Multiplexed sensing of mercury(II) and silver(I) ions: a new class of DNA electrochemiluminescent-molecular logic gates

Controllable DNA nanodevices regulated by logic gates for multi-stimulus recognition

DNA biosensors have attracted considerable attention due to their great potential in environmental monitoring and medical diagnosis. Despite the great achievements, the single function and uncontrollability of the sensors restrict their further application. Therefore, it is necessary to construct controllable nanodevices with both sensing and responding capabilities to external stimuli. Herein, we develop a strategy to engineer structure-switching biosensors which can respond to external stimuli while preserving the sensing capability. The engineered nanodevice consists of an actuation module and a sensing module. Initially, the sensing module is disabled by a blocker strand which acts as an allosteric switch. Once the stimuli-responsive actuation module displaces the blocker DNA, the sensing module is activated. Based on the strategy, the engineered nanodevice could recognize both the target and external stimuli. As a demonstration of this strategy, a controllable Hg²⁺ sensor was designed, in which a 'YES', 'AND', and 'OR' logic gate is employed as the actuation module respectively to facilitate recognition of oligonucleotide inputs. The modular nature of the proposed strategy makes it easily generalizable to other structure-switching sensors. As a demonstration of this, we successfully apply it to the ATP sensor. The proposed strategy has potential in the fields of programmable biosensing, disease diagnosis, DNA computing, and intelligent nanodevices.

Detection of Ag+ ions via an anti-aggregation mechanism using unmodified gold nanoparticles in the presence of thiamazole

The present study proposed a novel and highly selective and sensitive method for Ag⁺ ion detection based on gold nanoparticles (AuNPs) anti-aggregation. Thiamazole can induce AuNPs aggregation due to electrostatic interactions, which result in color transitions in the AuNPs solution from red to blue. However, the presence of Ag⁺ ions results in the preferential combination of the pyridinic nitrogen of thiamazole with the Ag⁺ ions. In addition, the Ag⁺ ions oxidize the sulfhydryl groups(-SH), which inhibit AuNPs aggregation and prompt a color change from blue to red. As a result, the present study established a method for Ag⁺ ion determination by AuNPs-thiamazole colorimetric probe based on the aforementioned anti-aggregation mechanism. The probe dynamic range was easily tuned via adjustments of the thiamazole amount. The relationship between the Ag⁺ concentration and AuNPs aggregation was monitored by ultraviolet-visible light (UV-Vis) spectroscopy at a dynamic range of 0.1 nM-9 μM and at a detection limit of 0.042 nM. The river water and tap water recovery analysis validated the successful operation of this colorimetric sensor in environmental monitoring.

Ultrasensitive detection of miRNA based on efficient immobilization of probe and electrochemiluminescent quenching of Ru(bpy)32+ by methylene blue

A high performance miRNA biosensor based on effective click chemistry assembly of a Ru(bpy)₃²⁺ labeled DNA probe and efficient electrochemiluminescence (ECL) quenching of the Ru(bpy)₃²⁺/BDEA (BDEA = N-butyldiethanolamine) system by surface-confined electroactive methylene blue (MB) dye is reported. When the target miRNA was present, the ECL signal instantly changed from "light off" to "light on" status. Using the specific miRNA let-7d as the target analyte, this biosensor provided sensitive detection over approximately six orders of magnitude (10 fM-10 nM), with a limit of detection of 10 fM (S/N = 3). Detailed study of the ECL quenching behavior of the Ru(bpy)₃²⁺/BDEA system by MB in solution suggested that the ECL quenching involves a combination of photoluminescence dynamic quenching and quenching processes directly associated with the redox reactions, as well as resonance energy transfer. A large binding constant of 4.7 × 10¹¹ M^-1 between let-7d and the DNA hairpin was estimated using an ECL-based extended Langmuir isotherm model, suggesting remarkably strong binding of the target to the probe. Furthermore, our biosensor exhibited excellent specificity and reproducibility. Using the developed system, the concentration of the target miRNA extracted from the A549 cell line could be obtained, demonstrating the potential application of the developed biosensor to practical biological sample analysis.

