A novel label-free fluorescent sensor for the detection of potassium ion based on DNAzyme

Nanoscale potassium sensing based on valinomycin-anchored fluorescent gold nanoclusters

Gold nanoclusters are a smart platform for sensing potassium ions (K+). They have been synthesized using bovine serum albumin (BSA) and valinomycin (Val) to protect and cap the nanoclusters. The nanoclusters (Val-AuNCs) produced have a red emission at 616 nm under excitation with 470 nm. In the presence of K+, the valinomycin polar groups switch to the molecule's interior by complexing with K+, forming a bracelet structure, and being surrounded by the hydrophobic exterior conformation. This structure allows a proposed fluorometric method for detecting K+ by switching between the Val-AuNCs' hydrophilicity and hydrophobicity, which induces the aggregation of gold nanoclusters. As a result, significant quenching is seen in fluorescence after adding K+. The quenching in fluorescence in the presence of K+ is attributed to the aggregation mechanism. This sensing technique provides a highly precise and selective sensing method for K+ in the range 0.78 to 8 µM with LOD equal to 233 nM. The selectivity of Val-AuNCs toward K+ ions was investigated compared to other ions. Furthermore, the Val-AuNCs have novel possibilities as favorable sensor candidates for various imaging applications. Our detection technique was validated by determining K+ ions in postmortem vitreous humor samples, which yielded promising results.

Fluorescence 'turn-off-on' assays for neomycin sulphate and K+ ions with orange-red fluorescent molybdenum nanoclusters

Fluorescent metal nanoclusters (MNCs) have found extensive application in recognizing molecular species. Here, orange-red fluorescent Arg-A. paniculata-MoNCs were synthesized using Andrographis paniculata leaf extract, arginine as a ligand, and MoCl5 as a metal precursor. The Arg-A. paniculata-MoNCs complex exhibited a quantum yield (QY) of 16.91% and excitation/emission wavelengths of 400/665 nm. The synthesized Arg-A. paniculata-MoNCs successfully acted as a probe for assaying neomycin sulphate (NS) via fluorescence turn-off and K+ ions via fluorescence turn-on mechanisms, respectively. Moreover, the developed probe was effectively used to develop a cellulose paper strip-based sensor for detection of NS and K+ ions. Arg-A. paniculata-MoNCs demonstrated great potential for sensing NS and K+ ions, with concentration ranges of 0.1-80 and 0.25-110 μM for NS and K+ ions, respectively. The as-synthesized Arg-A. paniculata-MoNCs efficiently detected NS and K+ ions in food and biofluid samples, respectively.

Engineered DNAzyme Enables Homogeneous Detection of Cereulide via Polychromic Fluorescence Modality

Cereulide, the exotoxin of emetic Bacillus cereus, has garnered considerable attention due to its capacity to produce foodborne poisonings and great chemical stability. Herein, a G-quadruplex-hemin DNAzyme-based biosensor was developed to detect cereulide in the homogeneous solution. Due to the special ring structure and high affinity to K+, cereulide can be attracted and intercalated into the G-quadruplex; thus, the properties of the G4 DNAzyme can be altered. The melting temperature (Tm) of the G4 DNAzyme in the presence or absence of cereulide was 58.75 and 50.10 °C, respectively, proving the intercalation of cereulide into the G4 DNAzyme. By using the polychromic fluorescence modality of CdTe quantum dots and o-phenylenediamine to assess the variation in the catalytic activity of the DNAzyme, the intercalation of cereulide had bidirectional effects in G4 DNAzyme-mediated reactions, showing that the fluorescence intensity of CdTe quantum dots displayed a linear relationship with the concentration of cereulide from 0.16 to 40 μg/mL with the limit of detection (LOD) of 0.10 μg/mL, while the fluorescence intensity of DAP exhibited a linear relationship with the concentration of cereulide from 0.02 to 40 μg/mL with the LOD of 0.01 μg/mL. It will be a perspective step of controlling cereulide as a hazardous material in food or the environment.

Fluorescence-Based Kinetic Measurements for RNA-Cleaving DNAzymes

Studying the catalytic behavior of biocatalysts under different conditions including temperature, buffer conditions, and cofactor concentrations is an important tool to understand their reaction mechanism. We describe two protocols that allow for the investigation of the catalysis of RNA-cleaving DNAzymes. The techniques include the use of FRET-labeled RNA substrates for studying the RNA-cleavage reaction in real-time under high throughput as well as RNA substrates labeled with a fluorescein molecule at the 5' end for gel-based assays. Both methods allow for an accurate determination of rate constants given a reaction model.

