G-triplex/hemin DNAzyme mediated colorimetric aptasensor for Escherichia coli O157:H7 detection based on exonuclease III-assisted amplification and aptamers-functionalized magnetic beads

Escherichia coli O157: H7 (E. coli O157: H7) is one of the most common foodborne pathogens and is widespread in food and the environment. Thus, it is significant for rapidly detecting E. coli O157: H7. In this study, a colorimetric aptasensor based on aptamer-functionalized magnetic beads, exonuclease III (Exo III), and G-triplex/hemin was proposed for the detection of E. coli O157: H7. The functional hairpin HP was designed in the system, which includes two parts of a stem containing the G-triplex sequence and a tail complementary to cDNA. E. coli O157: H7 competed to bind the aptamer (Apt) in the Apt-cDNA complex to obtain cDNA. The cDNA then bound to the tail of HP to trigger Exo III digestion and release the single-stranded DNA containing the G-triplex sequence. G-triplex/hemin DNAzyme could catalyze TMB to produce visible color changes and detectable absorbance signals in the presence of H2O2. Based on the optimal conditions, E. coli O157: H7 could be detected down to 1.3 × 103 CFU/mL, with a wide linear range from 1.3 × 103 to 1.3 × 107 CFU/mL. This method had a distinguished ability to non-target bacteria, which showed good specificity. In addition, the system was successfully applied to detect E. coli O157: H7 in milk samples.

Construction of a novel "self-regenerative" electrochemical biosensor based on metal-organic frameworks and its application to the detection of Mycoplasma ovine pneumonia

This study aimed to prepare a novel "self-regenerative" electrochemical biosensor by successively modifying gold nanoparticles, four-arm polyethylene glycol-NH₂, and NH₂-MIL-53 (Al) (MOF) on the glassy carbon electrode interface. A hairpin G-triplex-mediated DNA (G3 probe) as a part of the mycoplasma ovine pneumonia (MO) gene was loosely adsorbed to MOF. Based on the mechanism of hybridization induction, the G3 probe could effectively detach from the MOF only after introducing the target DNA. Subsequently, its guanine-rich nucleic acid sequences were exposed to solution of methylene blue. As a result, the diffusion current of the sensor system showed a sharp decline. The developed biosensor showed excellent selectivity, and the concentration of target DNA exhibited a good correlation in the range 10^-10 to 10^-6 M with a detection limit of 1.00 pM (S/N = 3), even in 10% goat serum. Most interestingly, this biosensor interface automatically started the regeneration program. Moreover, regeneration could be effectively achieved at least seven times, and the recovery rate of the electrode interface and sensing efficiency was up to 90%. Additionally, this platform could be used for other clinical assays in various systems by simply changing the DNA sequence of the probe.

Peroxidase-Mimicking DNAzymes as Receptors for Label-Free Discriminating Heavy Metal Ions by Chemiluminescence Sensor Arrays

Receptors are crucial to the analytical performance of sensor arrays. Different from the previous receptors in sensor arrays, herein, peroxidase-mimicking DNAzymes were innovatively used as receptors to develop a label-free chemiluminescence sensor array for discriminating various heavy metal ions in complex samples. The peroxidase-mimicking DNAzymes are composed of functional oligonucleotides and hemin, including G-triplex-hemin DNAzyme (G3-DNAzyme), G-quadruplex-hemin DNAzyme (G4-DNAzyme), and the dimer of G-quadruplex-hemin DNAzyme (dG4-DNAzyme). Circular dichroism (CD) spectroscopy demonstrated that different metal ions diversely affect the conformation of G-quadruplex and G-triplex, resulting in a change in the activity of peroxidase-mimicking DNAzyme. Thus, the unique fingerprints formed to easily discriminate seven kinds of heavy metal ions by principal component analysis (PCA) within 20 min. The discrimination of unknown metal ions in tap water further confirmed its ability for discriminating multiple heavy metal ions. Moreover, it will not bring water pollution due to the good biocompatibility of DNA. Therefore, it not only merely offers a label-free, rapid, environment-friendly, and cheap (1.49 $) sensor assay for discriminating metal ions but also comes up with an innovative way for developing sensor arrays.

Telomere G-triplex lights up Thioflavin T for RNA detection: new wine in an old bottle

Few reports are found working on the features and functions of the human telomere G-triplex (ht-G3) though the telomere G-quadruplex has been intensely studied and widely implemented to develop various biosensors. We herein report that ht-G3 lights up Thioflavin T (ThT) and establish a sensitive biosensing platform for RNA detection by introducing a target recycling strategy. An optimal condition was selected out for ht-G3 to promote ThT to generate a strong fluorescence. Accordingly, an ht-G3-based molecular beacon was successfully designed against the corresponding RNA sequence of the SARS-CoV-2 N-gene. The sensitivity for the non-amplified RNA target achieves 0.01 nM, improved 100 times over the conventional ThT-based method. We believe this ht-G3/ThT-based label-free strategy could be widely applied for RNA detection.

