Nanoengineered electrically contacted enzymes on DNA scaffolds: functional assemblies for the selective analysis of Hg2+ ions

Supramolecular Assembly of Single-Tail ssDNA-Amphiphiles through π-π Interactions

In this work, we demonstrate the formation of supramolecular architectures from the assembly of single-tail single stranded DNA (ssDNA)-amphiphiles. Short ssDNA sequences of 10 nucleotides that were either unstructured or formed G-quadruplex secondary structures were conjugated to a single 4-(hexadecyloxy)benzamide tail, either directly or through a polycarbon (C₁₂) spacer. Conjugation of the ssDNA to the tail did not interfere with the G-quadruplex secondary structure of the ssDNA sequence. The ssDNA-amphiphiles self-assembled into ellipsoidal micelles, vesicles, nanotapes, and nanotubes. These nanotubes appeared to be formed by the rolling up of nanotapes. The increase of the hydrophobic block of the ssDNA-amphiphiles through the addition of a C₁₂ spacer led to an increase in wall thickness and nanotube diameter. The presence of π-π interactions, through the benzoic group, was verified via X-ray diffraction (XRD) and played a critical role in the formation of the different nanostructures. In contrast, ssDNA-amphiphiles with a single heptadecanoic acid tail self-assembled only into ellipsoidal micelles.

Au nanoparticle-hydrogel nanozyme-based colorimetric detection for on-site monitoring of mercury in river water

A sensitive on-site mercury sensing platform was developed for simple and effective monitoring of mercury levels in the field. The simple and practical mercury detection system was designed by integrating an Au nanoparticle-PEG hydrogel block nanozyme (Au-HBNz) into a polymer film-based colorimetric device. Upon addition of Hg²⁺ ions, Au-HBNz exhibited excellent peroxidase-like activity, catalyzing the oxidation of 3,3',5,5'-tetramethylbenzidine into a blue-colored product, which has a maximum absorbance at 652 nm. The resulting color intensity change was evaluated using a smartphone for simple and rapid Hg²⁺ detection with a broad detection range (0.008-20 μg∙mL^-1) and a linear concentration-response relationship (R² = 0.96). The detection limit (1.10 ng∙mL^-1) was lower than the maximum permissible Hg²⁺ levels in drinking water set by the World Health Organization (6 ng∙mL^-1) and U.S. Environmental Protection Agency (2 ng∙mL^-1). The recoveries of Hg²⁺ determination in river water by spiking Hg²⁺ samples ranged from 92 to 106%, which indicated high validity and applicability of the Hg²⁺ detection system for field measurements. Thus, the developed sensor enables highly selective and efficient real-time monitoring of Hg²⁺.

Silver enriched silver phosphate microcubes as an efficient recyclable SERS substrate for the detection of heavy metal ions

A rapid, cost-effective and accurate detection of heavy metal ions is crucial for human health monitoring and environmental protection. Surface-enhanced Raman spectroscopy (SERS) has become a reliable method due to its outstanding performance for the identification of contaminants. In this paper, silver phosphate microcubes (Ag₃PO₄) were fabricated using two different precipitation methods for ultrasensitive SERS detection of heavy metal ions. The use of an organic linker (BPy) with Ag₃PO₄ enabled the immobilization of Hg²⁺ and Pb²⁺ ions. The formation of Ag₃PO₄ was confirmed by XRD, UV-DRS, FESEM coupled with EDX and HRTEM. The analytical enhancement factor (AEF) obtained was 10¹⁰ with a detection limit of 10^-15 M indicating high sensitivity. Based on these results, the possible SERS mechanism has been proposed and discussed. Moreover, an excellent reusability of Ag₃PO₄ substrate for at least four cycles was achieved upon the light exposure on heavy metal loaded substrate due to its superior catalytic ability for the degradation of heavy metal ions. The as-prepared substrate demonstrated remarkable stability, selectivity and SERS sensitivity towards real samples. The results conclude that Ag₃PO₄ microcubes offer a great prospect in recyclable SERS applications.

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.