Highly Selective Detection of K+ Based on a Dimerized G-Quadruplex DNAzyme

Potassium ion (K⁺) plays a crucial role in biological systems, such as maintaining cellular processes and causing diseases. However, specifically, the detection of K⁺ is extremely challenging because of the coexistence of the chemically similar ion of Na⁺ under physiological conditions. In this work, a K⁺ specific biosensor is constructed on the basis of a dimerized G-quadruplex (GQ) DNA, which is promoted by K⁺, and the enzymatic activity of the resulting DNAzyme depends on the concentration of the K⁺. The K⁺ in a 1-200 mM concentration range can be selectively detected by visual color, UV-Vis absorbance or fluorescence even if the concentration of the accompanying Na⁺ is up to 140 mM at an ambient condition up to 45 °C. In addition, this system can also be used to selectively detect NH₄⁺ in a 5-200 mM concentration range. This dimerized DNAzyme offers a new type of biosensor with a potential application in the biological system.

Fluorogenic Aptasensors with Small Molecules

Aptamers are single-stranded DNA or RNA molecules that can be identified through an iterative in vitro selection–amplification process. Among them, fluorogenic aptamers in response to small molecules have been of great interest in biosensing and bioimaging due to their rapid fluorescence turn-on signals with high target specificity and low background noise. In this review, we report recent advances in fluorogenic aptasensors and their applications to in vitro diagnosis and cellular imaging. These aptasensors modulated by small molecules have been implemented in different modalities that include duplex or molecular beacon-type aptasensors, aptazymes, and fluorogen-activating aptamer reporters. We highlight the working principles, target molecules, modifications, and performance characteristics of fluorogenic aptasensors, and discuss their potential roles in the field of biosensor and bioimaging with future directions and challenges.

A wearable battery-free wireless and skin-interfaced microfluidics integrated electrochemical sensing patch for on-site biomarkers monitoring in human perspiration

In this study, an ultra-high sensitive, flexible, wireless, battery-free, and fully integrated (no external analysis equipment) electrochemical sensing patch system, including a microfluidic-sweat collecting unit, was newly developed for the on-site monitoring of the [K⁺] concentration in human sweat. Multiwalled carbon nanotube (MWCNT) and MXene-Ti₃C₂T_X based hybrid multi-dimensional networks were applied to obtain a high surface activation area and faster charge transfer rate, strongly adsorbing the valinomycin membrane to protect the ionophore for effective transshipment and immobilization of the [K⁺]. Furthermore, the controllable porosity of carbon-based materials can accelerate the kinetic process of ion diffusion. This hybrid nanonetwork structure effectively enhanced electrochemical stability and sensitivity, addressing the noise and signal drifting problems experienced with low concentration detection. The fabricated sensor exhibited a high ion concentration sensitivity of 63 mV/dec with excellent selectivity, amplified to 173 mV/dec with the integrated amplification system. The Near Field Communication (NFC) is used to transmit measurements to a smartphone wirelessly. A microfluidic channel was integrated with the electrochemical sensor patch to efficiently collect sweat on the human skin surface and mitigate the sensor surface contamination problem. Furthermore, the developed sensing patch can also be applied to other biomarkers on-site detection after modifying the working electrode with the corresponding selective membranes.

Electrochemical device based on nonspecific DNAzyme for the high-accuracy determination of Ca2+ with Pb2+ interference

Calcium is one of the most abundant and indispensable elements in biology, as it is a vital component of nerves, bones, and muscles and maintains the excitability of normal neuromuscular muscles. However, it may be harmful to the human body and even damage the organs if the calcium content exceeds the standard value by several times. To evaluate the level of calcium ions (Ca²⁺), an electrochemical biosensor (FET/SWNTs/Cazyme) was developed using a nonspecific DNAzyme with high stability, which combined the unique advantage of field-effect transistors and single-walled carbon nanotubes, while being easy-to-use and having excellent sensitivity. The incubation time and voltage after optimization were 15 min and +0.02 V. The nonspecific DNAzyme-based biosensor was sensitive to Ca²⁺, but it was also interfered with by Pb²⁺, which affected the detection accuracy. To solve this shortcoming, an electrochemical device was proposed, in which FET/SWNTs/Cazyme combined with other specific biosensors for Pb²⁺, and then established some data processing models were established through support vector machine regression (SVMR) and artificial neural network fitting (ANNF). For the optimal SVMR, the electrochemical device can determine the Ca²⁺ concentration in the range of 7.5-1000 μM with a detection limit of 5.48 μM. Finally, the prepared electrochemical device was employed to detect the Ca²⁺ in different milk and water samples.

