Cascade Fluorescent Sensors Based on Isothermal Signal Amplification for the Detection of Mercury and Silver Ions

In this study, novel fluorescent DNA biosensors for mercury (Hg2+) and silver (Ag+) ions were developed based on thymine (T)- and cytosine (C)-rich recognition elements in combination with exonuclease III and a mismatch-catalyzed hairpin assembly (MCHA)-based cascade isothermal signal-amplification strategy. In the presence of the respective target analytes, the recognition element terminals form so-called T-Hg2+-T or C-Ag+-C structures, resulting in cleavage by Exo III and the release of the trigger strand for MCHA. This binds to the H1 hairpin, which is fluorescently labeled with carboxyfluorescein (FAM) and tetramethylrhodamine (TAMRA), disrupting fluorescence resonance energy transfer between them and, thus, restoring FAM fluorescence, generating a strong signal at 520 nm. The linear range of the Hg2+ sensor is 0.5 to 3 pM, with a detection limit of 0.07 pM. The recovery range in actual spiked water samples is between 98.5% and 105.2%, with a relative standard deviation (RSD) ranging from 2.0% to 4.2%. The linear range of the Ag+ sensor is 10 to 90 pM, with a detection limit of 7.6 pM. The recovery range in actual spiked water samples is between 96.2% and 104.1%, with an RSD ranging from 3.2% to 6.3%. The cascade isothermal signal amplification strategy effectively enhances sensor sensitivity, while MCHA decreases the false-positive rate. The aptamer sensor exhibits high specificity, is resistant to interference, and can be used for the detection of Hg2+ and Ag+ in environmental water samples.

Dimerizing DNA-AgNCs via a C-Ag+-C structure for fluorescence sensing with dual-output signals

The unique insertion capability of Ag+ into cytosine-cytosine (C-Ag+-C) mismatch-base pairs enables precise fabrication of DNA-trapped silver nanoclusters (DNA-AgNCs) through varying the DNA sequences, thereby offering precise assembly of DNA-AgNCs and demonstrating great fluorescence applications. However, most of the DNA-AgNC-based fluorescence sensors have a single output signal. Herein, we developed a dimerized DNA-AgNC system through C-Ag+-C connection at the 3'-end of a designed DNA. The formation and crack-up of C-Ag+-C endows DNA-AgNCs with the ability to identify Ag+ and cysteine (Cys) with dual-output signals, changed fluorescence intensity (FI) and wavelength-shift in NIR emission around 815 nm via photoinduced electron transfer (PET), respectively. Superior linearity of FI for Cys and Ag+ concentrations was demonstrated. Meanwhile, the practical utility of this platform was also successfully verified in milk and lake water.

A DNA Logic Circuit Equipped with a Biological Amplifier Loaded into Biomimetic ZIF-8 Nanoparticles Enables Accurate Identification of Specific Cancers In Vivo

DNA logic circuits (DLC) enable the accurate identification of specific cell types, such as cancer cells, but they face the challenges of weak output signals and a lack of competent platforms that can efficiently deliver DLC components to the target site in the living body. To address these issues, we rationally introduced a cascaded biological amplifier module based on the Primer Exchange Reaction inspired by electronic circuit amplifier devices. As a paradigm, three abnormally expressed Hela cell microRNAs (-30a, -17, and -21) were chosen as "AND" gate inputs. DLC response to these inputs was boosted by the amplifier markedly enhancing the output signal. More importantly, the encapsulation of DLC and amplifier components into ZIF-8 nanoparticles resulted in their efficient delivery to the target site, successfully distinguishing the Hela tumor subtype from other tumors in vivo. Thus, we envision that this strategy has great potential for clinical cancer diagnosis.

Fluorescent cysteine probe based on a signal amplification unit, a catalyzed hairpin assembly reaction and Förster resonance energy transfer

This work developed a sensitive DNA-based fluorescent probe comprising a cysteine binding unit and a signal amplification unit based on a catalyzed hairpin assembly (CHA) reaction. The cysteine binding unit comprises a homodimer of single-stranded DNA (ssDNA) rich in cytosine and held together by silver ions. In the presence of cysteine, the homodimer is disintegrated because of cysteine-silver binding that liberates the ssDNA, which drives the CHA reaction in the signal amplification unit. Förster resonance energy transfer (FRET) was used to report the generation of the amplified double-stranded DNA (dsDNA) product. Under the optimal conditions, the probe provided a good linearity (100-1200 nM), a good detection limit (47.8 ± 2.7 nM) and quantification limit (159.3 ± 5.3 nM), and a good sensitivity (1.900 ± 0.045μM^-1). The probe was then used to detect cysteine in nine real food supplement samples. All results provided good recoveries that are acceptable by the AOAC, indicating that it has potential for practical applications.