Sodium Alginate Micelle-Encapsulating Zinc Phthalocyanine Dye-Sensitized Photoelectrochemical Biosensor with CdS as the Photoelectric Material for Hg2+ Detection

A simple and selective photoelectrochemical (PEC) biosensor was constructed for Hg²⁺ detection based on zinc phthalocyanine (ZnPc) dye-sensitized CdS using alginate not only as a carrier but also as a binder. First, CdS as a photoactive material was in situ modified on the electrode surface using a rapid and simple electrodeposition to obtain an initial photocurrent signal. Second, ZnPc was loaded in the amphiphilic alginate micelle and then was coated onto the CdS film surface via alginate as the binder. The photocurrent was subsequently enhanced due to the favorable dye sensitization effect of ZnPc to CdS. Finally, the thymine-rich probe DNA was immobilized on the modified ITO surface via coupling reaction between the carbonyl groups of the amphiphilic polymer and the amino groups of the probe DNA. In the presence of Hg²⁺, the thymine-Hg²⁺-thymine (T-Hg²⁺-T) structure was formed due to the specific bond of Hg²⁺ with thymine, resulting in the decrease of photocurrent due to the increase of steric hindrance on the modified electrode surface. The proposed PEC biosensor for Hg²⁺ detection possessed a wide linear range from 10 pM to 1.0 μM with a detection limit of 5.7 pM. This biosensor provides a promising platform for detecting other biomolecules of interest.

Filter-Assisted Separation of Multiple Nanomaterials: Mechanism and Application in Atomic/Mass Spectrometry/Fluorescence Label-Free Multimode Bioassays

Atomic spectrometry (AS) has been widely used in bioassay, but it requires steps to immobilize or separate the signal molecules. In this work, based on the phenomenon that the filter membrane can selectively separate multiple nanomaterials (nanoparticles (NPs) and quantum dots (QDs)) and its related ions, including poly(thymine)-templated Cu NPs and free Cu²⁺, Ag NPs and free Ag⁺, CdTe QDs and Cd²⁺, we constructed multimode and label-free biosensors by chemical vapor generation-atomic fluorescence spectrometry (CVG-AFS), inductively coupled plasma mass spectrometry (ICP-MS), and fluorescence. In this strategy, terminal deoxynucleotidyl transferase (TdT) and polynucleotide kinase (PNK), H₂O₂, and mucin 1 can be sensitively detected using Cu²⁺, Ag⁺, and Cd²⁺ as the signal probe, respectively. As a result, TdT and T4 PNK in single cells level can be accurately quantified. In addition, the possible separation mechanism of filter membrane was proposed, both Donnan repulsion by charged functional layer and entrapment effect by nanomaterials size contributed to the outstanding separation performance. Subsequently, on the basis that CdTe QDs can selectively identify Cu NPs/Cu²⁺, Ag NPs/Ag⁺, and C-Ag⁺-C/Ag⁺, cation-exchange reaction (CER) was introduced in this platform due to its unique advantages, including improving the sensitivity of the above system (an order of magnitude), converting the non-CVG metal elements into CVG elements, and using low-cost AFS to substitute the high-cost ICP-MS. In addition, we performed theoretical calculations of the selective CER using density functional theory (DFT). Therefore, this label-free and simple separation AS/ICP-MS sensing platform shows great potential for biomarker analysis.

Indirect determination of mercury(II) by using magnetic nanoparticles, CdS quantum dots and mercury(II)-binding aptamers, and quantitation of released CdS by graphite furnace AAS

This work describes an aptamer based method for highly sensitive determination of Hg(II). A Hg(II)-binding ssDNA aptamer was linked to silica-coated magnetic nanoparticles (magNPs). Then, a conjugate composed of graphene and CdS quantum dots (Gr-CdS) was linked to the complementary ssDNA. On mixing the two components, a duplex of type magNP-dsNNA-Gr/CdS is generated. If Hg(II) is added, it wills capturing the aptamer, and this leads to the release of Gr/CdS because of the formation of a stable thymine-Hg²⁺-thymine link. External magnetic force is used to remove the remaining complex. The released graphene-CdS is decomposed by HNO₃ and injected into a graphite furnace AAS. The detectable amount of Cd is proportional to the concentration of Hg(II) in the sample. Under the optimal conditions, the method has a linear response in the 2.50 aM to 0.25 nM Hg(II) concentration range, and the detection limit is as low as 7.6 aM (at S/N = 3). It has high selectivity for Hg(II) over other metal ions. Graphical abstract.

Concerted dynamics of metallo-base pairs in an A/B-form helical transition

Metal-mediated base pairs expand the repertoire of nucleic acid structures and dynamics. Here we report solution structures and dynamics of duplex DNA containing two all-natural C-HgII-T metallo base pairs separated by six canonical base pairs. NMR experiments reveal a 3:1 ratio of well-resolved structures in dynamic equilibrium. The major species contains two (N3)T-HgII-(N3)C base pairs in a predominantly B-form helix. The minor species contains (N3)T-HgII-(N4)C base pairs and greater A-form characteristics. Ten-fold different 1J coupling constants (15N,199Hg) are observed for (N3)C-HgII (114 Hz) versus (N4)C-HgII (1052 Hz) connectivities, reflecting differences in cytosine ionization and metal-bonding strengths. Dynamic interconversion between the two types of C-HgII-T base pairs are coupled to a global conformational exchange between the helices. These observations inspired the design of a repetitive DNA sequence capable of undergoing a global B-to-A-form helical transition upon adding HgII, demonstrating that C-HgII-T has unique switching potential in DNA-based materials and devices.

