Simultaneous fluorescent detection of multiple metal ions based on the DNAzymes and graphene oxide

Target-promoted autocatalytic hairpin assembly of bivalent DNAzymes for sensitive and label-free electrochemical metallothionein assay

Metallothionein (MT) has shown to be an important biomarker for environmental monitoring and various diseases, due to its significant binding ability to heavy metal ions. On the basis of such a characteristic and the Hg2+-stabilized DNA duplex (Hg2+-dsDNA) probe, as well as a new autocatalytic hairpin assembly (aCHA)/DNAzyme cascaded signal enhancement strategy, the construction of a highly sensitive and label-free electrochemical MT biosensor is described. Target MT molecules bind Hg2+ in Hg2+-dsDNA to disrupt the duplex structure and to release ssDNA sequences, which trigger subsequent aCHA for efficient production of mimic aCHA triggering strands and many bivalent DNAzymes. The signal hairpins on the electrode are then cyclically cleaved by DNAzyme amplification cascade to liberate plenty G-quadruplex sequences, which bind hemin and yield largely enhanced currents for sensitive assay of MT with a detection limit of 0.217 nM in a label-free approach. Such sensor also shows selective discrimination capability to MT against other interfering proteins and assay of MT in normal serums with dilution has also been verified, indicating its potential for highly sensitive detection of different heavy metal ion binding molecules for various application scenarios.

Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials

Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.

Smart Nucleic Acid Hydrogels with High Stimuli-Responsiveness in Biomedical Fields

Due to their hydrophilic, biocompatible and adjustability properties, hydrogels have received a lot of attention. The introduction of nucleic acids has made hydrogels highly stimuli-responsiveness and they have become a new generation of intelligent biomaterials. In this review, the development and utilization of smart nucleic acid hydrogels (NAHs) with a high stimulation responsiveness were elaborated systematically. We discussed NAHs with a high stimuli-responsiveness, including pure NAHs and hybrid NAHs. In particular, four stimulation factors of NAHs were described in details, including pH, ions, small molecular substances, and temperature. The research progress of nucleic acid hydrogels in biomedical applications in recent years is comprehensively discussed. Finally, the opportunities and challenges facing the future development of nucleic acid hydrogels are also discussed.

DNAzyme-Functionalized Nanomaterials: Recent Preparation, Current Applications, and Future Challenges

DNAzyme-nanomaterial bioconjugates are a popular hybrid and have received major attention for diverse biomedical applications, such as bioimaging, biosensor development, cancer therapy, and drug delivery. Therefore, significant efforts are made to develop different strategies for the preparation of inorganic and organic nanoparticles (NPs) with specific morphologies and properties. DNAzymes functionalized with metal-organic frameworks (MOFs), gold nanoparticles (AuNPs), graphene oxide (GO), and molybdenum disulfide (MoS₂ ) are introduced and summarized in detail in this review. Moreover, the focus is on representative examples of applications of DNAzyme-nanomaterials over recent years, especially in bioimaging, biosensing, phototherapy, and stimulation response delivery in living systems, with their several advantages and drawbacks. Finally, the perspective regarding the future directions of research addressing these challenges is also discussed and highlighted.

Simultaneous detection of mercury (II), lead (II) and silver (I) based on fluorescently labelled aptamer probes and graphene oxide

We have developed a fluorescence quantitative analysis method for the simultaneous detection of Hg²⁺, Pb²⁺ and Ag⁺ based on fluorescently labelled nucleic acid aptamer probes and graphene oxide (GO). By this method, three nucleic acid aptamer probes (P_Hg, P_Pb, P_Ag) were designed. The carboxyl fluorescein (FAM), tetramethyl-6-carboxyrhodamine (TAMRA) and cyanine-5 (Cy-5) were respectively selected as fluorophore of aptamer probes, and GO was chosen as quencher. In general, these probes were on free single-stranded state and adsorbed on the surface of GO via π-π interactions, which brought fluorophores of probes and GO into close proximity. Due to the fluorescence resonance energy transfer occurred between fluorophores and GO, the fluorescence was quenched and fluorescence signals were all weak. Under the optimal condition, fluorescence intensities of three fluorophores exhibited a good linear dependence on corresponding ions concentration. The detection limit for Hg²⁺, Pb²⁺ and Ag⁺ were 0.2, 0.5 and 2 nmol/L (3σ, n = 11). Average recoveries of this method were 97.56-104.92%, which indicated the method had a high accuracy and low detection limit. In addition, this proposed method has good selectivity, and there was no crosstalk effect among these probes.