A sensitive aptasensor based on rolling circle amplification and G-rich ssDNA/terbium (III) luminescence enhancement for ofloxacin detection in food

As the light-harvesting "antenna", G-rich oligonucleotides (such as the G-quadruplex) can interact with lanthanide (III) to bring a luminescent enhancement response. In this study, phenomenon of luminescent enhancement of G-triplex/terbium (III) (G3/Tb³⁺) and interaction between G3 and Tb³⁺ were first reported and characterized. Based on G3/Tb³⁺ luminescence, a label-free aptasensor for the detection of ofloxacin (OFL) residues in the food was developed. The OFL triggered the action of rolling circle amplification (RCA) allowed for the amplification product of G3-forming sequences in the single-stranded DNA, which promoted the conformational transition of the G3/Tb³⁺ complexes once the addition of Tb³⁺. Under the optimal conditions, the logarithmic correlation between the G3/Tb³⁺ luminescence intensity and the concentration of OFL was found to be linear in the range of 5-1000 pmol L^-1 (R² = 0.9949). The limit of detection was 0.18 pmol L^-1 (3σ/slope). Additionally, the good recoveries of 90.19-108.89 % and the relative standard deviations values of 0.59-5.87 % were obtained in the application of the aptasensor detecting OFL in the practical samples. These results confirmed that the present aptasensor has a good analytical performance and bright prospect for detecting ofloxacin residues in food.

Stimuli-Responsive and Reversible Nanoassemblies of G-Triplexes

G-triplex (G3) structures formed with three consecutive G-tracts have recently been identified as a new emerging guanine-rich DNA fold. There could likely be a wide range of biological functions for G3s as occurring for G-quadruplex (G4) structures formed with four consecutive G-tracts. However, in comparison to the many reports on G4 nanoassemblies that organize monomers together in a controllable manner, G3-favored nanoassemblies have yet to be explored. In this work, we found that a natural alkaloid of sanguinarine can serve as a dynamic ligand glue to reversibly switch the dimeric nanoassemblies of the thrombin binding aptamer G3 (TBA-G3). The glue planarity was considered to be a crucial factor for realizing this switching. More importantly, external stimuli including pH, sulfite, O₂ and H₂ O₂ can be employed as common regulators to easily modulate the glue's adhesivity for constructing and destructing the G3 nanoassemblies as a result of the ligand converting between isoforms. However, this assembly behavior does not occur with the counterpart TBA-G4. Our work demonstrates that higher-order G3 nanoassemblies can be reversibly operated by manipulating ligand adhesivity. This provides an alternative understanding of the unique behavior of guanine-rich sequences and focuses attention on the G3 fold since the nanoassembly event investigated herein might occur in living cells.

G-triplex: A new type of CRISPR-Cas12a reporter enabling highly sensitive nucleic acid detection

CRISPR-Cas12a (Cpf1) trans-cleaves ssDNA and this feature has been widely harnessed for nucleic acid detection. Herein, we introduce a new type of Cas12a reporter, G-triplex (G3), and a highly sensitive biosensor termed G-CRISPR. We proved that Cas12a trans-cleaves G3 structures in about 10 min and G3 can serve as an excellent reporter based on the cleavage-induced high-order structure disruption. G3 reporter improves the analytical sensitivity up to 20 folds, enabling the detection of unamplified and amplified DNA as low as 50 pmol and 0.1 amol (one copy/reaction), respectively. G-CRISPR has been utilized for the analysis of 27 PCR-amplified patient samples with HPV infection risk based on both fluorescence and lateral flow assays, resulting in 100% concordance between the two. In comparison with the clinical results, it achieved overall specificity and sensitivity of 100% and 94.7%, respectively. These results suggest that G-CRISPR can serve as a rapid, sensitive, and reliable biosensor, and could further expand the CRISPR toolbox in biomedical diagnostics.

A new G-triplex-based strategy for sensitivity enhancement of the detection of endonuclease activity and inhibition

EcoRI is an important biomacromolecule in live cells and protects bacterial cells against foreign DNA. In this work, we developed a simple and convenient G-triplex (G3) (5′-TGGGAAGGGAGGGAATTCCCT-3′)-based colorimetric assay for the rapid and selective detection of EcoRI activity and inhibition. The sequence specifically responds to EcoRI in the presence of K⁺ and hemin to form a G-triplex/hemin complex. Taking advantage of G-triplex, EcoRI activity was investigated under the optimized conditions. The absorption intensity ratio displayed a linear relationship against the concentration of EcoRI in the range 0 to 100 U mL⁻¹, and the detection limit was 5.7 U mL⁻¹. Furthermore, G3 showed good selectivity, and the ability to be used to screen for EcoRI inhibitors, indicating its potential in detection and analysis applications.