Ultrasensitive impedimetric mercury(II) sensor based on thymine-Hg(II)-thymine interaction and subsequent disintegration of multiple sandwich-structured DNA chains

An impedimetric method is described for ultrasensitive analysis of mercury(II). It is based on thymine-Hg(II)-thymine interaction which causes the disintegration of multiple-sandwich structured DNA chains. DNA strands were selected that are partially complementary to the T-rich Hg(II)-specific oligonucleotides (MSO). They were immobilized on a gold electrode via Au-S interaction. Next, the MSO and the bridging strands (BS) that can connect adjacent MSOs were alternately attached through layer-by-layer hybridization. Thus, a multiple-sandwich structured interface in created that carries numerous MSOs. This leads to a change-transfer resistance (R_ct) values of the electrode-electrolyte interface at faradic electrochemical impedance spectroscopy measurements in the presence of the hexacyanoferrate(II)/(III) redox probe at 0.2 V (vs. Ag/AgCl). If Hg(II) is added to the solution, the MSOs selectively interact with Hg(II) to produce T-Hg(II)-T structures. Hence, the multiple-sandwich hybridization chains become disintegrated, and this causes a decrease in resistivity. The effect can be used to quantify Hg(II) over an analytical range that extends over four orders of magnitude (1 fM to 10 pM), and it has a 0.16 fM limit of detection under optimal conditions. Graphical abstract An electrochemical sensor for femtomolar level detection of Hg²⁺ is realized on the basis of thymine-Hg²⁺-thymine interaction which causes disintegration of multiple sandwich DNA hybridization strands.

Structure-Switching Electrochemical Aptasensor for Single-Step and Specific Detection of Trace Mercury in Dairy Products

A reagentless and single-step electrochemical aptasensor with separation-free fashion and rapid response is developed for the Hg²⁺ assay in dairy products. Herein, the sensing strategy is established on Hg²⁺-induced structural transition of the methylene-blue-tagged single-stranded DNA (ssDNA) from a flexible manner to rigid hairpin-shaped double-stranded DNA (dsDNA), generating an improved peak current for the Hg²⁺ assay with a detection limit of 0.62 fM. Importantly, the best signal-to-noise ratio value can be obtained by exploiting Au flowers as sensing material and the optimal ssDNA concentration. The proposed sensor also exhibits high selectivity as a result of the specific thymine-Hg²⁺-thymine (T-Hg²⁺-T) coordination chemistry and can be applied to detect Hg²⁺ in dairy products. With the use of the electric "signal-on" switch, the electrochemical aptasensor has the advantages of simplicity, ease of operation, and high sensitivity and specificity, offering a promising method to assess the safety of dairy products polluted with Hg²⁺.

Facile Ag-Film Based Surface Enhanced Raman Spectroscopy Using DNA Molecular Switch for Ultra-Sensitive Mercury Ions Detection

Heavy metal pollution has long been the focus of attention because of its serious threat to human health and the environment. Surface enhanced Raman spectroscopy (SERS) has shown great potential for metal detection owing to many advantages, including, requiring fewer samples, its minimal damage to specimen, and its high sensitivity. In this work, we proposed a simple and distinctive method, based on SERS, using facile silver film (Ag-film) combined with a DNA molecular switch, which allowed for the highly specific detection of heavy metal mercury ions (Hg²⁺). When in the presence of Hg²⁺ ions, the signals from Raman probes attach to single-stranded DNA, which will be dramatically enhanced due to the specific structural change of DNA strands-resulting from the interaction between Hg²⁺ ions and DNA bases. This SERS sensor could achieve an ultralow limit of detection (1.35 × 10^-15 M) for Hg²⁺ detection. In addition, we applied this SERS sensor to detect Hg²⁺ in real blood samples. The results suggested that this SERS platform could be a promising alternative tool for Hg²⁺ detection in clinical, environmental, and food inspection.