Smart and Functionalized Development of Nucleic Acid-Based Hydrogels: Assembly Strategies, Recent Advances, and Challenges

Nucleic acid-based hydrogels that integrate intrinsic biological properties of nucleic acids and mechanical behavior of their advanced assemblies are appealing bioanalysis and biomedical studies for the development of new-generation smart biomaterials. It is inseparable from development and incorporation of novel structural and functional units. This review highlights different functional units of nucleic acids, polymers, and novel nanomaterials in the order of structures, properties, and functions, and their assembly strategies for the fabrication of nucleic acid-based hydrogels. Also, recent advances in the design of multifunctional and stimuli-responsive nucleic acid-based hydrogels in bioanalysis and biomedical science are discussed, focusing on the applications of customized hydrogels for emerging directions, including 3D cell cultivation and 3D bioprinting. Finally, the key challenge and future perspectives are outlined.

Simultaneous and ultra-sensitive detection of Cu2+ and Mg2+ in wine and beer based on dual DNA tweezers and entropy-driven three-dimensional DNA nanomachine

Simultaneous and ultra-sensitive detection strategy of Cu²⁺ and Mg²⁺ in wine and beer was developed based on dual DNA tweezers and entropy-driven three-dimensional DNA nanomachine. The dual DNAzyme can simultaneously respond to two kinds of metal ions and cause two kinds of "turn-on" fluorescent signals. The working principle of this strategy was indirectly proven. In addition, some key experimental parameters were also optimized. Under the optimum conditions, the limit of detection was 10 pM for Cu²⁺ and 2 nM for Mg²⁺ respectively which was significantly improved by entropy driven amplification. This strategy also showed good selectivity and specificity. It was successfully used to detect of Cu²⁺ and Mg²⁺ in wine and beer with 5.26% to 9.12% of relative standard deviation and 90.4% to 110.5% of recoveries.

Nanomaterial-based fluorescent sensors for the detection of lead ions

Lead (Pb) poisoning has been a scourge to the human to pose sighnificant health risks (e.g., organ disorders, carcinogenicity, and genotoxicity) as observed from many different parts of the world, especially in developing countries. The demand for accurate sensors for its detection, especially in environmental media (soil, water, food, etc.) has hence been growing steadily over the years. The potential utility of fluorescent nanosensors as an important analytical tool is recognized due to their astonishing characteristics (e.g., high sensitivity/selectivity, enhanced detection performance, low cost, portability, and rapid on-site detection ability). This review is organized to offer insight into the recent developments in fluorescent nanosensing technology for the detection of lead ions (Pb²⁺). To this end, different types of nanomaterials explored for such applications have been classified and evaluated with respect to performance, especially in terms of sensitivity. This review will help researchers gain a better knowledge on the status and importance of optical nanosensors so as to remediate the contamination of lead and associated problems. The technical challenges and prospects in the development of nanosensing systems for Pb²⁺ are also discussed.

Nanomaterial and Aptamer-Based Sensing: Target Binding versus Target Adsorption Illustrated by the Detection of Adenosine and ATP on Metal Oxides and Graphene Oxide

Target molecule-induced desorption of aptamer probes from nanomaterials has been a very popular sensing method, taking advantage of the fluorescence quenching or catalytic activity of nanomaterials for signal generation. While it is generally conceived that aptamers desorb due to binding to target molecules, in this work, we examined the effect of competitive target adsorption. From five metal oxide nanoparticles including CeO₂, ZnO, NiO, Fe₃O₄, and TiO₂, only ATP was able to induce desorption of its aptamer. Adenosine could not, even though it had an even higher affinity than ATP to the aptamer. The same conclusion was also observed with a random DNA that cannot bind ATP, indicating that the desorption of DNA was due to competitive adsorption of ATP instead of aptamer binding. On graphene oxide, however, adenosine produced slightly more aptamer desorption than ATP under most of the conditions, and this can be partially attributed to the weaker interaction of negatively charged ATP with negatively charged graphene oxide. For such surface-based biosensors, it is recommended that a nonaptamer control DNA be tested side-by-side to ensure the sensing mechanism to be related to aptamer binding instead of target adsorption.