Versatile Triple-Output Molecular Logic Gate for Cysteine and Silver (I) in Foods and the Environment Based on I-Motif DNA Modulation

DNA-based molecular logic gates have been developed rapidly but most of them have a single output mode. This study is to develop a triple-output label-free fluorescent DNA-based multifunctional molecular logic gate with berberine as a fluorescent signal and a Ag⁺-aptamer as a recognition matrix. The Ag⁺-aptamer has been identified to switch from a random coil to an i-motif structure of C-Ag⁺-C from a Ag⁺-induced responsive conformational change. As a fluorescent probe, berberine is ultrasensitive to the changes of microenvironments, and the binding to i-motif DNA's more rigid structure causes a significant increase in fluorescence, anisotropy, and lifetime. The addition of cysteine to the berberine/C-Ag⁺-C system disintegrates the i-motif DNA structure because of the strong coordination between Ag⁺ and cysteine, and then the triple-output signals are almost retrieved. Given this, a highly sensitive triple-output molecular logic gate for the analyses of Ag⁺ and cysteine is constructed with high specificity. Moreover, this simple and cost-effective molecular logic gate has been applied for the detection of cysteine and Ag⁺ in various real environmental samples including river water, PM_2.5, soil, and food samples with satisfactory recoveries from 89.83 to 106.04%.

A review on silver-mediated DNA base pairs: methodology and application

The investigation of the interaction between metal ions and DNA has always attracted much attention in the fields of bioinorganic chemistry, supramolecular coordination chemistry, and DNA nanotechnology. Its mode of action can be simply divided into two aspects. On the one hand, it is non-specific electrostatic adsorption, mainly including Na⁺, K⁺, Mg²⁺, Ca²⁺ and other physiologically regulating ions; on the other hand, it is specific covalent binding, such as Pt²⁺, Hg²⁺, Ag⁺ and other heavy metal ions. This article focuses on the mechanism of action between Ag⁺ and DNA mismatch pair C-C, and summarizes its main characterization methods and various applications. It aims to provide a certain reference for the field of biological devices. With the development of cryo-electron microscopy and liquidcell TEM, the structure of C-Ag⁺-C is expected to be further characterized, which will be more widely used.

Enhanced 3D paper-based devices with a personal glucose meter for highly sensitive and portable biosensing of silver ion

A variety of routine methods are available for the detection of silver (I) (Ag⁺) ions, but most of them rely on expensive, sophisticated and desktop instruments. Herein, a low-cost, instrument-free and portable Ag⁺ biosensor was described by initially designing a new class of 3D origami microfluidic paper-based analytical devices (μPADs) into each of which one piece of reagent-loaded nanoporous membrane was integrated. It combines analyte-triggered self-growing of silver nanoparticles to block the membrane's pores in situ for rapid yet efficient signal amplification with a handheld personal glucose meter for a portable and sensitive quantitative readout based on the biocatalytic reactions between the glucose oxidase and glucose. Its utility is well demonstrated with the specific detection of the analyte with a limit of detection as low as ∼58.1 pM (3σ), which makes this new biosensing method one of the most sensitive Ag⁺ assays in comparison with many other typical methods recently reported. Moreover, the satisfactory recovery of analyzing several types of real water examples, i.e., tap water, drinking water, pond water and soil water, additionally validates its feasibility for practical applications.

A Sensitive Fluorescence Biosensor for Silver Ions (Ag+) Detection Based on C-Ag+-C Structure and Exonuclease III-Assisted Dual-Recycling Amplification

A C-Ag⁺-C structure-based fluorescence biosensor with novel combination design of exonuclease III (Exo III) dual-recycling amplification is proposed for the application of silver ions (Ag⁺) detection. Since oligo-1 involves C-C mismatches, the presence of Ag⁺ can be captured to form C-Ag⁺-C base pairs, which results in a double-helix structure with a blunt terminus. The double-helix structure can be cleaved by EXO III to release short mononucleotide fragments (trigger DNA) and Ag⁺. Released Ag⁺ can form new bindings with oligo-1, and other trigger DNA can be produced in the digestion cycles. Hybridization with the signal DNA (oligo-2) transforms a trigger DNA into double-stranded DNA with blunt terminus which can be cleaved by Exo III to reproduce the trigger DNA and form guanine- (G-) quadruplex DNA. The trigger DNA returns free to the solution and hybridizes with another signal DNA, which realizes the dual-recycling amplification. The G-quadruplex DNA can be reported by N-methylmesoporphyrin IX (NMM), a specific G-quadruplex DNA fluorochrome. This method allows Ag⁺ to be determined in the 5 to 1500 pmol/L concentration range, with a 2 pmol/L detection limit, and it has been successfully applied to the detection of Ag⁺ in real samples.

