A versatile nanomachine for the sensitive detection of platelet-derived growth factor-BB utilizing a G-quadruplex-selective iridium(III) complex

A robust luminescent assay for screening alkyladenine DNA glycosylase inhibitors to overcome DNA repair and temozolomide drug resistance

Temozolomide (TMZ) is an anticancer agent used to treat glioblastoma, typically following radiation therapy and/or surgical resection. However, despite its effectiveness, at least 50% of patients do not respond to TMZ, which is associated with repair and/or tolerance of TMZ-induced DNA lesions. Studies have demonstrated that alkyladenine DNA glycosylase (AAG), an enzyme that triggers the base excision repair (BER) pathway by excising TMZ-induced N3-methyladenine (3meA) and N7-methylguanine lesions, is overexpressed in glioblastoma tissues compared to normal tissues. Therefore, it is essential to develop a rapid and efficient screening method for AAG inhibitors to overcome TMZ resistance in glioblastomas. Herein, we report a robust time-resolved photoluminescence platform for identifying AAG inhibitors with improved sensitivity compared to conventional steady-state spectroscopic methods. As a proof-of-concept, this assay was used to screen 1440 food and drug administration-approved drugs against AAG, resulting in the repurposing of sunitinib as a potential AAG inhibitor. Sunitinib restored glioblastoma (GBM) cancer cell sensitivity to TMZ, inhibited GBM cell proliferation and stem cell characteristics, and induced GBM cell cycle arrest. Overall, this strategy offers a new method for the rapid identification of small-molecule inhibitors of BER enzyme activities that can prevent false negatives due to a fluorescent background.

A Novel Colorimetric Nano Aptasensor for Ultrasensitive Detection of Aflatoxin B1 Based on the Exonuclease III-Assisted Signal Amplification Approach

The detection of aflatoxin B1 (AFB1) has recently garnered much attention on the issue of food safety. In this study, a novel and sensitive aptasensor towards AFB1 is proposed using an Exonuclease III (Exo III)-integrated signal amplification strategy. This reported sensing strategy is regulated by aptamer-functionalized nanobeads that can target AFB1; furthermore, complementary DNA (cDNA) strands can lock the immobilized aptamer strands, preventing the signal amplification function of Exo III in the absence of AFB1. The presence of AFB1 triggers the displacement of cDNA, which will then activate the Exo III-integrated signal amplification procedure, resulting in the generation of a guanine (G)-rich sequence to form a G-4/hemin DNAzyme, which can catalyze the substrate of ABTS to produce a green color. Using this method, a practical detection limit of 0.0032 ng/mL and a dynamic range of detection from 0.0032 to 50 ng/mL were obtained. Additionally, the practical application of the established sensing method for AFB1 in complex matrices was demonstrated through recovery experiments. The recovery rate and relative standard deviations (RSD) in three kinds of cereal samples ranged from 93.83% to 111.58%, and 0.82% to 7.20%, respectively, which were comparable with or better than previously reported methods.

Target-induced activation of polymerase activity for recycling signal amplification cascades for sensitive aptamer-based detection of biomarkers

It is of great importance to develop biosensing methods for the sensitive and selective analysis of biomarkers at very low levels in biological samples. Using a new target-induced activation of the DNA polymerase activity for recycling amplification cascades, we describe an aptamer-based method for highly sensitive detection of platelet-derived growth factor BB (PDGF-BB) in human serums. The polymerase activity is initially inhibited by the binding of the polymerase to the enzyme aptamer sequence. PDGF-BB associates with and switches a PDGF-BB binding aptamer to trigger the release of an active polymerase, which further initiates the simultaneous recycling of the target PDGF-BB molecules and the enzyme aptamer sequence for the subsequent displacement of the fluorescently quenched probes to recover the fluorescence. Due to two recycling cascades, substantial fluorescence magnification is obtained for the highly sensitive detection of PDGF-BB with a low detection limit of 5.1 pM. Moreover, the potential applicability of this method for real samples was verified by determining PDGF-BB in diluted human serums, relying on the excellent specificity and selectivity of the aptamer. The demonstration of the PDGF-BB assay method here thus can be expanded for the construction of diverse sensing platforms for detecting different trace biomarkers with the integration of an elaborate design of the aptamer probes.

Recent Progress and Development of G-Quadruplex-Based Luminescent Assays for Ochratoxin A Detection

Ochratoxin A (OTA) is a mycotoxin that is widespread throughout the world. It contaminates foods such as vegetables, fruits, and rice. It harms human health and has potential carcinogenic effects. The G-quadruplex (G4) is a tetraplexed DNA structure generated from guanine-rich DNA that has found emerging use in aptamer-based sensing systems. This review outlines the status of OTA contamination and conventional detection methods for OTA. Various G4-based methods to detect OTA developed in recent years are summarized along with their advantages and disadvantages compared to existing approaches.