Fabrication of Electrochemical-Based Bioelectronic Device and Biosensor Composed of Biomaterial-Nanomaterial Hybrid

The field of bioelectronics has paved the way for the development of biochips, biomedical devices, biosensors and biocomputation devices. Various biosensors and biomedical devices have been developed to commercialize laboratory products and transform them into industry products in the clinical, pharmaceutical, environmental fields. Recently, the electrochemical bioelectronic devices that mimicked the functionality of living organisms in nature were applied to the use of bioelectronics device and biosensors. In particular, the electrochemical-based bioelectronic devices and biosensors composed of biomolecule-nanoparticle hybrids have been proposed to generate new functionality as alternatives to silicon-based electronic computation devices, such as information storage, process, computations and detection. In this chapter, we described the recent progress of bioelectronic devices and biosensors based on biomaterial-nanomaterial hybrid.

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.

Lateral flow test for visual detection of silver (I) based on cytosine-Ag(I)-cytosine interaction in C-rich oligonucleotides

The authors describe an oligonucleotide-based lateral flow test for visual detection of Ag(I). The assay is based on cytosine-Ag(I)-cytosine [C-Ag(I)-C] coordination chemistry to capture gold nanoparticle (AuNP) tags in the test zone. A thiolated C-rich oligonucleotide probe was immobilized on the AuNPs via gold-thiol chemistry, and a biotinylated C-rich oligonucleotide probe was immobilized on the test zone. The AuNPs labelled with C-rich oligonucleotides are captured by Ag(I) ions in the test zone through the C-Ag(I)-C coordination. The resulting accumulation of AuNPs produces a readily visible red band in the test zone. Under optimized conditions, the test is capable of visually detecting 1.0 ppb of Ag(I) which is 50 times lower than the maximum allowable concentration as defined by the US Environmental Protection Agency for drinking water. Hence, the test is inexpensive and highly sensitive. It was applied to the detection of Ag(I) in spiked samples of tap water and river water. In our perception, the test is a particularly valuable tool in limited resource settings.

Nanozyme-based bio-barcode assay for high sensitive and logic-controlled specific detection of multiple DNAs

Since HCV and HIV share a common transmission path, high sensitive detection of HIV and HCV gene is of significant importance to improve diagnosis accuracy and cure rate at early stage for HIV virus-infected patients. In our investigation, a novel nanozyme-based bio-barcode fluorescence amplified assay is successfully developed for simultaneous detection of HIV and HCV DNAs with excellent sensitivity in an enzyme-free and label-free condition. Here, bimetallic nanoparticles, PtAu_NPs, present outstanding peroxidase-like activity and act as barcode to catalyze oxidation of nonfluorescent substrate of amplex red (AR) into fluorescent resorufin generating stable and sensitive "Turn On" fluorescent output signal, which is for the first time to be integrated with bio-barcode strategy for fluorescence detection DNA. Furthermore, the provided strategy presents excellent specificity and can distinguish single-base mismatched mutant from target DNA. What interesting is that cascaded INHIBIT-OR logic gate is integrated with biosensors for the first time to distinguish individual target DNA from each other under logic function control, which presents great application in development of rapid and intelligent detection.

Quencher-Free Fluorescence Method for the Detection of Mercury(II) Based on Polymerase-Aided Photoinduced Electron Transfer Strategy

A new quencher-free Hg²⁺ ion assay method was developed based on polymerase-assisted photoinduced electron transfer (PIET). In this approach, a probe is designed with a mercury ion recognition sequence (MRS) that is composed of two T-rich functional areas separated by a spacer of random bases at the 3′-end, and a sequence of stacked cytosines at the 5′-end, to which a fluorescein (FAM) is attached. Upon addition of Hg²⁺ ions into this sensing system, the MRS folds into a hairpin structure at the 3′-end with Hg²⁺-mediated base pairs. In the presence of DNA polymerase, it will catalyze the extension reaction, resulting in the formation of stacked guanines, which will instantly quench the fluorescence of FAM through PIET. Under optimal conditions, the limit of detection for Hg²⁺ ions was estimated to be 5 nM which is higher than the US Environmental Protection Agency (EPA) standard limit. In addition, no labeling with a quencher was requiring, and the present method is fairly simple, fast and low cost. It is expected that this cost-effective fluorescence method might hold considerable potential in the detection of Hg²⁺ ions in real biological and environmental samples.