Recent Developments in Fluorescent Materials for Heavy Metal Ions Analysis From the Perspective of Forensic Chemistry

Forensic chemistry deals with the analysis of various types of physical evidences related to crime, corresponding to the detection of target substances or elements in complex matrices. There is a vital need for highly selective, rapid, and sensitive biosensing technologies in heavy metal ions analysis especially those from living persons, autopsy, food, water, soil, and other identified substances at very preliminary stages. Fluorescent materials-based method for heavy metal ions detection is one of the most important analytical methods, resulting in the ability to measure analytes in complex matrices with unsurpassed selectivity and sensitivity. In this mini review, different fluorescent materials-based analytical methods aiming at several heavy metal ions detection are exclusively reviewed through a comprehensive literature survey. In addition, current challenges to achieve integrated evidence analysis process are briefly discussed to provide an outlook for heavy metal ions detection based on fluorescent analytical methods in the forensic chemistry field.

A low-cost paper-based aptasensor for simultaneous trace-level monitoring of mercury (II) and silver (I) ions

Mercury (Hg²⁺) and silver (Ag⁺) ions possess the harmful effects on public health and environment that makes it essential to develop the sensing techniques with great sensitivity for the ions. Metal ions commonly coexist in the different biological and environmental systems. Hence, it is an urgent demand to design a simple method for the simultaneous detection of metal ions, peculiarly in the case of coexisting Hg²⁺ and Ag⁺. This study introduces a low-cost paper-based aptasensor to monitor Hg²⁺ and Ag⁺, simultaneously. The strategy of the sensing array is according to the conformational changes of Hg²⁺- and Ag⁺-specific aptamers and their release from the GO surface after the injection of the target sample on the sensing platform. Through monitoring the fluorescence recovery changes against the concentrations of the ions, Hg²⁺ and Ag⁺ can be determined as low as 1.33 and 1.01 pM. The paper-based aptasensor can simultaneously detect the ions within about 10 min. The aptasensor is applied prosperously to monitor Hg²⁺ and Ag⁺ in human serum, water, and milk. The designed aptasensor with the main advantages of simplicity and feasibility holds the supreme potential to develop a cost-effective sensing method for environmental monitoring, food control, and human diagnostics.

A simple and programmed DNA tweezer probes for one-step and amplified detection of UO22

A simple DNA tweezer was proposed for one-step and amplified detection of UO₂²⁺ based on DNAzyme catalytic cleavage. The two arms of DNA tweezers are close in the original form. Thus, the fluorescent signal of fluorophore at the end of arm is dramatically quenched. However, the structure of DNA tweezers can be changed from "close" to "open" in the presence of UO₂²⁺, resulting the strong fluorescent signal. The linear range was obtained in the range of 0.1 nM to 60 nM and the limit of detection was 25 pM with the amplification of DNAzyme catalytic cleavage reaction. Importantly, the whole detection process is very simple and only one operation step is required. In addition, it shows great potential and promising prospects for uranyl detection in practical application.

Engineering DNAzyme cascade for signal transduction and amplification

Inspired by the natural enzyme cascade reaction, a multiple DNAzyme cascade platform is engineered to imitate the intracellular process of signal transduction and signal amplification. In this design, when particular stimuli appear, an activated upstream DNAzyme will cleave a well-designed intermediary S1, releasing a downstream DNAzyme that can cleave the reporter substrate S2 to output signals. Thus, the signal is passed from the upstream DNAzyme to the downstream DNAzyme through a well-designed intermediary, accomplishing signal transduction and signal amplification. According to the experimental results, the DNAzyme cascades are capable of improving sensitivity for bioassays compared with that for single DNAzyme-based biocatalysis, which holds promise for potential applications, such as biomolecular computing, logic circuits and precision medicine.

