G-quadruplex DNAzyme-based Hg2+ and cysteine sensors utilizing Hg2+-mediated oligonucleotide switching

Reusable fluorescence nanoprobe based on DNA-functionalized metal-organic framework for ratiometric detection of mercury (II) ions

A reusable fluorescent nanoprobe was developed using DNA-functionalized metal-organic framework (MOF) for ratiometric detection of Hg2+. We utilized a zirconium-based MOF (UiO-66) to encapsulate tris(bipyridine) ruthenium(II) chloride (Ru(bpy)32+), resulting in Ru(bpy)32+@UiO-66 (RU) with red fluorescence. The unsaturated metal sites in UiO-66 facilitate the attachment of thymine-rich single-strand DNA (T-ssDNA) through Zr-O-P bond, producing T-ssDNA-functionalized RU complex (RUT). The T-ssDNA selectively binds to Hg2+, forming stable T-Hg2+-T base pairs and folding into double-stranded DNA, which permits the intercalation of SYBR Green I (SGI) and activates its green fluorescence. In the presence of Hg2+, SGI fluorescence increases in a dose-dependent manner, while Ru(bpy)32+ fluorescence remains constant. This fluorescence contrast enables RUT to serve as an effective ratiometric nanoprobe for Hg2+ detection, with a detection limit of 3.37 nM. Additionally, RUT demonstrates exceptional reusability due to the ability of cysteine to remove Hg2+, given its stronger affinity for thiol groups. The RUT was successfully applied to detect Hg2+ in real water samples. This work advances the development of ratiometric fluorescence nanoprobe based on DNA-functionalized MOFs.

A Fluorescence Biosensor Based on Carbon Quantum Dots Prepared from Pomegranate Peel and T-Hg2+-T Mismatch for Hg2+ Detection

Mercury ions (Hg2+) can cause damage to human health, and thus, the study of the detection of Hg2+ is extraordinarily important in daily life. This work reported a fluorescence biosensor for the detection of Hg2+. The key point of this strategy was that the fluorescence of carbon quantum dots made from pomegranate peel (P-CQDs) was quenched by hemin, and restored after G-quadruplex binding with hemin. The presence of Hg2+ caused thymine (T)-rich DNA fragments to form T-Hg2+-T mismatches, and this change allowed the release of G-quadruplex. G-quadruplex could change the fluorescence of hemin/P-CQDs. P-CQDs exhibited excellent properties through characterization analysis, such as transmission electron microscope, X-ray photoelectron spectroscopy and Fourier transform infrared. This proposed fluorescence detection strategy established the linear ranges of Hg2+ from 1 nM to 50 nM. In conclusion, this simple biosensor had the advantages of strong sensitivity, high selectivity, and low cost for Hg2+ detection in environmental water samples.

DNAzyme-based biosensors for mercury (Ⅱ) detection: Rational construction, advances and perspectives

Mercury contamination is one of the most severe issues in society due to its threats to public health and the ecological system. However, traditional methods for mercury ion detection are still limited by their time-consuming procedures, requirement of expensive instruments, and low selectivity. In recent decades, tremendous progress has been made in the development of functional nucleic acid-based, especially DNAzyme sensors for mercury (Ⅱ) (Hg²⁺) determination, including RNA-cleaving DNAzymes and G-quadruplex-based DNAzymes in particular. Researchers have heavily studied the construction of Hg²⁺ sensors, mainly originating from in vitro selection-derived DNAzymes, by incorporating T-Hg²⁺-T recognition moieties in existing DNAzyme scaffolds, and interfacing Hg²⁺-sensitive sequences with nanomaterials. In the last case, the employment of materials (as quenchers, signal transducers and DNA immobilizers) enriches the application scenarios of current Hg²⁺-DNAzymes, due to a combination of their functions. We summarize a broad range of sensing approaches, including optical, electrochemical, and other sensing methods, and compare their features. This review elaborates on the rational design strategies for engineering DNAzymes to selectively sense Hg²⁺, critically discusses their properties in different application scenarios, and summarizes recent advances in this field. Additionally, current progress, challenges and future perspectives are also discussed. This minireview provides deeper insights into the chemistry of these functional nucleic acids when working with Hg²⁺, explains the design ideas of DNAzyme-sensors in each platform, and reveals potential opportunities in developing more advanced DNAzyme sensors for the highly selective and sensitive recognition of Hg²⁺. ENVIRONMENTAL IMPLICATION: Mercury is one of the most toxic metallic contaminants due to its high toxicity, non-biodegradability, and serious human health risks when accumulated in the body. In the recent decade, intensive studies have focused on exploring mercury sensors by combining DNAzymes with various sensing methods, paving a promising avenue to gain ultra-high sensitivity and selectivity. However, so far, no review has introduced the recent advances on DNAzyme-based sensors for mercury detection in a critical way. In this review, we comprehensively summarized the studies on DNAzyme-based sensors for mercury detection using various sensing techniques including optical, electrochemical and other sensing methods.

