection of Ag⁺ in the presence of Cd²⁺, Hg²⁺, and Cu²⁺ based on gold nanoclusters (AuNCs). That is, bovine serum albumin (BSA) templated AuNCs with double emission peaks were synthesized using BSA as a protective agent. AuNCs with uniform distribution and average size between 2.0 and 2.2 nm were synthesized using a green and simple method, and showed bright orange-red fluorescence under ultraviolet light. AuNCs have two emission peaks at 450 nm and 630 nm with an excitation wavelength of 365 nm. Under alkaline conditions, Cd²⁺ can combine with the surface sulfhydryl groups of BSA–AuNCs to form Cd–S bonds, which cause AuNCs to aggregate, resulting in an increase in fluorescence intensity at 630 nm. Conversely, due to the d¹⁰–d¹⁰ metal affinity interaction, the addition of Hg²⁺ can reduce the fluorescence peak at 630 nm. Ag⁺ was reduced to Ag⁰ by gold nuclei in AuNCs, forming a stable hybrid Au@ AgNCs species with blue-shifted and enhanced fluorescence. Finally, the paramagnetic behavior of Cu²⁺ combined with BSA causes the excited electrons of the gold cluster to lose their energy via ISC, eventually leading to simultaneous quenching of the two emission peaks. The results show that the limit of detection (LOD) of Ag⁺, Hg²⁺, Cd²⁺ and Cu²⁺ is 1.19 μM, 3.39 μM, 1.83 μM and 5.95 μM, respectively.

A fluorescence method was developed for selective detection of Ag⁺ in the presence of Cd²⁺, Hg²⁺, and Cu²⁺ based on gold nanoclusters. The limit of detection for Ag⁺, Hg²⁺, Cd²⁺ and Cu²⁺ is 1.19 μM, 3.39 μM, 1.83 μM and 5.95 μM, respectively.

A review on nanostructure-based mercury (II) detection and monitoring focusing on aptamer and oligonucleotide biosensors

Heavy metal ion pollution is a severe problem in environmental protection and especially in human health due to their bioaccumulation in organisms. Mercury (II) (Hg²⁺), even at low concentrations, can lead to DNA damage and give permanent harm to the central nervous system by easily passing through biological membranes. Therefore, sensitive detection and monitoring of Hg²⁺ is of particular interest with significant specificity. In this review, aptamer-based strategies in combination with nanostructures as well as several other strategies to solve addressed problems in sensor development for Hg²⁺ are discussed in detail. In particular, the analytical performance of different aptamer and oligonucleotide-based strategies using different signal improvement approaches based on nanoparticles were compared within each strategy and in between. Although quite a number of the suggested methodologies analyzed in this review fulfills the standard requirements, further development is still needed on real sample analysis and analytical performance parameters.

Label-Free and Regenerable Aptasensor for Real-Time Detection of Cadmium(II) by Dual Polarization Interferometry

Recently, numerous aptamer-based biosensors have been developed to detect heavy metal ions. Most of aptamer-based biosensors only can be used to get some quantitative information. The mechanism of the interaction between aptamer and metal ions, however, is rarely studied. In this work, a label-free and regenerable aptamer-based biosensor was constructed using dual polarization interferometry (DPI). This aptasensor was used to investigate the real-time interaction process between cadmium(II) and its aptamer. According to the information on mass, thickness, and density obtained by DPI, a Cd²⁺ concentration-dependent interaction mechanism and conformation of aptamer was proposed. At low Cd²⁺ concentration, Cd²⁺ mainly interacted with phosphate groups on aptamer, resulting in the stretched ssDNA and a few vertical hairpin structures. When adding the high concentration of Cd²⁺, Cd²⁺ primarily bound with bases of DNA by coordination interaction and the conformation of aptamer transferred to a tight and short hairpin structure. In addition, the association rate constant (k_a), dissociation rate constant (k_d) and disassociation constant (K_D) between Cd²⁺ and its aptamer were calculated to be 96 M^-1 S^-1, 2.11 × 10^-5 S^-1, and 220 nM, respectively. The proposed aptasensor showed high sensitivity for Cd²⁺ detection with the detection limit of 0.61 μg/L, which was far below the 5.0 μg/L ranked by the U.S. Environmental Protection Agency. The biosensor also exhibited excellent regenerability and could be used for three cycles without obvious change in response signal. Therefore, the developed method could not only provide quantitative information, but also offered the information on conformation and kinetics for molecular interaction. This method can facilely extend to study the interaction of DNA with other ions, small molecules, or biomacromolecules.