A Multicolor Fluorescence Nanoprobe Platform Using Two-Dimensional Metal Organic Framework Nanosheets and Double Stirring Bar Assisted Target Replacement for Multiple Bioanalytical Applications

Multicolor fluorescence probes can show fluorescence of different colors when detecting different targets, and the excellent feature can create a highly differentiated multicolor sensing platform. However, most of the previously reported multicolor luminescent materials usually suffer from high toxicity and photobleaching, complex preparation procedures, and poor water solubility, which may not be conducive to bioanalytical applications. Two-dimensional metal organic frameworks (2D MOFs), which have large specific surface areas with long-range fluorescence quenching coupled with biomolecular recognition events, have encouraged innovation in biomolecular probing. Here, we propose a 2D-MOF-based multicolor fluorescent aptamer nanoprobe using a double stirring bar assisted target replacement system for enzyme-free signal amplification. It utilizes the interaction between 2D MOFs and DNA molecules to detect multiple antibiotics quickly, sensitively, and selectively. Since 2D MOFs have excellent quenching efficiency for luminescence of fluorescent-dye-labeled single-strand DNA (ssDNA), the background fluorescence can be largely reduced and the signal-to-noise ratio can be improved. When the adsorbed ssDNA formed double helix double-stranded DNA with its complementary ssDNA, its fluorescence can be almost fully recovered. The assay was tested by detecting chloramphenicol (CAP), oxytocin (OTC), and kanamycin (KANA) in biological samples. The developed aptasensor was sufficiently sensitive to detect the antibiotic residues as low as 1.5 pM CAP, 2.4 pM OTC, and 1 pM KANA (S/N = 3). It has been preliminarily used for multicolor imaging of three different antibiotics in fish tissue slices with satisfactory results.

Wavelength distinguishable signal quenching and enhancing toward photoactive material 3,4,9,10-perylenetetracarboxylic dianhydride for simultaneous assay of dual metal ions

Photoelectrochemical (PEC) assay with low background, simple instrumentation and high sensitivity has deemed as one of the most potential strategies to simultaneous multi-component detection. How to distinguish photocurrent changes caused by various targets on a single sensing platform thus becomes the key issue to be resolved. Herein, we innovatively proposed a multiplex PEC biosensor based on wavelength distinguishable signal quenching and enhancing toward photoactive material 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) for simultaneous assay of dual metal ions. Briefly, S1 and S2 ssDNA containing sensitizer methylene blue and quencher ferrocene (termed as MB-S1 and Fc-S2), respectively, were first generated through target Pb²⁺ and Mg²⁺-induced DNAzyme-assisted target recycling, which thereafter were modified on PTCDA sensing platform specifically via host-guest recognition with β-cyclodextrin (β-CD). Interestingly, the sensitizer MB could enhance photocurrent of PTCDA under the excitation wavelength of 623 nm and 590 nm, respectively, while the quencher Fc just quencher the photocurrent of PTCDA under the excitation wavelength of 590 nm, thereby achieving wavelength distinguishable signal quenching and enhancing toward photoactive material PTCDA for simultaneous assay of dual metal ions. As a result, the conceived biosensor for Mg²⁺ and Pb²⁺ detection realized high sensitivity with detection limit of 0.3 pM and 0.3 nM, respectively. The proposed strategy not only for the first time achieved the discrimination of varied PEC signal caused by two targets with usage of sole photoelectric material, but also realized the simultaneous multiplex assay on a single sensing platform, providing a new way for constructing effective and sensitive PEC biosensor for multi-component detection.