Enzyme-induced multicolor colorimetric and electrochemiluminescence sensor with a smartphone for visual and selective detection of Hg2

In this study, we developed a novel dual-analytical platform for the visual, sensitive, and reliable analysis of mercury ions (Hg²⁺) in environmental water samples. Importantly, thymine (T)-rich DNA probes were utilized to form T-Hg²⁺-T base pairs in the presence of Hg²⁺ to ensure the specificity of the method. We synthesized new luminescent tris(4,4'-dicarboxylicacid-2,2'-bipyridyl) ruthenium (II) dichloride (Ru(dcbpy)₃²⁺)-modified metal-polydopamine frameworks (MPFs@Ru), which were then applied to construct an electrochemiluminescence (ECL) system for the first time, and it achieved accurate and sensitive quantitative detection of Hg²⁺. To achieve rapid on-site determination, a multicolorimetric system based on a smartphone was established by inducing deposition of silver shells on gold nanorods (Au NRs). Under optimized conditions, the dual-modal assay showed an excellent response for Hg²⁺ in the linear range of 2 pmol L^-1 to 500 nmol L^-1, with a low detection limit of 0.32 pmol L^-1. Moreover, the proposed method demonstrated satisfactory selectivity, stability, and acceptable reproducibility for the detection of Hg²⁺. The recovery of lake water samples ranged from 98.53% to 111.97% for the ECL method and from 95.04% to 106.11% for the colorimetric method, indicating the potential applicability of the proposed method for monitoring environmental water samples.

A visual Hg2+ detection strategy based on distance as readout by G-quadruplex DNAzyme on microfluidic paper

In this work, we have developed a simple, fast and visual Hg²⁺ detection strategy based on distance as readout on paper chip by the Hg²⁺-mediated formation of G-quadruplex-hemin DNAzymes. In the presence of Hg²⁺, the two oligonucleotides hybridize to form G-quadruplex DNA by T-Hg²⁺-T base pair, which was able to bind hemin to form the catalytically active G-quadruplex-hemin DNAzymes. Once DNAzymes were added to react with the precipitated 3,3,5,5-tetramethyl benzidine (TMB) immobilized on the sample area, a visible color band was produced, and the formed length was positively correlated with the concentration of Hg²⁺. This biosensor is capable of selectively detecting mercuric ions with good reproducibility and satisfactory dynamic range. The limit of detection was low to 0.23 nM. Therefore, this strategy not only provides a visual and quick screen of Hg²⁺, but also shows a promising future in monitoring analysis of other metal ions in POC diagnostic field.