A new G-triplex-based probe was developed for detecting EcoRI activity and inhibition. The probe showed good selectivity towards EcoRI. The assay was colorimetric and can be monitored by the naked eye.

A pH-triggered G-triplex switch with K+ tolerance

A pH-triggered G-triplex (G3) switch is demonstrated to operate in K⁺ using a planar ligand enabling reversible iminium-alkanolamine conversion as the G3 structuring-destructuring initiator.

G-triplex based molecular beacon with duplex-specific nuclease amplification for the specific detection of microRNA

Based on the G-triplex molecular beacon (MBG3), we have developed a duplex-specific nuclease signal amplification (DSNSA) assay for highly selective miRNA detection.

An ultrathin iron-porphyrin based nanocapsule with high peroxidase-like activity for highly sensitive glucose detection

For the first time, an ultrathin iron-porphyrin based polymer nanocapsule with multiple peroxidase-like catalytic centers was constructed by covalently assembling iron-porphyrin monomers; this nanocapsule with a single molecule thickness shell acted as a highly efficient artificial enzyme for mimicking peroxidase. On the basis of the peroxidase-like activity of Fe-TPyP based nanocapsules (Fe-TPyP NCs), a highly sensitive colorimetric sensor for glucose determination was fabricated, the limit of detection was found to be as low as 0.098 μM. This study provided a novel strategy for developing artificial enzymes based on covalently assembled nanostructures. Furthermore, the colorimetric sensor for glucose determination showed potential applications in biomedicine and biology.

The G-quadruplex fluorescent probe 3,6-bis(1-methyl-2-vinyl-pyridinium) carbazole diiodide as a biosensor for human cancers

Using time-gated fluorescence lifetime imaging microscopy, significantly more signals from 3,6-bis(1-methyl-2-vinyl-pyridinium) carbazole diiodide (o-BMVC) foci, characterized by the longer fluorescent decay time of o-BMVC, were detected in six types of cancer cells than in three types of normal cells. Accumulating evidence suggested that the o-BMVC foci are mainly the G-quadruplex foci. The large contrast in the number of o-BMVC foci can be considered as a common signature to distinguish cancer cells from normal cells. Further study of tissue biopsy showed that the o-BMVC test provides a high accuracy for clinical detection of head and neck cancers.

Stable and Label-Free Fluorescent Probe Based on G-triplex DNA and Thioflavin T

G-triplexes have recently been identified as a new kind of DNA structures. They perhaps possess specific biological and chemical functions similar as identified G-quadruplex but can be formed by shorter G-rich sequences with only three G-tracts. However, until now, limited G-triplexes sequences have been reported, which might be due to the fact that their stability is one of the biggest concerns during their functional studies and application research. Herein, we found a G-rich sequence (5'-TGGGTAGGGCGGG-3') which can form a stable G-triplex (Tm ∼ 60 °C) at room temperature. The stable G-triplex can combine with thioflavin T and function as an efficient fluorescence light-up probe. Comparing with the traditional G-quadruplex based probe, this triplex based probe was easy to be controlled and excited. Finally, the probe was successfully applied into constructing a label-free molecular beacon for miRNA detection. Taking advantage of these abilities of the G-triplex based fluorescent probe, the challenges faced during designing G-rich sequences based fluorescent biosensors can be efficiently solved. These findings provide important information for the future application of G-triplex.

A G-triplex luminescent switch-on probe for the detection of mung bean nuclease activity

A G-triplex luminescent switch-on probe for the detection of nuclease activity.

Cu(II)-coordinated GpG-duplex DNA as peroxidase mimetics and its application for label-free detection of Cu2+ ions

Herein a facile method is proposed to construct DNA-based peroxidase mimetics simply assembled by polymorphic DNA and Cu(2+) ions. The Cu(II)-catalyzed oxidation of TMB in the presence of H2O2 can be significantly accelerated through Cu(II)-coordination with DNA scaffolds, of which a colorimetric change can be discerned by naked-eye. The reaction rates of DNA-Cu(II) complexes are directly associated with sequence composition as well as the secondary structure of DNA scaffold, e.g., the reaction rate decreases in the following order: GpG-duplex ≈ G-rich coil > G-quadruplex > C-rich coil > i-motif. It is the first report to explore a colorimetric Cu(2+) sensing system on the basis of peroxidase mimicking activities of polymorphic DNA-Cu(II) complexes. One of our most intriguing results is that the GpG-duplex DNA demonstrates the ability to sense Cu(2+) ions in aqueous solution without significant interference from other metal ions. The Cu(2+) detection limit of 1.2 nM is achieved with a linear response range of 1.2-100 nM, and the developed sensing system is potentially applicable for quantitative determination of Cu(2+) in drinking water samples.