The analytical and biomedical potential of cytosine-rich oligonucleotides: A review

Polycytosine DNA strands are often found among natural sequences, including the ends of telomeres, centromeres, and introns or in the regulatory regions of genes. A characteristic feature of oligonucleotides that are rich in cytosine (C-rich) is their ability to associate under acidic conditions to form a tetraplex i-motif consisting of two parallel stranded cytosine-hemiprotonated cytosine (C·C+) base-paired duplexes that are mutually intercalated in an antiparallel orientation. Nanotechnology has been exploiting the advantages of i-motif pH-dependent formation to fabricate nanomachines, nanoswitches, electrodes and intelligent nanosurfaces or nanomaterials. Although a few reviews regarding the structure, properties and applications of i-motifs have been published, this review focuses on recently developed biosensors (e.g., to detect pH, glucose or silver ions) and drug-delivery biomaterials. Furthermore, we have included examples of sensors based on parallel C-rich triplexes and silver nanoclusters (AgNCs) fabricated on cytosine-rich DNA strands. The potential diagnostic and therapeutic applications of this type of material are discussed.

Molecular logic gates based on DNA tweezers responsive to multiplex restriction endonucleases

Self-assembled DNA tweezers containing four different restriction endonuclease recognition sites were designed and a set of logic gates were constructed.

Electrochemiluminescent molecular logic gates based on MCNTs for the multiplexed analysis of mercury(ii) and silver(i) ions

In this paper, logic gates with electrochemiluminescence (ECL) signal as outputs were constructed based on the use of the thymine (T)-rich (S₁) or cytosine (C)-rich (S₂) oligonucleotides for the selective analysis of mercury ions (Hg²⁺) or silver ions (Ag⁺).

Label-free colorimetric logic gates based on free gold nanoparticles and the coordination strategy between cytosine and silver ions

A colorimetric sensing strategy combined with logic gates was demonstrated by taking advantage of the dispersion and aggregation of gold nanoparticles.

Functional nucleic acid-based sensors for heavy metal ion assays

Heavy metal contaminants such as lead ions (Pb(2+)), mercury ions (Hg(2+)) and silver ions (Ag(+)) can cause significant harm to humans and generate enduring bioaccumulation in ecological systems. Even though a variety of methods have been developed for Pb(2+), Hg(2+) and Ag(+) assays, most of them are usually laborious and time-consuming with poor sensitivity. Due to their unique advantages of excellent catalytic properties and high affinity for heavy metal ions, functional nucleic acids such as DNAzymes and aptamers show great promise in the development of novel sensors for heavy metal ion assays. In this review, we summarize the development of functional nucleic acid-based sensors for the detection of Pb(2+), Hg(2+) and Ag(+), and especially focus on two categories including the direct assay and the amplification-based assay. We highlight the emerging trends in the development of sensitive and selective sensors for heavy metal ion assays as well.

A new fluorescent nitrogen-doped carbon dot system modified by the fluorophore-labeled ssDNA for the analysis of 6-mercaptopurine and Hg (II)

A simple, environmentally friendly hydrothermal method was used to prepare strongly luminescent, nitrogen-doped carbon dots (NCDs) with the use of Chinese yams as a source of carbon and nitrogen. Such NCDs have an average size of 2.7±1.4 nm; they emit blue light at 420 nm and have a quantum yield of up to 9.3%. Thus, carboxyfluorescein (FAM)-DNA macro-molecules were assembled on the surfaces of the NCDs, and stabilised by strong π-π stacking; the so formed hybrid nano-sensors were found to have an ultra-sensitive response to 6-mercaptopurine (6-MP). A strong emission and enhancement of yellow radiation was observed from FAM. Furthermore, due to the specific interactions between DNA and Hg(2+), which resulted in the formation of the T-Hg(2+)-T (T: thymine base) complex - a large, conjugated system, which formed between NCDs, DNA and 6-MP, was broken up. Thus, the fluorescence from FAM was quenched. The detection limits for 6-MP and Hg(2+) were 0.67 and 1.26 nM, respectively. The proposed method was applied for the determination of 6-MP in human serum and Hg(2+) in water samples with satisfactory results.