Extremely sensitive and wide-range silver ion detection via assessing the integrated surface potential of a DNA-capped gold nanoparticle

With the rapid development of nanotechnology and its associated waste stream, public concern is growing over the potential toxicity exposure to heavy metal ions poses to the human body and the environment. Herein, we report an extremely sensitive Kelvin probe force microscopy (KPFM)-based platform for detecting nanotoxic materials (e.g. Ag⁺) accomplished by probing the integrated surface potential differences of a single gold nanoparticle on which an interaction between probe DNA and target DNA occurs. This interaction can amplify the surface potential of the nanoparticle owing to the coordination bond mediated by Ag⁺ (cytosine-Ag⁺-cytosine base pairs). Interestingly, compared with conventional methods, this platform is capable of extremely sensitive Ag⁺ detection (∼1 fM) in a remarkably wide-range (1 fM to 1 μM). Furthermore, this platform enables Ag⁺ detection in a practical sample (general drinking water), and this KPFM-based technique may have the potential to detect other toxic heavy metal ions and single nucleotide polymorphisms by designing specific DNA sequences.

The construction of DNAzyme-based logic gates for amplified microRNA detection and cancer recognition

A series of duplex-specific nuclease-based DNAzyme logic gates was established for detecting multiple low-abundance microRNAs.

DNA-functionalized gold nanoparticle-based fluorescence polarization for the sensitive detection of silver ions

Despite their practical applications, Ag⁺ ions are environmental pollutants and affect human health. So the effective detection methods of Ag⁺ ions are imperative. Herein, we developed a simple, sensitive, selective, and cost-effective fluorescence polarization sensor for Ag⁺ detection in aqueous solution using thiol-DNA-functionalized gold nanoparticles (AuNPs). In this sensing strategy, Ag⁺ ions can specifically interact with a cytosine-cytosine (CC) mismatch in DNA duplexes and form stable metal-mediated cytosine-Ag⁺-cytosine (C-Ag⁺-C) base pairs. The formation of the C-Ag⁺-C complex results in evident changes in the molecular volume and fluorescence polarization signal. To achieve our aims, we prepared two complementary DNA strands containing C-base mismatches (probe A: 5'-SH-A₁₀-TACCACTCCTCAC-3' and probe B: 5'-TCCTCACCAGTCCTA-FAM-3'). The stable hybridization between probe A and probe B occurs with the formation of the C-Ag⁺-C complex in the presence of Ag⁺ ions, leading to obvious fluorescence quenching in comparison to the system without AuNP enhancement. The assay can be used to identify nanomolar levels of Ag⁺ within 6 min at room temperature, and has extremely high specificity for Ag⁺, even in the presence of higher concentrations of interfering metal ions. Furthermore, the sensor was successfully applied to the detection of Ag⁺ ions in environmental water samples and showed excellent selectivity and high sensitivity, implying its promising application in the future.

Reversible regulation of the supramolecular chirality of a cyanine dye by using the G-quadruplex structure as a template

Multiple cycle regulation of the supramolecular chirality of a cyanine dye has been successfully achieved by using DNA G-quadruplexes as templates, which is easily controllable by repeated addition of Ag(+) and cysteine (Cys). This work provides an easy and controllable strategy for the chiral regulation of supramolecules.

A simple and sensitive sensor for silver ions based on unmodified gold nanoparticles by using dynamic light scattering techniques

A simple and sensitive assay for Ag+ was developed with unmodified gold nanoparticles (AuNPs) by using dynamic light scattering techniques. Ag+ could induce the oligonucleotide (5′-ATC ACT ATA TCA TAT ACT CAT-3′) to change from a single-stranded structure to a double-stranded structure and desorb from the surface of AuNPs, which triggered the aggregation of AuNPs in the salt solution. The average hydrodynamic diameter of aggregated AuNPs could be detected by using dynamic light scattering techniques. Under the optimum conditions, the average hydrodynamic diameter of AuNPs is proportional to the concentration of Ag+ within the range of 13.3–100.0 nmol/L, with a detection limit of 3.2 nmol/L. The method is easy to operate and has low sample consumption, high sensitivity and selectivity.