A general scheme for fluorometric detection of multiple oligonucleotides by using RNA-cleaving DNAzymes: application to the determination of microRNA-141 and H5N1 virus DNA

A widely applicably method is described for fluorometric determination of targets such as microRNA and viral DNA. It is making use of a Mg(II)-dependent DNAzyme and a G-quadruplex. In the absence of analyte, an inactive DNAzyme is formed by the hybridization of split DNAzymes and substrate. On addition of target analyte, the end of each strand of the split DNAzymes bind the analyte. This leads to the generation of an active DNAzyme. In the presence of Mg(II), the activated DNAzyme is formed and can cleave the substrate strand. Hence, the caged G-quadruplex sequences will be released. These released G-quadruplexes combine with thioflavin T to generate a G-quadruplex/thioflavin T complex and thereby cause amplified fluorescence. The method shows a 70 pM detection limit for H5N1 and works over a wide linear range 1 nM to 400 nM. Conceivably, this detection scheme has a wide scope in that it may be applied to other assays for microRNAs and DNAs by variation of the type of DNAzyme. Graphical abstract Schematic presentation of target detection: the DNAzyme cannot cleave the substrate strand when target is absent. Once the target is added, the active DNAzyme can cleave the substrate strand in the presence of Mg²⁺, resulting in significant fluorescence enhancement when the release of the caged G-quadruplex sequences binding with 2-[4-(dimethylamino)phenyl]-3,6-dimethylbenzothiazolium chloride (ThT).

A simple paper-based aptasensor for ultrasensitive detection of lead (II) ion

In this study, a simple paper-based aptasensor has been developed for the ultrasensitive detection of lead (Pb²⁺) ion within about 10 min. The aptasensor has been successfully designed by taking advantages of the Förster Resonance Energy Transfer (FRET) process and the super fluorescence quenching property of graphene oxide (GO) sheet. The sensing mechanism of the aptasensor is based on the conformational switch of the Pb²⁺-specific aptamer from a random coil to a G-quadruplex structure. An injection of Pb²⁺ on the paper-based platform induces the release of the specific aptamer from the GO surface that recovers the fluorescence emission. Under the optimal experimental conditions, there is a good linear relationship between the fluorescence recovery and the Pb²⁺concentration in the ranges of 5-70 pM and 0.07-20 nM. Moreover, the aptasensing array exhibits a high sensitivity to Pb²⁺ with an ultra-low detection limit of 0.5 pM. The developed aptasensor has been successfully applied to determine Pb²⁺ in tap water, lake water, milk, and human blood serum. The paper-based aptasensor can be efficiently utilized to detect other metal ions and biological molecules by substituting target specific aptamer.

Synthesis of dual-emission fluorescent carbon quantum dots and their ratiometric fluorescence detection for arginine in 100% water solution

The dual-emission carbon dots (CDs) can detect arginine in 100% water via ratiometric fluorescent method. The CDs exhibits good photostability, selectivity, and anti-interference ability, fast response time, and wide pH detection range.

Multiplex microRNA imaging in living cells using DNA-capped-Au assembled hydrogels

Non-invasively imaging multiplex microRNAs (miRNAs) in living cells is pivotal to understanding their physiological functions and pathological development due to the key regulatory roles of miRNAs in gene expression. However, developing smart delivery systems with large gene loading capacity, biocompatibility and responsiveness remains a significant challenge. Herein, we successfully incorporated DNA-capped Au nanoparticles (NPs) and their complementary fluorescent DNA sequences into a porous 3D hydrogel network (AuDH), in which hairpin-locked DNAzyme strands and active metal ions were loaded (AuDH/M n+/H) for simultaneously imaging multiplex miRNAs in living cells. After transfection into cells, the specific miRNAs trigger the strand-displacement reaction and sequentially activate the DNAzyme-assisted target recycling, leading to a strong increase in the corresponding fluorescence intensity for imaging. This enables simultaneous assessment of the abundance of multiplex cancer-related miRNAs, even if at a very low expression level, in different cells through the different fluorescence intensities due to the dual signal amplification, and the change in abundance of miRNAs induced by siRNA or miRNA mimics in living cells can also be efficiently monitored. The versatile and responsive DNA hydrogel system holds great potential for miRNA biomedical applications.

Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application

Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.