HgII binds to C-T mismatches with high affinity

Binding reactions of HgII and AgI to pyrimidine-pyrimidine mismatches in duplex DNA were characterized using fluorescent nucleobase analogs, thermal denaturation and 1H NMR. Unlike AgI, HgII exhibited stoichiometric, site-specific binding of C-T mismatches. The on- and off-rates of HgII binding were approximately 10-fold faster to C-T mismatches (kon ≈ 105 M-1 s-1, koff ≈ 10-3 s-1) as compared to T-T mismatches (kon ≈ 104 M-1 s-1, koff ≈ 10-4 s-1), resulting in very similar equilibrium binding affinities for both types of 'all natural' metallo base pairs (Kd ≈ 10-150 nM). These results are in contrast to thermal denaturation analyses, where duplexes containing T-T mismatches exhibited much larger increases in thermal stability upon addition of HgII (ΔTm = 6-19°C), as compared to those containing C-T mismatches (ΔTm = 1-4°C). In addition to revealing the high thermodynamic and kinetic stabilities of C-HgII-T base pairs, our results demonstrate that fluorescent nucleobase analogs enable highly sensitive detection and characterization of metal-mediated base pairs - even in situations where metal binding has little or no impact on the thermal stability of the duplex.

Triplex DNA Nanostructures: From Basic Properties to Applications

Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.

Highly effective target converting strategy for ultrasensitive electrochemical assay of Hg2+

An electrochemical sensing system based on a highly effective Hg²⁺ converting strategy and RCA has been developed for the ultrasensitive detection of Hg²⁺.

Nanoarchitectonics of Small Molecule and DNA for Ultrasensitive Detection of Mercury

Reliable and ultrasensitive detection of mercury ions is of paramount importance for toxicology assessment, environmental protection, and human health. Herein, we present a novel optoelectronic approach based on nanoarchitectonics of small-molecule templated DNA system that consists of an adenine (A)-conjugated small organic semiconductor (BNA) and deoxyribo-oligothymidine (dT_n). This mutually templated dynamic chiral coassembly system (BNAn-dT_n) with tunable chiroptical, morphological, and electrical properties is tapped in to enable ultrasensitive and selective detection of inorganic and organometallic mercury in water. We observe a rapid transformation of the BNA_n-dT_n coassembly into a metallo-DNA duplex [dT-Hg-dT]_n in the presence of mercury, which is utilized for a chiro-optical and conductivity-based rapid and subnanomolar sensitivity (≥0.1 nM, 0.02 ppb) to mercury ions in water (∼100 times lower than United States Environmental Protection Agency tolerance limit). This ultrasensitive detection of inorganic and organometallic mercury is driven by a novel chemical design principle that allows strong mercury thymine interaction. This study is anticipated to inspire the development of future templated DNA nanotechnology-based optoelectronic devices for the rapid and ultrasensitive detection of numerous other toxic analytes.

Bottom-Up Synthesis and Sensor Applications of Biomimetic Nanostructures

The combination of nanotechnology, biology, and bioengineering greatly improved the developments of nanomaterials with unique functions and properties. Biomolecules as the nanoscale building blocks play very important roles for the final formation of functional nanostructures. Many kinds of novel nanostructures have been created by using the bioinspired self-assembly and subsequent binding with various nanoparticles. In this review, we summarized the studies on the fabrications and sensor applications of biomimetic nanostructures. The strategies for creating different bottom-up nanostructures by using biomolecules like DNA, protein, peptide, and virus, as well as microorganisms like bacteria and plant leaf are introduced. In addition, the potential applications of the synthesized biomimetic nanostructures for colorimetry, fluorescence, surface plasmon resonance, surface-enhanced Raman scattering, electrical resistance, electrochemistry, and quartz crystal microbalance sensors are presented. This review will promote the understanding of relationships between biomolecules/microorganisms and functional nanomaterials in one way, and in another way it will guide the design and synthesis of biomimetic nanomaterials with unique properties in the future.

Label-free and dual-amplified electrochemical detection of Hg2+ based on self-assembled DNA nanostructures and target-triggered exonuclease cleavage activity

An electrochemical biosensor for Hg²⁺ detection via HCR and Hg²⁺-triggered Exo III-assisted target recycling for signal amplification.

A strongly coupled Au/Fe3O4/GO hybrid material with enhanced nanozyme activity for highly sensitive colorimetric detection, and rapid and efficient removal of Hg(2+) in aqueous solutions

We have developed an efficient strategy for synthesizing a strongly coupled Au/Fe3O4/GO hybrid material to improve the catalytic activity, stability, and separation capability of Au nanoparticles (NPs) and Hg(2+). The hybrid material can be synthesized by the direct anchoring of Au and Fe3O4 NPs on the functional groups of GO. This approach affords strong chemical attachments between the NPs and GO, allowing this hybrid material to ultrasensitively detect Hg(2+) in aqueous solutions with a detection limit as low as 0.15 nM. In addition, the deposition of Hg(0) on the surface of Au/Fe3O4/GO could be quickly (within 30 min) and efficiently (>99% elimination efficiency) removed by the simple application of an external magnetic field and then Au/Fe3O4/GO could be subsequently reused at least 15 times, with the elimination efficiency remaining high (>96%).