A dual-fluorophore sensor approach for ratiometric fluorescence imaging of potassium in living cells

Potassium is the most abundant intracellular metal in the body, playing vital roles in regulating intracellular fluid volume, nutrient transport, and cell-to-cell communication through nerve and muscle contraction. On the other hand, aberrant alterations in K+ homeostasis contribute to a diverse array of diseases spanning cardiovascular and neurological disorders to diabetes to kidney disease to cancer. There is an unmet need for studies of K+ physiology and pathology owing to the large differences in intracellular versus extracellular K+ concentrations ([K+]intra = 150 mM, [K+]extra = 3-5 mM). With a relative dearth of methods to reliably measure dynamic changes in intracellular K+ in biological specimens that meet the dual challenges of low affinity and high selectivity for K+, particularly over Na+, currently available fluorescent K+ sensors are largely optimized with high-affinity receptors that are more amenable for extracellular K+ detection. We report the design, synthesis, and biological evaluation of Ratiometric Potassium Sensor 1 (RPS-1), a dual-fluorophore sensor that enables ratiometric fluorescence imaging of intracellular potassium in living systems. RPS-1 links a potassium-responsive fluorescent sensor fragment (PS525) with a low-affinity, high-selectivity crown ether receptor for K+ to a potassium-insensitive reference fluorophore (Coumarin 343) as an internal calibration standard through ester bonds. Upon intracellular delivery, esterase-directed cleavage splits these two dyes into separate fragments to enable ratiometric detection of K+. RPS-1 responds to K+ in aqueous buffer with high selectivity over competing metal ions and is sensitive to potassium ions at steady-state intracellular levels and can respond to decreases or increases from that basal set point. Moreover, RPS-1 was applied for comparative screening of K+ pools across a panel of different cancer cell lines, revealing elevations in basal intracellular K+ in metastatic breast cancer cell lines vs. normal breast cells. This work provides a unique chemical tool for the study of intracellular potassium dynamics and a starting point for the design of other ratiometric fluorescent sensors based on two-fluorophore approaches that do not rely on FRET or related energy transfer designs.

Aptamers as potential recognition elements for detection of vitamins and minerals: a systematic and critical review

Background: Vitamin and mineral deficiencies are prevalent globally, and extensive efforts have been made to assess their status. Most traditional methods are expensive and time-consuming; therefore, developments of rapid, simple, specific, and sensitive methods for the assessment of vitamins and minerals in biological samples are of high importance in research. Aptamers are synthetic nucleic acid single-stranded DNA or RNA that can be synthesized in vitro. They can be engineered to be analyte-specific and have been suggested as a substitute for monoclonal antibodies, due to their high sensitivity and affinity. In addition, aptamers can be chemically synthesized and readily modified for use as biosensors. These features make aptamers a promising tool for the detection of biological analytes. In this review, we provide an overview of the potential use of aptamer-based biosensors.Methods: Search terms were conducted on several online databases, including Google Scholar, PubMed, Scopus, and Science Direct from January 2000 to August 2019. Eligibility criteria were used and quality evaluation was performed. Following the review of 4349 articles, 39 articles met the inclusion criteria.Results: Aptasensors have recently been developed for the detection of vitamins by using optical methods, with a detection range from 74 pM to 204 pM, and lower limit of detection of 2.4 pM. Both electrochemical and optical methods have been used for detection of minerals, however electrochemical methods show a wider linear range and lower detection limits compared to optical methods with a wide linear range from 0.2 fM to 1.0 mM and limit of detection of 14.7 fM.Conclusion: The current report reviews recent developments in aptamer-based biosensors for detection of vitamins and minerals. Studies have shown that aptasensors' properties are suitable for the quantification of vitamins and minerals with high sensitivity, affinity, and specificity. Nevertheless, the limitations and future directions of aptamers require further research and new technological innovation.

Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges

DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.

Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications

DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes is expected to open the door to several healthcare applications. Therefore, a significant portion of this review is dedicated to various biological applications of DNAzymes, such as sensing, therapeutics, and nanodevices. In addition, discussion is further extended to the barriers encountered for the real-life application of these DNAzymes to provide a foundation for future research.

A "Turn-On" Fluorescence Copper Biosensor Based on DNA Cleavage-Dependent Graphene Oxide-dsDNA-CdTe Quantum Dots Complex

A novel “turn-on” fluorescent copper biosensor is developed successfully based on the graphene oxide (GO)-dsDNA-CdTe quantum dots (QDs) complex via chemical crosslink method. The optical and structure properties of GO-dsDNA-CdTe QDs complex are studied by fluorescence (FL) spectra and transmission electron microscopy (TEM) in detail. It is demonstrated that the fluorescence quenching of CdTe QDs is a process of fluorescence resonance energy transfer (FRET) due to the essential surface and quenching properties of two-dimensional GO. Copper ions induce the catalytic reaction of DNA chain and irreversibly break at the cleavage site, which will cause the G-quadruplex formation, moreover further result in the CdTe QDs separated from GO and restored its fluorescence. Therefore, a significant recovery effect on the fluorescence of the GO-dsDNA-CdTe QDs complex is observed in the presence of copper ions. The fluorescence responses are concentration-dependent and can be well described by a linear equation. Compared with other metal ions, the sensor performs good selectivity for copper ions.

Colorimetric Detection of Uranyl Using a Litmus Test

Ingestion of water containing toxic contaminants above levels deemed safe for human consumption can occur unknowingly since numerous common contaminants in drinking water are colorless and odorless. Uranyl is particularly problematic as it has been found at dangerous levels in sources of drinking water. Detection of this heavy metal-ion species in drinking water currently requires sending a sample to a laboratory where trained personnel use equipment to perform the analysis and turn-around times can be long. A pH-responsive colorimetric biosensor was developed to enable detection of uranyl in water which coupled the uranyl-specific 39E DNAzyme as a recognition element, and an enzyme capable of producing a pH change as the reporter element. The rapid colorimetric assay presented herein can detect uranyl in lake and well water at concentrations relevant for environmental monitoring, as demonstrated by the detection of uranyl at levels below the limits set for drinking water by major regulatory agencies including the World Health Organization (30 μg/L). This simple and inexpensive DNAzyme-based assay enabled equipment-free visual detection of 15 μg/L uranyl, using both solution-based and paper-based pH-dependent visualization strategies.

Colorimetric detection of microRNA based on DNAzyme and nuclease-assisted catalytic hairpin assembly signal amplification

Accurate and quantitative analysis of microRNA (miRNA) expression is critical for the diagnostics and theranostics of a disease. Herein, a proof-of-concept of a colorimetric horseradish peroxidase-mimicking DNAzyme (HRP-DNAzyme) biosensor for miRNA assay based on nuclease-assisted catalytic hairpin assembly (CHA) signal amplification was demonstrated. Duplex-specific nuclease (DSN) was employed to cleave the single-stranded DNA (ssDNA) chimeric probe (CP) on the magnetic bead (MB) surface via hybridization of the CP and target miRNA. The regenerated miRNA can cleave a large number of ssDNA CP to produce CHA initiator sequence fragments. The CP consists of two main regions: a target miRNA recognition DNA sequence at the 5' end and a CHA initiator (CI) sequence at the 3' end. The catalyzed assembly process of CHA produces a large amount of G-rich DNA. In the presence of hemin, the G-rich DNA forms G-quadruplex/hemin complex and mimics the horseradish peroxidase activity, which catalyzes a colorimetric reaction. For the proof-of-concept, microRNA-21 (miR-21) was selected as the model target to authenticate this strategy as a versatile assay platform. The proposed strategy allowed quantitation of the sequence specificity of miRNA-21 with a detection limit of 9.2 fM in a dynamic range from 10 fM-1 nM, with an excellent ability to discriminate the differences in miRNAs. Additionally, the miRNA assay in real samples was satisfactory, thereby confirming its applicability. Therefore, this method exhibited a great potential as a miRNA quantification method in biomedical research and clinical diagnosis.