Modeling Gene Expression Instability by Programmed and Switchable Polymerization/Nicking DNA Nanomachineries

Models for gene expression instability by noncanonical DNA-nanostructures are introduced. The systems consist of a promoter-template scaffold that acts as a polymerization/nicking machinery that models, in the presence of polymerase/Nt.BbvCI and dNTPs, the autonomous synthesis of displaced strands mimicking the native "genes". Incorporation of noncanonical DNA structures into the scaffolds consisting of Sr²⁺-ion-stabilized G-quadruplexes, T-A·T triplexes, or ATP-aptamer complexes results in the perturbation of the polymerization/nicking DNA machineries and the synthesis of displaced strands-"genes" exhibiting other structures. By the dissociation of the noncanonical blockage units, the regeneration of the synthesis of the original intact displaced strands-"genes" is demonstrated. The study introduces conceptual means to eliminate destructive gene expression instability pathways.

A Metal-Organic Framework Nanosheet-Assembled Frame Film with High Permeability and Stability

The engineering of metal-organic frameworks (MOFs) into membranes and films is being investigated, to transform laboratory-synthesized MOFs into industrially viable products for a range of attractive applications. However, rational design and construction of highly permeable MOF thin films, without trade-offs in terms of structural mechanical stability, remains a significant challenge. Herein, a simple, general strategy is reported to prepare thin MOF nanosheet (NS)-assembled frame film via heteroepitaxial growth from metal hydroxide film. As the thin MOF NS-assembled film significantly enhances the permeability of mass though the film, the resultant gold nanoparticle (Au NP)@MOF film exhibits much higher catalytic efficiency than the Au NP@MOF bulk film. Meanwhile, the unique framework of the MOF NS-assembled film resists torsion and collapse, so the composite catalyst exhibits long-term stability.

Nonlinear Plasmonic Sensing for Label-Free and Selective Detection of Mercury at Picomolar Level

We present the concept of a nonlinear plasmonic sensing approach for rapid, sensitive, and label-free detection of mercury. Nonlinear plasmonic sensing of mercury relies on a systematic combination of nonlinear optics (NLO) with well-known concepts of amalgamation chemistry and plasmonic properties of gold nanorods. Exploiting the extreme sensitivity of the NLO process toward Hg-induced change in the local electric field of plasmonic nanorods, we succeed in improving the limit of detection (LOD) of mercury by 2-3 orders of magnitude as compared to the commonly used linear localized surface plasmon resonance (LSPR) based sensing. Using our method, an LOD of as low as 58 pM (11 ppt) has been achieved with high selectivity. Nonlinear plasmonic sensing aproach is found to work excellently for detecting mercury in real samples like blood plasma.

Heteroleptic Pt(II)-dithiolene-based Colorimetric Chemosensors: Selectivity Control for Hg(II) Ion Sensing