Room-temperature phosphorescence logic gates developed from nucleic acid functionalized carbon dots and graphene oxide

Room-temperature phosphorescence (RTP) logic gates were developed using capture ssDNA (cDNA) modified carbon dots and graphene oxide (GO). The experimental results suggested the feasibility of these developed RTP-based "OR", "INHIBIT" and "OR-INHIBIT" logic gate operations, using Hg(2+), target ssDNA (tDNA) and doxorubicin (DOX) as inputs.

Molecular encoder-decoder based on an assembly of graphene oxide with dye-labelled DNA

A general strategy was developed to fabricate 2-to-1, 4-to-2 and 8-to-3 molecular encoders and a 1-to-2 decoder by assembling graphene oxide with various dye-labeled DNAs.

Colorimetric logic response based on aptamer functionalized colloidal crystal hydrogels

A novel colorimetric logic system based on the aptamer-cross-linked colloidal crystal hydrogel (CCH) was developed. With the input stimuli of Hg(2+) and Ag(+), the CCH displayed shrinking response and colour change corresponding to the logical "OR" and "AND" gate. The visualization of the logic output signals is realized.

Biosensors with built-in biomolecular logic gates for practical applications

Molecular logic gates, designs constructed with biological and chemical molecules, have emerged as an alternative computing approach to silicon-based logic operations. These molecular computers are capable of receiving and integrating multiple stimuli of biochemical significance to generate a definitive output, opening a new research avenue to advanced diagnostics and therapeutics which demand handling of complex factors and precise control. In molecularly gated devices, Boolean logic computations can be activated by specific inputs and accurately processed via bio-recognition, bio-catalysis, and selective chemical reactions. In this review, we survey recent advances of the molecular logic approaches to practical applications of biosensors, including designs constructed with proteins, enzymes, nucleic acids, nanomaterials, and organic compounds, as well as the research avenues for future development of digitally operating “sense and act” schemes that logically process biochemical signals through networked circuits to implement intelligent control systems.

Retracted Article: Upconversion luminescent logic gates and turn-on sensing of glutathione based on two-photon excited quantum dots conjugated with dopamine

This article reported the two-photon excited quantum dots-based novel upconversion luminescent logic gates for turn-on sensing of glutathione.

Fluorometric/colorimetric logic gates based on BODIPY-functionalized mesoporous silica

We have demonstrated that metal ions acting as modulators in BODIPY-functionalized SiO₂ nanoparticles can generate absorbance changes in accordance with the operation of a half-adder digital circuit.

Logical regulation of the enzyme-like activity of gold nanoparticles by using heavy metal ions

In this study we employed self-deposition and competitive or synergistic interactions between metal ions and gold nanoparticles (Au NPs) to develop OR, AND, INHIBIT, and XOR logic gates through regulation of the enzyme-like activity of Au NPs. In the presence of various metal ions (Ag(+), Bi(3+), Pb(2+), Pt(4+), and Hg(2+)), we found that Au NPs (13 nm) exhibited peroxidase-, oxidase-, or catalase-like activity. After Ag(+), Bi(3+), or Pb(2+) ions had been deposited on the Au NPs, the particles displayed strong peroxidase-like activity; on the other hand, they exhibited strong oxidase- and catalase-like activities after reactions with Ag(+)/Hg(2+) and Hg(2+)/Bi(3+) ions, respectively. The catalytic activities of these Au NPs arose mainly from the various oxidation states of the surface metal atoms/ions. Taking advantage of this behavior, we constructed multiplex logic operations-OR, AND, INHIBIT, and XOR logic gates-through regulation of the enzyme-like activity after the introduction of metal ions into the Au NP solution. When we deposited Hg(2+) and/or Bi(3+) ions onto the Au NPs, the catalase-like activities of the Au NPs were strongly enhanced (>100-fold). Therefore, we could construct an OR logic gate by using Hg(2+)/Bi(3+) as inputs and the catalase-like activity of the Au NPs as the output. Likewise, we constructed an AND logic gate by using Pt(4+) and Hg(2+) as inputs and the oxidase-like activity of the Au NPs as the output; the co-deposition of Pt and Hg atoms/ions on the Au NPs was responsible for this oxidase-like activity. Competition between Pb(2+) and Hg(2+) ions for the Au NPs allowed us to develop an INHIBIT logic gate-using Pb(2+) and Hg(2+) as inputs and the peroxidase-like activity of the Au NPs as the output. Finally, regulation of the peroxidase-like activity of the Au NPs through the two inputs Ag(+) and Bi(3+) enabled us to construct an XOR logic gate.