Structural basis for stabilization of human telomeric G-quadruplex [d-(TTAGGGT)]4 by anticancer drug adriamycin

Besides inhibiting DNA duplication, DNA dependent RNA synthesis and topoisomerase-II enzyme action, anticancer drug adriamycin is found to cause telomere dysfunction and shows multiple strategies of action on gene functioning. We present evidence of binding of adriamycin to parallel stranded intermolecular [d-(TTAGGGT)]₄ G-quadruplex DNA comprising human telomeric DNA by proton and phosphorus-31 nuclear magnetic resonance spectroscopy. Diffusion ordered spectroscopy shows formation of complex between the two molecules. Changes in chemical shift and line broadening of DNA and adriamycin protons suggest participation of specific chemical groups/moieties in interaction. Presence of sequential nuclear Overhauser enhancements at all base quartet steps and absence of large downfield shifts in ³¹P resonances give clear proof of absence of intercalation of adriamycin chromophore between base quartets. Restrained molecular dynamics simulations using observed 15 short intermolecular inter proton distance contacts depict stacking of ring D of adriamycin with terminal G6 quartet by displacing T7 base and external groove binding close to T1-T2-A3 bases. The disappearance of imino protons monitored as a function of temperature and differential scanning calorimetry experiments yield thermal stabilization of 24 °C, which is likely to come in the way of telomerase association with telomeres. The findings pave the way for design of alternate anthracycline based drugs with specific modifications at ring D to enhance induced thermal stabilization and use alternate mechanism of binding to G-quadruplex DNA for interference in functional pathway of telomere maintenance by telomerase enzyme besides their well known action on duplex DNA. Communicated by Ramaswamy H. Sarma.

Switch-on effect on conformation-specific arylamine-DNA adduct by cyclometalated Ir(III) complexes

Arylamines are known to form covalent-DNA adducts upon metabolic activation. These covalent adducts adopt different conformational attributes, viz., major groove (B), stacked (S), and minor groove (W), and lead to different types of mutations. The conformation depends on the flanking and next flanking bases at the 3' position of the adduct. Early detection of these conformations by simple probes is an ideal and challenging task. Here, we have reported two Ir(III)-based cyclometalated complexes, viz., [Ir(ppy)₂(imiphen)]⁺ (1) (ppy: 2-phenylpyridine; imiphen: 2-(1H-imidazol-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline) and [Ir(ppy)₂(furphen)]⁺ (2) (furphen: 2-(furan-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline) and its interaction with N-acetyl-2-aminofluorene-dG (AAF-dG). The sequences used in this work are NarI sequence (-CG₁G₂CG₃CX-) in which Gs are modified with AAF and X is either C or T. Luminescence studies reveal that the Ir(III) complexes bind to AAF-dG adduct with high specificity toward G₁ and G₃ compared to G₂ and unmodified control. The selectivity also depends on the next flanking base as cytosine favors G₃^AAF, while thymine favors G₁^AAF in complex 1 and vice versa for complex 2. The quenching studies confirm that Ir(III) complexes bind with AAF-dG sequences through the minor groove. The outcome of this work reveals that the switch-on effect by the complexes can be utilized for determining the conformational heterogeneity of the adduct and also for similar covalent-DNA adducts.

Dual mode of binding of anti cancer drug epirubicin to G-quadruplex [d-(TTAGGGT)]4 containing human telomeric DNA sequence induces thermal stabilization

Epirubicin exerts its anti cancer action by blocking DNA/RNA synthesis and inhibition of topoisomerase-II enzyme. Recent reports on its influence on telomere maintenance, suggest interaction with G-quadruplex DNA leading to multiple strategies of action. The binding of epirubicin with parallel stranded inter molecular G-quadruplex DNA [d-(TTAGGGT)]₄ comprising human telomeric DNA sequence TTAGGG was investigated by absorption, fluorescence, circular dichroism and nuclear magnetic resonance spectroscopy. The epirubicin binds as monomer to G-quadruplex DNA with affinity, K_b1 = 3.8 × 10⁶ M^-1 and K_b2 = 2.7 × 10⁶ M^-1, at two independent sites externally. The specific interactions induce thermal stabilization of DNA by 13.2-26.3 °C, which is likely to come in the way of telomere association with telomerase enzyme and contribute to epirubicin-induced apoptosis in cancer cell lines. The findings pave the way for drug designing in view of the possibility of altering substituent groups on anthracyclines to enhance efficacy using alternate mechanism of its interaction with G4 DNA, causing interference in telomere maintenance pathway by inducing telomere dysfunction.