Hg²⁺ ions can accumulate in the natural environment and in organisms, where they cause damage to the central nervous system. Therefore, the detection of Hg²⁺ ions is essential for monitoring environmental contamination and human health. Herein, we demonstrate a simple method for tuning chemosensor signal ratios that significantly increased chemosensor selectivity for Hg²⁺ detection. Selectivity tuning was accomplished for chemosensors of the type (diphosphine)Pt(dmit), bearing the two different terminal groups 1,2-bis(diphenylphosphino)ethane (dppe) and 1,2-bis[bis(pentafluorophenyl)phosphino]ethane) (dfppe) due to the modulation of specific intermolecular interactions between the dmit ligand and Hg²⁺ ion. The structure exhibited a large pseudo-Stokes shift, which was advantageous for the internal reference signal and for eliminating potential artifacts. Straightforward chain-end manipulation enabled the tuning of chemosensor properties without additional chemical alterations. Based on these findings, we propose a new platform for improving the selectivity and sensitivity of colorimetric cation sensors. The results of this study will facilitate the designing of organic materials whose certain properties can be enhanced through precise control of the materials’ chemical hybridization by simple functional end-group manipulation.

Aggregation-based determination of mercury(II) using DNA-modified single gold nanoparticle, T-Hg(II)-T interaction, and single-particle ICP-MS

An ultrasensitive assay is described for the detection and determination of Hg²⁺(aq) in water samples based on single-particle inductively-coupled plasma/mass spectrometry (spICP-MS). In the presence of Hg²⁺(aq), AuNPs modified with a segment of single-stranded DNA aggregate due to the formation of the well-known thymine (T)-Hg²⁺-T complex. Single particle (sp) ICP-MS is used quantify the degree of aggregation by the overall decrease in number of detected AuNPs or NP aggregates. Compared with most other Hg²⁺ assays that use the same principle of aggregation-dispersion with DNA modified AuNPs, this method has a much lower detection limit of (0.031 ng L^-1, 155 fM) and a wider (10,000-fold) linear range (up to 1 μg L^-1). The method also showed good practical potential because of its minimal interference from the water sample matrix. Graphical abstractSchematic representation of Hg²⁺ determination by using modified AuNP probes measured by spICP-MS. AuNPs pulses detected in ICP-MS is relative to the aggregation status of AuNPs based on thymine-Hg²⁺-thymine interaction.

Visible sensing of conformational transition in model silk peptides based on a gold nanoparticles indicator

To understand protein structural transition and β-sheet formation is of importance in disparate areas such as silk protein processing and disease related β-amyloid behavior. Herein, GAGSGAGAGSGAGY (GY-14), a tetradecapeptide based on the crystallizable sequence of silk fibroin, was employed as a model peptide of the crystalline regions of silk fibroin. Due to the incorporation of tyrosine (Y), GY-14 was able to reduce Au³⁺ to Au NPs and further stabilize them without any external reducing or capping reagents to produce GY-14 stabilized Au NPs (GY-14@Au NPs). The in situ prepared GY-14@Au NPs were utilized as a built-in colorimetric indicator. The influences of specified physiological factors including decreasing the pH, the addition of calcium ions and isopropanol treatment on the self-assembly behavior of GY-14@Au NPs in aqueous solution have been studied. On the basis of transmission electron microscopy (TEM), dynamic light scattering (DLS), atomic force microscopy (AFM), Fourier transform infrared (FT-IR) spectroscopy and circular dichroism (CD) measurements, the color changes and the UV-Vis absorption peak shift of GY-14@Au NPs were attributed to the conformational change of the GY-14 peptide. The colorimetric readout can be seen with the naked eye, providing an efficient indicator to study the conformational changes of peptides exposed to various environmental stimuli.

Ion-induced PCR strategy for mercury detection

Mercury contamination is one of the most serious environmental problems. It can cause serious effects on the human health, such as case damage in the brain, nervous system, immune system, and kidney failure. Therefore, development of an accurate, sensitive, and simple operational detection method for mercury is very necessary. Herein, we report a new strategy for mercury ion detection based on commonly used PCR technique. High selectivity and sensitivity were achieved by the formation of the thymine-Hg-thymine (T-Hg-T) unnatural base pair at the 3'-end of PCR primers. The detection results of PCR amplification in presence of mercury ion could be reported either by using agarose gel analysis or through real-time fluorometric dye tracing for different detection purposes. To our knowledge, this study represents the first application of PCR based technique to the detection of metal ions.