A quantum dot-labelled aptamer/graphene oxide system for the construction of a half-adder and half-subtractor with high resettability

By a combination of quantum dot-labelled aptamers and graphene oxide, a hybrid molecular system was developed for the integration of multiple logic gates to implement half adder and half subtractor functions. On the merits of quantum dots, repetitious arithmetic operations and a reliable fluorescent switch were demonstrated.

A novel universal colorimetric sensor for simultaneous dual target detection through DNA-directed self-assembly of graphene oxide and magnetic separation

A novel universal colorimetric sensor for simultaneous dual target detection through DNA-directed self-assembly of graphene oxide and magnetic separation was designed for the first time.

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.

Determination of Ag+ ions by a graphene oxide based dual-output nanosensor with high selectivity

A new highly selective chemosensor for Ag⁺ ions was designed and synthesized by covalently introducing well-known fluorophore 1,8-diaminonaphthalene (DAN) onto graphene oxide (GO) sheets.

DNA assembled metal nanoclusters: synthesis to novel applications

In this review, we have discussed the emergence of promising environmental-benign DNA assembled fluorescent metal nanoclusters and their unique electronic structures, unusual physical and chemical properties.

A colorimetric and fluorometric dual-modal DNA logic gate based on the response of a cyanine dye supramolecule to G-quadruplexes

The INHIBIT DNA logic gate with dual-modal outputs based on the response of MTC aggregates to G-quadruplexes.

Graphene oxide-based selection and identification of ofloxacin-specific single-stranded DNA aptamers

ssDNA aptamers specific to ofloxacin with high affinity were screened using graphene oxide-SELEX.

Metal ion triggers for reversible switching of DNA polymerase

A new strategy to modulate DNA polymerase activity in a reversible and switchable manner was devised by using the novel interactions between DNA bases and metal ions.

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.

Triple Raman Label-Encoded Gold Nanoparticle Trimers for Simultaneous Heavy Metal Ion Detection

Here, a triple Raman label-encoded gold nanoparticle (AuNP) trimer is fabricated for heavy metal ion detection. In the presence of target ions, the gold nanoparticles modified with different Raman labels are assembled into trimers and produce different enhancements of Raman reporters, which are functionalized as Raman probes for simultaneous silver and mercury ion detection. Under optimized conditions, the limits of detection of Ag(+) and Hg(2+) reach 8.42 × 10(-12) and 16.78 × 10(-12) m, respectively.

A turn-on fluorescent aptasensor for adenosine detection based on split aptamers and graphene oxide

A simple, sensitive and selective turn-on fluorescent aptasensor for adenosine detection was developed based on target-induced split aptamer fragment conjunction and different interactions of graphene oxide and the two states of the designed aptamer sequences.

Enzyme-free and DNA-based multiplexer and demultiplexer

A DNA-based 2:1 multiplexer and 1:2 demultiplexer have been conceptually realized in enzyme-free conditions.

Fluorescence sensing systems for gold and silver species

Here, we provide an overview of the reported fluorescent detection systems for gold and silver species, and discuss their sensing properties with promising features.

A DNA logic gate based on strand displacement reaction and rolling circle amplification, responding to multiple low-abundance DNA fragment input signals, and its application in detecting miRNAs

A conveniently amplified DNA AND logic gate platform was designed for the highly sensitive detection of low-abundance DNA fragment inputs based on strand displacement reaction and rolling circle amplification strategy.

A metal (Co)–organic framework-based chemiluminescence system for selective detection of l-cysteine

A metal (Co)–Organic Framework–luminol chemiluminescence system was successfully established for the determination of l-cysteine.

A benzimidazolium-based organic trication: a selective fluorescent sensor for detecting cysteine in water

A benzimidazolium- and imidazolium-based trication was developed as a selective fluorescence probe for cysteine.

The graphene/nucleic acid nanobiointerface

In this critical review, we present the recent advances in the design and fabrication of graphene/nucleic acid nanobiointerfaces, as well as the fundamental understanding of their interfacial properties and various nanobiotechnological applications.

Construction of DNA logic gates utilizing a H+/Ag+ induced i-motif structure

A simple technology to construct diverse DNA logic gates (OR and INHIBIT) has been designed utilizing a H(+) and/or Ag(+) induced i-motif structure. The logic gates are easily controlled and also show a real time response towards inputs. The research provides a new insight for designing DNA logic gates using an i-motif DNA structure.