Incorporation of surface plasmon resonance with novel valinomycin doped chitosan-graphene oxide thin film for sensing potassium ion

In this study, the combination of novel valinomycin doped chitosan-graphene oxide (C-GO-V) thin film and surface plasmon resonance (SPR) system for potassium ion (K⁺) detection has been developed. The novel C-GO-V thin film was deposited on the gold surface using spin coating technique. The system was used to monitor SPR signal for K⁺ in solution with and without C-GO-V thin film. The K⁺ can be detected by measuring the SPR signal when C-GO-V thin film is exposed to K⁺ in solution. The sensor produces a linear response for K⁺ ion up to 100ppm with sensitivity and detection limit of 0.00948°ppm^-1 and 0.001ppm, respectively. These results indicate that the C-GO-V film is high potential as a sensor element for K⁺ that has been proved by the SPR measurement.

Sensitive Fluorescent Sensor for Recognition of HIV-1 dsDNA by Using Glucose Oxidase and Triplex DNA

A sensitive fluorescent sensor for sequence-specific recognition of double-stranded DNA (dsDNA) was developed on the surface of silver-coated glass slide (SCGS). Oligonucleotide-1 (Oligo-1) was designed to assemble on the surface of SCGS and act as capture DNA, and oligonucleotide-2 (Oligo-2) was designed as signal DNA. Upon addition of target HIV-1 dsDNA (Oligo-3•Oligo-4), signal DNA could bind on the surface of silver-coated glass because of the formation of C•GoC in parallel triplex DNA structure. Biotin-labeled glucose oxidase (biotin-GOx) could bind to signal DNA through the specific interaction of biotin-streptavidin, thereby GOx was attached to the surface of SCGS, which was dependent on the concentration of target HIV-1 dsDNA. GOx could catalyze the oxidation of glucose and yield H₂O₂, and the HPPA can be oxidized into a fluorescent product in the presence of HRP. Therefore, the concentration of target HIV-1 dsDNA could be estimated with fluorescence intensity. Under the optimum conditions, the fluorescence intensity was proportional to the concentration of target HIV-1 dsDNA over the range of 10 pM to 1000 pM, the detection limit was 3 pM. Moreover, the sensor had good sequence selectivity and practicability and might be applied for the diagnosis of HIV disease in the future.

Facile Determination of Sodium Ion and Osmolarity in Artificial Tears by Sequential DNAzymes

Despite high relevance of tear osmolarity and eye abnormality, numerous methods for detecting tear osmolarity rely upon expensive osmometers. We report a reliable method for simply determining sodium ion-based osmolarity in artificial tears using sequential DNAzymes. When sodium ion-specific DNAzyme and peroxidase-like DNAzyme were used as a sensing and detecting probe, respectively, the concentration of Na⁺ in artificial tears could be measured by absorbance or fluorescence intensity, which was highly correlated with osmolarity over the diagnostic range (R² > 0.98). Our approach is useful for studying eye diseases in relation to osmolarity.

Rapid and sensitive detection of potassium ion based on K(+)-induced G-quadruplex and guanine chemiluminescence

A simple and rapid method for detection of potassium ion (K(+)) based on a guanine chemiluminescence (CL) system is presented. In this system, one guanine-rich DNA molecule is used as the recognition element. K(+) can cause the guanine-rich DNA to form a G-quadruplex conformation, resulting in remarkable quenching of the guanine CL intensity of guanine-rich DNA. The CL intensity of this CL system decreased with increasing K(+) concentration, revealing a linear relationship in K(+) concentration range from 3 × 10(-5) to 1 × 10(-3) M. A complete detection process can be accomplished in about 5 min. Other common cations (such as Na(+), NH4 (+), Mg(2+), Ca(2+), Zn(2+), and Pb(2+)) did not notably interfere with K(+) detection. The mechanism of this strategy is also discussed. The sensing strategy is low cost and simple without the requirement of complex labeling of probe DNA. The scheme is applicable to the detection of other guanine-rich aptamer-binding chemicals or biomolecules.

Label-free fluorescent aptasensor for potassium ion using structure-switching aptamers and berberine

A simple, rapid and label-free fluorescent aptasensor was fabricated for the detection of potassium ion (K(+) ion) in aqueous solution using K(+) ion-stabilized single stranded DNA (ssDNA) with G-rich sequence as the recognition element and a fluorescent dye, berberine, as the fluorescence probe. In the presence of K(+) ion, the G-rich ssDNA is promoted to form the aptamer-target complex with a G-quadruplex conformation, and berberine binding to the G-quadruplex structure results in the enhancement of its fluorescence. The fluorescence intensity of the sensing system displayed a calibration response for K(+) ion in the range of 0-1600μM with a detection limit of 31nM (S/N=3) and a relative standard deviation (RSD) of 0.45%. This label-free fluorescence aptasensor is conveniently and effectively applicable for analysis of K(+) ion in blood serum samples with the recovery range of 81.7-105.3%. The assay for detection of potassium ion is easy, economical, robust, and stable in rough conditions.