Noble Metal Nanoparticles-Based Colorimetric Biosensor for Visual Quantification: A Mini Review

Nobel metal can be used to form a category of nanoparticles, termed noble metal nanoparticles (NMNPs), which are inert (resistant to oxidation/corrosion) and have unique physical and optical properties. NMNPs, particularly gold and silver nanoparticles (AuNPs and AgNPs), are highly accurate and sensitive visual biosensors for the analytical detection of a wide range of inorganic and organic compounds. The interaction between noble metal nanoparticles (NMNPs) and inorganic/organic molecules produces colorimetric shifts that enable the accurate and sensitive detection of toxins, heavy metal ions, nucleic acids, lipids, proteins, antibodies, and other molecules. Hydrogen bonding, electrostatic interactions, and steric effects of inorganic/organic molecules with NMNPs surface can react or displacing capping agents, inducing crosslinking and non-crosslinking, broadening, or shifting local surface plasmon resonance absorption. NMNPs-based biosensors have been widely applied to a series of simple, rapid, and low-cost diagnostic products using colorimetric readout or simple visual assessment. In this mini review, we introduce the concepts and properties of NMNPs with chemical reduction synthesis, tunable optical property, and surface modification technique that benefit the development of NMNPs-based colorimetric biosensors, especially for the visual quantification. The “aggregation strategy” based detection principle of NMNPs colorimetric biosensors with the mechanism of crosslinking and non-crosslinking have been discussed, particularly, the critical coagulation concentration-based salt titration methodology have been exhibited by derived equations to explain non-crosslinking strategy be applied to NMNPs based visual quantification. Among the broad categories of NMNPs based biosensor detection analyses, we typically focused on four types of molecules (melamine, single/double strand DNA, mercury ions, and proteins) with discussion from the standpoint of the interaction between NMNPs surface with molecules, and DNA engineered NMNPs-based biosensor applications. Taken together, NMNPs-based colorimetric biosensors have the potential to serve as a simple yet reliable technique to enable visual quantification.

Effects of Small Molecules on DNA Adsorption by Gold Nanoparticles and a Case Study of Tris(2-carboxyethyl)phosphine (TCEP)

DNA-functionalized gold nanoparticles (AuNPs) often encounter various small molecules and ions such as backfilling agents, bifunctional cross-linkers, stabilizers, and molecules from biological fluids both during and after the DNA conjugation process. Small molecules and ions can influence the stability and property of the conjugate, but such interactions are yet to be fully explored. In this work, eight important molecules were studied and compared, including tris(2-carboxyethyl)phosphine hydrochloride (TCEP), 3-(2-pyridyldithio)propionic acid N-hydroxysuccinimide ester (SPDP), 4-maleimidobutyric acid N-hydroxysuccinimide ester (GMBS), 6-hydroxy-1-hexanethiol (MCH), l-glutathione (GSH), bromide (Br^-), bis(p-sulfonatophenyl)phenylphosphine (BSPP), and thiocyanate (SCN^-). Depending on the size, charge, and adsorption affinity on the AuNPs, they can either stabilize or destabilize the AuNPs. Their ability to displace thiolated DNA from AuNPs follows the order of MCH > SPDP > GSH > SCN^- > TCEP > Br^- > BSPP > GMBS. BSPP has the best stabilization effect for the colloidal stability of AuNPs, while it does not displace the adsorbed DNA. TCEP can be adsorbed on AuNPs and enhance the adsorption of A/C rich DNA in low-salt conditions. This work indicates that the effects of small molecules and ions cannot be ignored when studying the DNA-functionalized AuNPs, which ensures optimal applications and correct interpretation of the data.