Macrocyclic "tet a" derived colorimetric sensor for the detection of mercury cations and hydrogen sulphate anions and its bio-imaging in living cells

A mono-N-substituted probe L containing a bromosalicylaldehyde pendant arm attached to a tetraazamacrocyclic "tet a" moiety was synthesized via straight forward reaction. The probe L crystallizes in a monoclinic P2₁/n space group. The probe L displayed quick sensitivity and selectivity towards Hg²⁺ ions due to its hopeful Chelation Enhancement Quenching (CHEQ) feature. Interestingly, the probe L exhibits turn-off fluorescence response to Hg²⁺ ion and turn-on fluorescence signals to HSO₄^- ions. When the probe L was complexed with HSO₄^- in 1:1 mode (L + HSO₄^- formation), improved turn-on fluorescence emission was detected due to the chelation enhanced fluorescence effect through sensor complex. The macrocyclic "tet a" probe L exhibited a binding constant value of 3.89 × 10⁶ M^-1 and 5.58 × 10⁵ M^-1 for Hg²⁺ and HSO₄^-, respectively. Probe L exhibited good selectivity to Hg²⁺ rather than other common metal ions and HSO₄^- over other common anions. The limit of detection (LOD) of Hg²⁺ and HSO₄^- were found to be 1 nM and 7 μM, respectively. The time-resolved fluorescence emission single-photon counting study was used to determine the average lifetime value for the probe L and L + HSO₄^- ions as 0.47 and 1.02 ns, respectively. The practical application of the probe in visualizing intracellular Hg²⁺ and HSO₄^- ions distribution in live Artemia salina was demonstrated. Furthermore, the probe L with Hg²⁺cations was found to be cytotoxic against breast cancer cells in nature and can be delivered as an anticancer agent. Besides the probe L with HSO₄^- exhibit strong fluorescence emission with low cytotoxicity, and it can be recommended for live-cell imaging.

Dinuclear HgII tetracarbene complex-triggered aggregation-induced emission for rapid and selective sensing of Hg2+ and organomercury species

Mercury-mediated chelate ring formation and subsequent aggregation gives strong fluorescence for rapid and selective sensing of Hg²⁺ and organomercury.

Rapid, reliable and highly selective detection of mercury species, including Hg²⁺ ions and organomercury, is of significant importance for environmental protection and human health. Herein, a new fluorescent dye 1,1,2,2-tetrakis[4-(3-methyl-1H-benzimidazol-1-yl)phenyl ethylene tetraiodide (Tmbipe) with aggregation-induced emission (AIE) potential was prepared and characterized. The presence of four positively charged methylated benzimidazole groups endows Tmbipe with excellent water solubility and almost undetectable background fluorescence. However, it can coordinate with two Hg²⁺ ions or two organomercury molecules (e.g. methylmercury and phenylmercury) to form a planar dinuclear Hg^II tetracarbene complex, which can then self-aggregate to turn on AIE fluorescence. Such a fluorescence turn-on process can be completed in 3 min. In addition, synergic rigidification of the tetraphenylethylene-bridged Tmbipe molecule by mercury-mediated chelate ring formation and subsequent aggregation results in obviously higher fluorescence enhancement than that given by the single aggregation-induced one. Low background, high fluorescence enhancement and rapid response time make Tmbipe a good fluorescent probe for reliable, sensitive and highly selective quantitation of both inorganic and organic mercury species. This probe was also demonstrated to work well for identification of mercury species accumulation in living cells.

Silver-ion-mediated Mg2+-dependent DNAzyme activity for amplified fluorescence detection of cysteine

Schematic illustration of a DNAzyme-based fluorescent biosensor for amplified Cys detection.

A novel label-free colorimetric detection of l-histidine using Cu2+-modulated G-quadruplex-based DNAzymes

We proposed a colorimetric method for l-histidine detection based on Cu²⁺-mediated DNAzyme and G-quadruplex-hemin complex catalyzed oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS). In this system, after the addition of l-histidine, the formation of G-quadruplex-hemin complex will be disturbed, thus the colorimetric signal intensity conversely corresponds to the concentration of histidine. In this assay, a lower detection limit of l-histidine (50 nM) is addressed comparing to previously reported colorimetric methods. The cost is extremely low as the proposed design is both label-free and enzyme-free. All the more vitally, the colorimetric detection procedure is substantially straightforward with no further modification processes. By and large, the sensor can provide a promising plan for the detection of l-histidine.