Modified electrodes used for electrochemical detection of metal ions in environmental analysis

Heavy metal pollution is one of the most serious environmental problems, and regulations are becoming stricter. Many efforts have been made to develop sensors for monitoring heavy metals in the environment. This review aims at presenting the different label-free strategies used to develop electrochemical sensors for the detection of heavy metals such as lead, cadmium, mercury, arsenic etc. The first part of this review will be dedicated to stripping voltammetry techniques, on unmodified electrodes (mercury, bismuth or noble metals in the bulk form), or electrodes modified at their surface by nanoparticles, nanostructures (CNT, graphene) or other innovative materials such as boron-doped diamond. The second part will be dedicated to chemically modified electrodes especially those with conducting polymers. The last part of this review will focus on bio-modified electrodes. Special attention will be paid to strategies using biomolecules (DNA, peptide or proteins), enzymes or whole cells.

A new method to fabricate an electrochemical aptasensor to assay adenosine deaminase concentration using an assistance DNA

A novel strategy for the fabrication of electrochemical aptasensor is proposed in this work. This strategy has been employed to develop an aptasensor for the detection of adenosine deaminase concentration. A probe which contains adenosine aptamer and modified with ferrocene is adopted in our strategy as the core element. Moreover, an assistance DNA which can hybridize with the probe was also been employed in our strategy. The enzymatic reaction of adenosine catalyzed by adenosine deaminase plays a key role as well in the regulation of the hybridized complex. The formation of these regions of rigid, duplex DNA prevents the ferrocene tag from approaching the electrode surface, suppressing amperometric currents. The electroactive probe is to reflect the concentration of the enzyme indirectly but accurately. The detection limit is 1 U L(-1), which can be acceptable for clinical applications.

Sensitive and selective amplified detection of silver ion based on NEase-aided target recycling

A new Ag⁺ detection strategy that can be devised utilizing the advantages of both the nicking endonuclease-assisted signaling amplification (NEASA) method and the label-free architecture of G-quadruplex–hemin complex is reported.

Structures, physicochemical properties, and applications of T–HgII–T, C–AgI–C, and other metallo-base-pairs

In this feature article, recent progress and future perspectives of metal-mediated base-pairs such as T–Hg(ii)–T and C–Ag(i)–C are presented.

A bio-inspired sensor coupled with a bio-bar code and hybridization chain reaction for Hg2+ assay

In this article, a bio-inspired DNA sensor is developed, which coupled with bio-bar code and hybridization chain reaction. This bio-inspired sensor has high sensitivity to Hg²⁺, and has been used to assay Hg²⁺ in the extraction of traditional Chinese medicine.

Nitrogen-doped, thiol-functionalized carbon dots for ultrasensitive Hg(ii) detection

Nitrogen-doped, PEGylated carbon dots (C-dots) have been synthesized for the ultra sensitive detection of mercury ions (Hg²⁺).

A novel optical DNA biosensor for detection of trace amounts of mercuric ions using gold nanoparticles introduced onto modified glass surface

In this work we report a DNA spectrophotometric biosensor for detection of Hg2+ ions in which a pair of oligonucleotides with four thymine-thymine (T-T) mismatched bases was immobilized onto modified glass surface. Firstly, glass surface modified with 3-(mercaptopropyl) trimethoxysilane (MSPT) and gold nano-particles respectively and then one oligonucleotide (P1) modified with hexanthiol at 5-terminal was immobilized on gold nano-particles via self-assembly and inserted in methylene blue. Methylene blue can intercalate on single strand DNA (ss-DNA) and its absorption peak can measure spectrophotometrically. Then the other oligonucleotide was able to hybridize with P1 by forming thymine-Hg2+-thymine (T-Hg2+-T) complexes in the presence of Hg2+, and absorption signal of methylene blue reduced upon Hg2+ increasing concentration because inaccessibility of guanine base in DNA duplex. However, when Hg2+ was absent, the two oligonucleotides could not hybridize due to the T-T mismatched bases, and P2 could not be fixed on the modified glass surface and any change in absorption peak of methylene blue takes place. The UV-Vis spectrum showed a linear correlation between the absorption peak of methylene blue and the concentration of Hg2+ over the range from 10 nM to 10 μM (R2=0.9985) with a detection limit of 6 nM. This spectrophotometric biosensor could be widely used for selective detection of Hg2+.