Metal ion induced fluorescence resonance energy transfer between crown ether functionalized quantum dots and rhodamine B: selectivity of K+ ion

A ratiometric fluorescent metal ion sensor based on the mechanism of fluorescence resonance energy transfer between 15-crown-5-ether capped CdSe/ZnS quantum dots and 15-crown-5-ether attached rhodamine B.

A label-free fluorescence assay for potassium ions using riboflavin as a G-quadruplex ligand

A label-free fluorescence K⁺assay was developed using riboflavin, a new G-quadruplex ligand, and a G-quadruplex sequence (PW17).

Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems

This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.

G-quadruplex DNA biosensor for sensitive visible detection of genetically modified food

In this paper, a novel label-free G-quadruplex DNAzyme sensor has been proposed for colorimetric identification of GMO using CaMV 35S promoter sequence as the target. The binary probes can fold into G-quadruplex structure in the presence of DNA-T (Target DNA) and then combine with hemin to form a DNAzyme resembling horseradish peroxidase. The detection system consists of two G-rich probes with 2:2 split mode by using the absorbance and color of ABTS(2-) as signal reporter. Upon the addition of a target sequence, two probes both hybridize with target and then their G-rich sequences combine to form a G-quadruplex DNAzyme, and the DNAzyme can catalyze the reaction of ABTS(2-) with H2O2. Then the linear range is from 0.05 to 0.5 μM while detection limit is 5nM. These results demonstrate that the proposed G-quadruplex DNAzyme method could be used as a simple, sensitive and cost-effective approach for assays of GMO.

A fluorescent aptasensor for potassium ion detection-based triple-helix molecular switch

Here, a biosensor based on a quadruplex-forming aptamer for the determination of potassium ion (K(+)) is presented. The aptamer was used as a molecular recognition element; it was adjacent to two arm fragments and a dual-labeled oligonucleotide serving as a signal transduction probe (STP) that is complementary of the arm fragment sequence. In the presence of K(+), the aptamer was displaced from the STP, which was accompanied by decreased signal. The quenching percentage of fluorescence intensity was proportional to the concentration of K(+) in the range of 0.05 to 1.4mM. A detection limit of 0.014 mM was achieved. Furthermore, other metal ions, such as Na(+), Li(+), NH4(+), Mg(2+), and Ca(2+), caused no notable interference on the detection of K(+).

DNA as sensors and imaging agents for metal ions

Increasing interest in detecting metal ions in many chemical and biomedical fields has created demands for developing sensors and imaging agents for metal ions with high sensitivity and selectivity. This review covers recent progress in DNA-based sensors and imaging agents for metal ions. Through both combinatorial selection and rational design, a number of metal-ion-dependent DNAzymes and metal-ion-binding DNA structures that can selectively recognize specific metal ions have been obtained. By attachment of these DNA molecules with signal reporters such as fluorophores, chromophores, electrochemical tags, and Raman tags, a number of DNA-based sensors for both diamagnetic and paramagnetic metal ions have been developed for fluorescent, colorimetric, electrochemical, and surface Raman detection. These sensors are highly sensitive (with a detection limit down to 11 ppt) and selective (with selectivity up to millions-fold) toward specific metal ions. In addition, through further development to simplify the operation, such as the use of "dipstick tests", portable fluorometers, computer-readable disks, and widely available glucose meters, these sensors have been applied for on-site and real-time environmental monitoring and point-of-care medical diagnostics. The use of these sensors for in situ cellular imaging has also been reported. The generality of the combinatorial selection to obtain DNAzymes for almost any metal ion in any oxidation state and the ease of modification of the DNA with different signal reporters make DNA an emerging and promising class of molecules for metal-ion sensing and imaging in many fields of applications.