DNA-Functionalized Plasmonic Nanomaterials for Optical Biosensing

Plasmonic nanomaterials, especially Au and Ag nanomaterials, have shown attractive physicochemical properties, such as easy functionalization and tunable optical bands. The development of this active subfield paves the way to the fascinating biosensing platforms. In recent years, plasmonic nanomaterials-based sensors have been extensively investigated because they are useful for genetic diseases, biological processes, devices, and cell imaging. In this account, a brief introduction of the development of optical biosensors based on DNA-functionalized plasmonic nanomaterials is presented. Then the common strategies for the application of the optical sensors are summarized, including colorimetry, fluorescence, localized surface plasmon resonance, and surface-enhanced resonance scattering detection. The focus is on the fundamental aspect of detection methods, and then a few examples of each method are highlighted. Finally, the opportunities and challenges for the plasmonic nanomaterials-based biosensing are discussed with the development of modern technologies.

Hierarchically spacing DNA probes on bio-based nanocrystal for spatial detection requirements

Sterically spacing and locating functional matters at the nanoscale exert critical effects on their application, especially for the fluorescence probes whose aggregation causes emission quenching. Here we achieved a hierarchical spacing strategy of DNA fluorescence probes for ion detection via locating them separately on rod-like cellulose nanocrystals (CNCs) and further isolating CNCs by pre-grafting long molecular chains. Controlling chemical structure of CNC and location degree could adjust the inter-space of DNA probes (with a molecular length of ca. 3.6 nm) in a range of 3.5-6.5 nm with a gradient about 0.2 nm. A length up to micrometer scale of the CNC nanorods was necessary to provide DNA probes with well-separated grafting locations and enough freedom, which brought a vast linear detection range from 10 nmol/L to 5 μmol/L of Hg²⁺ concentration. The abundant reactive sites on CNC allowed a grafting pre-location of poly (tert-butyl acrylate) (PtBA) to promote the isolation of DNA probes. Controlled radical polymerization was employed to adjust the length of PtBA molecular chains, which increased the linear sensitivity coefficient of Hg²⁺ detection by ca. 2.5 times. This hierarchical nanoscale spacing concept based on chemical design can hopefully conduce to the development of biosensor and medical diagnosis. A hierarchical spacing strategy was applied to separate DNA fluorescent probes on CNCs and detect ion concentration linearly. The first-level spacing was to locate probes uniformly on CNCs, obtaining a wide linear range; and the second-level spacing was to isolate CNCs with polymer, obtaining an increased linear coefficient.

Dual sensing reporter system of assembled gold nanoparticles toward the sequential colorimetric detection of adenosine and Cr(III)

A facile and sensitive sequential colorimetric detection strategy for adenosine and Cr³⁺ has been presented by using the aptamer and 11-mercaptoundecanoic acid assembled gold nanoparticles. The thiolated DNA and 11-mercaptoundecanoic acid was simultaneously assembled to the surface of gold nanoparticles in one step by gold-sulfur interaction. Adenosine aptamer was linked to functionalized gold nanaoparticles based on the strict complementary nature of the DNA base pairs. Conformational change of aptamer will be induced due to its specific binding with targets. As a result, this aptamer tethered aggregated nanoparticles underwent fast disassembly into dispersed nanoparticles upon binding of adenosine, and this distance change between particles induced a distinct solution color changing from blue to red. The dispersed particles were sensitive to Cr³⁺ due to the chelation effect between the carboxyl group of 11-mercaptoundecanoic acid and metal ions, and further occurred obvious aggregation accompanying with a color change from red to blue. Depended on this principle, a sensitive and selective sequential colorimetric sensor for detection of adenosine and Cr³⁺ was developed. The proposed colorimetric sensor exhibited wide linear ranges and low detection limits towards the detection of adenosine and Cr³⁺. Regarding adenosine, linear range was 1 × 10^-7 ∼ 1 × 10^-4 M with low detection limit of 1.8 × 10^-8 M, and the naked eye detection limit was estimated as 20 μM. With regard to Cr³⁺, good linear relationship was ranged from 1 × 10^-10 to 1 × 10^-6 M with low detection limit of 1.7 × 10^-11 M，and the naked eye detection limit was as low as 0.1 nM. Meanwhile, bifunctional recognition was successfully used for practical human urine samples with good recoveries from 89.0% to 112.6% for adenosine and 90.2%-113.4% for Cr³⁺. It also highlights the potential applications of other aptamers and ligands in cascade analysis of other analytes.