A dual-channel homogeneous aptasensor combining colorimetric with electrochemical strategy for thrombin

In this protocol, a dual-channel homogeneous aptasenor was proposed for protein molecule determination, employing thrombin as target analyte. The colorimetric and electrochemical transducers were combined in a single analytical system for signal readout. In this dual-channel sensing strategy, the G-quadruplex sequence was released and incorporated with hemin to form DNAzyme for naked-eye colorimetric detection. Meanwhile, the hydroxyapatite nanoparticle as signal probe was combined with magnetic nanoparticles to construct sandwich-type structure for generating the electrochemical current when thrombin was present in solution. By introducing two kinds of reporter probes and transducers, this dual-channel sensor produced two different kinds of signal to improve the analytical accuracy and diversity. The results revealed that the dual-channel sensor achieved the quantatitive determination of thrombin with low limit of detection (0.40 fM) and wide range (0.1 fM to 1 nM), which offer a promise for rapid and accurate detection of biomolecule.

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 naked-eye colorimetric sensor for Hg2+ monitoring with cascade signal amplification based on target-induced conjunction of split DNAzyme fragments

We developed a naked-eye colorimetric sensor for Hg²⁺ monitoring with cascade signal amplification based on DNAzyme fragments and gold nanoparticles.

A dual-channel detection of mercuric ions using a label free G-quadruplex-based DNAzyme molecule

We have constructed a ‘turn-off’ and label free bio-sensor using a DNAzyme molecule.

Dual-channel detection of metallothioneins and mercury based on a mercury-mediated aptamer beacon using thymidine-mercury-thymidine complex as a quencher

A novel dual-channel strategy for the detection of metallothioneins (MTs) and Hg(2+) has been developed based on a mercury-mediated aptamer beacon (MAB) using thymidine-mercury-thymidine complex as a quencher for the first time. In the presence of Hg(2+), the T-rich oligonucleotide with a 6-carboxyfluorescein (TRO-FAM) can form an aptamer beacon via the formation of T-Hg(2+)-T base pairs, which results in a fluorescence quenching of the sensing system owing to the fluorescence resonance energy transfer (FRET) from the fluorophore of FAM to the terminated T-Hg(2+)-T base pair. The addition of MTs into this solution leads to the disruption of the T-Hg(2+)-T complex, resulting in an increase of the fluorescent signal of the system. In the optimizing condition, ΔF was directly proportional to the concentrations ranging from 5.63 nM to 0.275 μM for MTs, and 14.2 nM to 0.30 μM for Hg(2+) with the detection limits of 1.69 nM and 4.28 nM, respectively. The proposed dual-channel method avoids the label steps of a quencher in common molecular beacon strategies, without tedious procedure or the requirement of sophisticated equipment, and is rapid, inexpensive and sensitive.

Label-free luminescence switch-on detection of hepatitis C virus NS3 helicase activity using a G-quadruplex-selective probe

A series of luminescent Ir(iii) complexes were synthesised and evaluated for their ability to act as luminescent G-quadruplex-selective probes. The Ir(iii) complex 9, [Ir(phq)2(phen)]PF6 (where phq = 2-phenylquinoline; phen = 1,10-phenanthroline), exhibited high luminescence in the presence of G-quadruplex DNA compared to dsDNA and ssDNA, and was employed to construct a label-free G-quadruplex-based assay for hepatitis C virus NS3 helicase activity in aqueous solution. Moreover, the application of the assay for screening potential helicase inhibitors was demonstrated. To our knowledge, this is the first G-quadruplex-based assay for helicase activity.

"Turn on" and label-free core-shell Ag@SiO2 nanoparticles-based metal-enhanced fluorescent (MEF) aptasensor for Hg(2+)