Colorimetric detection of potassium ions using aptamer-functionalized gold nanoparticles

Herein, a simple and novel colorimetric method for detection of potassium ions (K(+)) was developed. The colorimetric experiments revealed that upon the addition of K(+), the conformation of anti-K(+) aptamer in solution changed from random coil structure to compact rigid G-quadruplex one. This compact rigid G-quadruplex structure could not protect AuNPs against K(+)-induced aggregation, and thus the visible color change from wine-red to blue-purple could be observed by the naked eye. The linear range of the colorimetric aptasensor covered a large variation of K(+) concentration from 5 nM to 1 μM and the detection limit of 5 nM was obtained. Moreover, this assay was able to detect K(+) with high selectivity and had great potential applications.

Aptamer biosensor for label-free impedance spectroscopy detection of potassium ion based on DNA G-quadruplex conformation

Herein, a label-free and highly sensitive electrochemical impedance spectroscopy (EIS) aptasensor for the detection of potassium ion (K⁺) was developed based on a conformational change in which a K⁺-stabilized single stranded DNA (ssDNA) with G-rich sequence was used as the recognition element. In the measurement of K⁺ ions, the change in interfacial electron transfer resistance (R(ct)) of the sensor using a redox couple of [Fe(CN)₆]³⁻/⁴⁻ as the probe was monitored. In the presence of K⁺, the G-rich DNA folded into the G-quadruplex structure, and then K⁺ can bind to the G-quadruplex structure, leading to an increase in the R(ct). The Rct increased with K⁺ concentration, and the plot of R(ct) against the logarithm of K⁺ concentration is linear over the range from 0.1 nM to 1 mM with a detection limit of 0.1 nM. Other metal ions, such as Ca²⁺, Mg²⁺, Na⁺, Li⁺, Al³⁺, Zn²⁺, Cu²⁺, and Ni²⁺ caused no notable interference on the detection of K⁺. The scheme reported herein is applicable to the detection of other kinds of G-rich aptamer-binding chemicals and biomolecules.

Input-dependent induction of G-quadruplex formation for detection of lead (II) by fluorescent ion logic gate

A label-free fluorescent AND logic gate has been developed utilizing ion-tuned configuration conversion of DNA probe with K(+) and Pb(2+) as two inputs. A well-designed hairpin DNA which is composed of a poly-G loop and a GR-5 DNAzyme stem serves as a recognition probe, and an derivative of aloe-emodin (AED) was designed and synthesized as signal probe. In the presence of Pb(2+), the substrate strand of DNAzyme is irreversibly and specifically cleaved at the cleavage site, which made the poly-G loop form G-quadruplex in the presence of a constant concentration of K(+). Such a structural change significantly affects the spectral behaviors of AED, which can be explored to ultra-sensitively detect Pb(2+) with a limit of detection of 22.8pM. By combing the high specificity of hairpin DNA and GR-5 DNAzyme, Pb(2+) can be highly selectively detected even when coexisted with other metal ions. Circular dichroism (CD), UV-vis absorption spectrometry and fluorescence polarization (FP) measurements further verified the reliability and reasonability of the sensing mechanism. Therefore, it provides a simple and label-free approach to detect ions with high sensitivity and specificity, and promises to provide a solid sensing platform for the detection of targets by altering the specific sequence of nucleic acid probe.

Specific binding of anionic porphyrin and phthalocyanine to the G-quadruplex with a variety of in vitro and in vivo applications

The G-quadruplex, a four-stranded DNA structure with stacked guanine tetrads (G-quartets), has recently been attracting attention because of its critical roles in vitro and in vivo. In particular, the G-quadruplex functions as ligands for metal ions and aptamers for various molecules. Interestingly, the G-quadruplex can show peroxidase-like activity with an anionic porphyrin, iron (III) protoporphyrin IX (hemin). Importantly, hemin binds to G-quadruplexes with high selectivity over single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), which is attributable to an electrostatic repulsion of phosphate groups in ssDNA and dsDNA. The G-quadruplex and hemin-G-quadruplex complex allow development of sensing techniques to detect DNA, metal ions and proteins. In addition to hemin, anionic phthalocyanines also bind to the G-quadruplex formed by human telomere DNA, specifically over ssDNA and dsDNA. Since the binding of anionic phthalocyanines to the G-quadruplex causes an inhibition of telomerase activity, which plays a role in the immortal growth of cancer cells, anionic phthalocyanines are promising as novel anticancer drug candidates. This review focuses on the specific binding of hemin and anionic phthalocyanines to G-quadruplexes and the applications in vitro and in vivo of this binding property.