1,3,9-Triaza-2-oxophenoxazine: An Artificial Nucleobase Forming Highly Stable Self-Base Pairs with Three AgI Ions in a Duplex

Metal-mediated base pairs (MMBPs) formed by natural or artificial nucleobases have recently been developed. The metal ions can be aligned linearly in a duplex by MMBP formation. The development of a three- or more-metal-coordinated MMBPs has the potential to improve the conductivity and enable the design of metal ion architectures in a duplex. This study aimed to develop artificial self-bases coordinated by three linearly aligned Ag^I ions within an MMBP. Thus, artificial nucleic acids with a 1,3,9-triaza-2-oxophenoxazine (9-TAP) nucleobase were designed and synthesized. In a DNA/DNA duplex, self-base pairs of 9-TAP could form highly stable MMBPs with three Ag^I ions. Nine equivalents of Ag^I led to the formation of three consecutive 9-TAP self-base pairs with extremely high stability. The complex structures of 9-TAP MMBPs were determined by using electrospray ionization mass spectrometry and UV titration experiments. Highly stable self-9-TAP MMBPs with three Ag^I ions are expected to be applicable to new DNA nanotechnologies.

Amplified MicroRNA Detection and Intracellular Imaging Based on an Autonomous and Catalytic Assembly of DNAzyme

Abnormal microRNAs (miRNAs) expression is demonstrated to associate with various important biological processes, including tumorigenesis, metastasis, and progression. Given the low miRNA expression at the earlier stage of diseases, its amplified detection still requires more efforts. Inspired by the two-stage arithmetic amplifier of electric devices, we reported an autonomous and catalytic assembly of DNAzyme strategy by integrating a DNAzyme biocatalyst and catalytic hairpin assembly (CHA) circuit. Here the catalytically inactive DNAzyme subunits were respectively grafted into these metastable CHA hairpin reactants that were kinetically impeded without false cross-hybridizations. The target catalyzed the nonenzymatic CHA-mediated successive assembly of dumbbell-like bis-DNAzyme nanostructures, leading to the efficient DNAzyme-mediated cleavage of fluorophore/quencher-modified substrate and to the generation of an amplified fluorescence signal. The present CHA-DNAzyme amplifier can be employed as a versatile and general sensing platform for analyzing other analytes (e.g., miRNA) by introducing a sensing module into the present system. Moreover, the homogeneous CHA-DNAzyme method could realize the sensitive intracellular miRNA imaging in living cells, which is attributed to the inherently synergistic amplification property between DNAzyme and CHA reactions. Given the attractive analytical features of the autonomous CHA-DNAzyme system, the present strategy shows great promise for analyzing additional different analytes in clinical research fields.

Engineering Nanozymes Using DNA for Catalytic Regulation

DNA treatment of metal nanoparticles provides a potent tool for tuning their native properties and constructing advanced materials. However, there have been limited studies on interactions between DNA and nanomaterial-based artificial enzymes (nanozymes) to influence their intrinsic peroxidase-like properties. Here, we present the utilization of DNA as a capping ligand to engineer various bio-nanointerfaces for high-precise and adjustable regulation of catalytic behaviors of nanozymes toward the oxidation of substrates. The treatment of stiff double-stranded DNA only induced a negligible enhancement of the catalytic activity of nanozymes, and both coil-like single-stranded DNA and hairpin DNA-capped nanoparticles produced a medium signal increase. Interestingly, hybridization chain reaction (HCR) product-treated nanoparticles showed the highest peroxidase-like activities among four DNA structures. Furthermore, significant parameters that influence HCR process and the modulation of catalysis, such as the concentration of the hairpin DNA, the ionic strength, and the amount of nanozyme, were also systematically investigated. On the basis of HCR amplification and iron oxide (Fe₃O₄) nanoparticles, we develop a simple, fast, label-free, and sensitive colorimetric strategy for sensing of a Yersinia pestis-relevant DNA sequence with a detection limit as low as 100 pM as well as single nucleotide polymorphism discrimination. These results highlight DNA engineering as a facile strategy to regulate the catalytic activities of nanozymes and understand the interactions between metallic nanoparticles and nucleic acids for biosensing applications.