Easy design of colorimetric logic gates based on nonnatural base pairing and controlled assembly of gold nanoparticles

Utilizing the principles of metal-ion-mediated base pairs (C-Ag-C and T-Hg-T), the pH-sensitive conformational transition of C-rich DNA strand, and the ligand-exchange process triggered by DL-dithiothreitol (DTT), a system of colorimetric logic gates (YES, AND, INHIBIT, and XOR) can be rationally constructed based on the aggregation of the DNA-modified Au NPs. The proposed logic operation system is simple, which consists of only T-/C-rich DNA-modified Au NPs, and it is unnecessary to exquisitely design and alter the DNA sequence for different multiple molecular logic operations. The nonnatural base pairing combined with unique optical properties of Au NPs promises great potential in multiplexed ion sensing, molecular-scale computers, and other computational logic devices.

Potentiometric aptasensing based on target-induced conformational switch of a DNA probe using a polymeric membrane silver ion-selective electrode

In this article, we introduce a general, sensitive, facile, and label-free potentiometric assay based on metal-mediated DNA base pairs. A nucleic acid with one adenosine-5'-triphosphate (ATP) binding sequence (aptamer) in the middle and two cytosine(C)-rich sequences at the lateral portions was employed as a model. A rigid hairpin structure can be formed in the presence of Ag(+) ions, in which the C residues of the spatially separated nucleotides are linked by the ions. The strong interaction between Ag(+) ions and cytosines forms a stable C-Ag(+)-C structure, which could reduce the concentration of silver ions released from the polymeric membrane silver ion-selective electrode (ISE) at the sample-membrane interface and decrease the potential response. In the presence of its target, the aptamer (the loop sequence of the probe) binds specifically to the target via reaction incubation. Such target-binding induced aptamer conformational change prevents the formation of C-Ag(+)-C structure, leaving more silver ions at the sample-membrane interface, which can be detected by the silver ISE. ATP can be quantified in the range of 0.5-3.0 μM with a detection limit of 0.37 μM. The relative standard deviation for 5 μM ATP is 5.5%. For the proposed method, the combination of using ion fluxes of silver ions as modulating reagents and as signal reporters greatly simplifies the detection procedures. In addition, by changing the binding sequence in the middle of the probe, the present detection method will be able to explore new applications of ISE for the detection of a large variety of targets.

Mercury-thymine interaction with a chair type G-quadruplex architecture

The T-Hg-T bond was utilized to cross-link two lateral loops of chair-type G-quadruplex DNA (G4-DNA) structures. Two out of five cross-linking geometries are able to increase the melting temperature and simultaneously reduce the polymorphism of the G4-DNA conformations.

Computational lateral flow biosensor for proteins and small molecules: a new class of strip logic gates

The first example of strip logic gates ("OR" and "AND" functions) for proteins and small molecules has been constructed on the basis of target-induced self-assembly of split aptamer fragments. Using thrombin and ATP as inputs, the corresponding split/integrated aptamers as molecular recognition elements, and gold nanoparticles as a tracer, the output signals can be directly visualized by observing the red bands on the test zones of the strips. The assay is simple, easy to perform, and cost-effective, allowing portable analysis at ambient temperature. The strip logic system is resistant to nonspecific interfering agents and can operate effectively even in human serum samples. Such logic strips hold great promise for application in intelligent point-of-care and in-field diagnostics.

A simple "molecular beacon"-based fluorescent sensing strategy for sensitive and selective detection of mercury (II)

A novel fluorescent sensor for the detection of Hg(2+) in aqueous media was developed. The method takes advantages of the highly selective thymine-Hg(2+)-thymine coordination and the sensitive "signal-on" structure-switching molecular beacon.