A turn on and label-free fluorescent apasensor for Hg(2+) with high sensitivity and selectivity has been demonstrated in this report. Firstly, core-shell Ag@SiO2 nanoparticles (NPs) were synthetized as a Metal-Enhanced Fluorescent (MEF) substrate, T-rich DNA aptamers were immobilized on the surface of Ag@SiO2 NPs and thiazole orange (TO) was selected as fluorescent reporter. After Hg(2+) was added to the aptamer-Ag@SiO2 NPs and TO mixture buffer solution, the aptamer strand can bind Hg(2+) to form T-Hg(2+)-T complex with a hairpin structure which TO can insert into. When clamped by the nucleic acid bases, the fluorescence quanta yield of TO will be increased under laser excitation and emitted a fluorescence emission. Furthermore, the fluorescence emission can be amplified largely by the MEF effect of the Ag@SiO2 NPs. The whole experiment can be finished within 30 min and the limit of detection is 0.33 nM even with interference by high concentrations of other metal ions. Finally, the sensor was applied for detecting Hg(2+) in different real water samples with satisfying recoveries over 94%.

An electrochemical sensing strategy based on a three dimensional ordered macroporous polyaniline–platinum platform and a mercury(ii) ion-mediated DNAzyme functionalized nanolabel

An Hg²⁺-switched DNA biosensor using a three dimensional ordered macroporous polyaniline–platinum platform and a G-rich sequence recognition probe was developed, with the detection limit of 8.7 × 10⁻¹⁴ M.

Fluorescent and colorimetric sensors for environmental mercury detection

The development of fluorescent and colorimetric sensing strategies for environmental mercury is described.

A label-free hemin/G-quadruplex DNAzyme biosensor developed on electrochemically modified electrodes for detection of a HBV DNA segment

A label-free biosensor based on Au/G–CMWCNTs-GCE was proposed for the detection of a HBV DNA segment with a low LOD.

Studies on the thymine–mercury–thymine base pairing in parallel and anti-parallel DNA duplexes

Parallel and anti-parallel T–Hg–T base pairs have different thermal stabilities and conformational influences on DNA duplex structures.

Visual detection of mercury(ii) based on recognition of the G-quadruplex conformational transition by a cyanine dye supramolecule

Visual detection of mercury(ii) based on recognition of the G-quadruplex conformational transition by a cyanine dye supramolecule is reported.

A colorimetric aptasensor for the highly sensitive detection of 8-hydroxy-2'-deoxyguanosine based on G-quadruplex-hemin DNAzyme

A highly sensitive, low-cost colorimetric aptasensor was developed for the determination of 8-hydroxy-2'-deoxyguanosine (8-OHdG) in human urine. The method is based on a conformational switching of the 8-OHdG aptamer to form a G-quadruplex structure in the presence of 8-OHdG. The resulting G-quadruplex assembles into a peroxidase-like DNAzyme with hemin, which effectively catalyzes the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS(2-)) by H2O2 to ABTS(+), resulting in an increase in the absorption signal at 416nm along with a color change of the solution. The response signals linearly correlated with the concentration of 8-OHdG, ranging from 466pM to 247nM with a detection limit of 141pM. The relative standard deviation and the recovery were 1.97-3.47% (n=11) and 98.8-100.2%, respectively. The proposed method avoids the label and derivatization steps in common methods and allows direct analysis of the samples by the naked eye without costly instruments, which is reliable, inexpensive, and sensitive.

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.

A highly sensitive label-free sensor for Mercury ion (Hg²⁺) by inhibiting thioflavin T as DNA G-quadruplexes fluorescent inducer

DNA sequences with guanine repeats can be induced to form G-quartets that adopt G-quadruplex structures in the presence of thioflavin T (ThT). ThT plays a dual role of inducing DNA sequences to fold into quadruplex structures and of sensing the change by its remarkable fluorescence enhancement. ThT binding to the DNA sequences with guanine repeats showed highly specific fluorescence enhancement compared with single/double-stranded DNA. In this work, we have utilized the conformational switch from G-quadruplex complex induced by fluorogenic dye ThT to Hg(2+) mediated T-Hg-T double-stranded DNA formation, thereby pioneering a facile approach to detect Hg(2+) with fluorescence spectrometry. Through this approach, Hg(2+) in aqueous solutions can be detected at 5 nM with fluorescence spectrometry in a facile way, with high selectivity against other metal ions. These results indicate the introduced label-free method for fluorescence spectrometric Hg(2+) detection is simple, quantitative, sensitive, and highly selective.