Application of hairpin DNA-based biosensors with various signal amplification strategies in clinical diagnosis

Biosensors have been commonly used in biomedical diagnostic tools in recent years, because of a wide range of application, such as point-of-care monitoring of treatment and disease progression, drug discovery, commonly use food control, environmental monitoring and biomedical research. Additionally, development of DNA biosensors has been increased enormously over the past few years as confirmed by the large number of scientific publications in this field. A wide range of techniques can be used for the development of DNA biosensors, such as DNA nano-machines and various signal amplification strategies. This article selectively reviews the recent advances in DNA base biosensors with various signal amplification strategies for detection of cancer DNA and microRNA, infectious microorganisms, and toxic metal ions.

Plasmonic spectral determination of Hg(II) based on surface etching of Au-Ag core-shell triangular nanoplates: From spectrum peak to dip

In this work, we develop a simple and selective sensing method for the detection of mercury ions based on surface plasmon resonance (SPR) spectrum change of Au-Ag core-shell triangular nanoplates. When the concentration of mercury is increased, the etching-induced change of particle size and shape also leads to the decrease of the absorption peak at the fixed wavelength, until a spectrum dip takes place. This spectral change of "peak-to-dip" greatly enlarges the detection range of mercury ions, which could be fine tuned by changing the initial thickness of the Ag coating. Under optimal conditions, the decrease of the logarithmic absorption intensity has a good linear response with the concentration of mercury ions increasing from 10 to 1000 μM, and the limit of detection (LOD) is 0.88 μM. Interference studies and real samples test indicate that, this new sensing method has a good selection for mercury ions and can be practically used in lake water. This work shows the surface etching-induced SPR shift can also leads to the intensity change with "peak-to-dip" fashion, which greatly enlarge the concentration range of the detection and could be widely applied in the spectroscopy sensing based on SPR.

Construction of a ratiometric phosphorescent assay with long-lived carbon quantum dots and inorganic nanoparticles for its application in environmental and biological systems

An effective ratiometric phosphorescence assay for Hg²⁺ detection is established based on carbon quantum dots and inorganic nanoparticles (CDs–CaTiO₃:Pr³⁺@SiO₂).

Growing prospects of DNA nanomaterials in novel biomedical applications

As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications.

Recent progress in DNA-based nanomaterials is summarized, ranging from applications in biosensors, biomedicine/imaging, and molecular logic gates to emerging nanomachines, as well as future perspective discussions.

Mix-&-Read Determination of Mercury(II) at Trace Levels with Hybrid Mesoporous Silica Materials Incorporating Fluorescent Probes by a Simple Mix-&-Load Technique

The synthesis, characterization, and application of mesoporous materials containing boron-dipyrromethene (BODIPY) moieties that allow the sensitive and selective detection of HgII in aqueous environments by fluorescence enhancement is reported. For this purpose, BODIPY dye I containing a thia-aza crown ether receptor as the fluorescent probe for the detection of HgII in aqueous environments is encapsulated into mesoporous materials to avoid self-quenching or aggregation in water. Determination of HgII is accomplished within a few seconds with high selectivity and sensitivity, reaching a limit of detection of 12 ppt. The determination of trace amounts of HgII in natural waters and in fish extracts is demonstrated by using our sensing material. The incorporation of the material into several μ-PAD strips yields a portable, cheap, quick, and easy-to-handle tool for trace HgII analysis in water.