An Enzyme- and Label-Free Fluorescence Aptasensor for Detection of Thrombin Based on Graphene Oxide and G-Quadruplex

An enzyme- and label-free aptamer-based assay is described for the determination of thrombin. A DNA strand (S) consisting of two parts was designed, where the first (Sa) is the thrombin-binding aptamer and the second (Se) is a G-quadruplex. In the absence of thrombin, Sa is readily adsorbed by graphene oxide (GO), which has a preference for ss-DNA rather than for ds-DNA. Upon the addition of the N-methyl-mesoporphyrin IX (NMM), its fluorescence (with excitation/emission at 399/610 nm) is quenched by GO. In contrast, in the presence of thrombin, the aptamer will bind thrombin, and thus, be separated from GO. As a result, fluorescence will be enhanced. The increase is linear in the 0.37 µM to 50 µM thrombin concentration range, and the detection limit is 0.37 nM. The method is highly selective over other proteins, cost-effective, and simple. In our perception, it represents a universal detection scheme that may be applied to other targets according to the proper choice of the aptamer sequence and formation of a suitable aptamer-target pair.

An allosteric switch-based hairpin for label-free chemiluminescence detection of ribonuclease H activity and inhibitors

To assay enzyme activities and screen its inhibitors, we demonstrated a novel label-free chemiluminescent (CL) aptasensor for the sensitive detection of RNase H activity based on hairpin technology. The specific hairpin structure was a DNA-RNA chimeric strand, which contained a streptavidin aptamer sequence and a blocked RNA sequence. RNase H could specifically recognize and cleave the RNA sequence of the DNA-RNA hybrid stem, liberating the streptavidin aptamer which could be accumulated by streptavidin-coated magnetic microspheres (SA-MP). Then the CL signal was generated due to an instantaneous derivatization reaction between the specific CL reagent 3,4,5-trimethoxyphenyl-glyoxal (TMPG) and the guanine (G) nucleotides in the SA aptamer. This novel assay method exhibited a good linear relationship in the range of 0.1-10 U mL-1 under the optimized conditions. Our results suggested that the developed system was a promising platform for monitoring the RNase H activity and showed great potential in biomedical studies and drug screening.

A fluorescence method for homogeneous detection of influenza A DNA sequence based on guanine-quadruplex-N-methylmesoporphyrin IX complex and assistance-DNA inhibition

In his study, we report a fluorescence method for homogeneous detection of influenza A (H1N1) DNA sequence based on G-quadruplex-NMM complex and assistance-DNA (A-DNA) inhibition. The quadruplex-based functional DNA (QBF-DNA), composed of a complementary probe to the target H1N1 DNA sequence and G-rich fragment, was designed as the signal DNA. The A-DNA consisted of two parts, one part was complementary to target H1N1 DNA and the other part was complementary to the signal DNA. In the absence of target H1N1 DNA, the G-rich fragment of QBF-DNA can form G-quadruplex-NMM complex, which outputted a fluorescent signal. With the presence of target H1N1 DNA, QBF-DNA, and A-DNA can simultaneously hybridize with target H1N1 DNA to form double-helix structure. In this case, the A-DNA partially hybridized with the QBF-DNA, which inhibited the formation of G-quadruplex-NMM complex, leading to the decrease of fluorescent signal. Under the optimum conditions, the fluorescence intensity was inversely proportional to the concentration of target H1N1 DNA over the range from 25 to 700 pmol/L with a detection limit of 8 pmol/L. In addition, the method is target specific and practicability, and would become a new diagnostic assay for H1N1 DNA sequence and other infectious diseases.

Development of a Luminescent Dinuclear Ir(III) Complex for Ultrasensitive Determination of Pesticides

To improve the G-quadruplex specificity of Ir(III) complexes, a novel dinuclear Ir(III) complex (Din Ir(III)-1) was designed and synthesized through connecting two mononuclear Ir(III) complexes via a diphenyl bridge. Din Ir(III)-1 presents 3.4-4.1-fold enhancements for G-quadruplex relative to ssDNA and 4.3-5.3-fold enhancements relative to dsDNA in luminescence intensity, respectively, demonstrating an excellent G-quadruplex selectivity. Ascribed to its superior specificity to G-quadruplex, Din Ir(III)-1 was employed to construct a highly sensitive luminescent pesticides' detection platform. The detection is based on acetylcholinesterase (AChE)-catalyzed hydrolysis product-induced DNA conformational transformation and subsequent terminal deoxynucleotidyl transferase (TdT) directed G-quadruplex formation. The assay exhibited a linear response between the emission intensity of Din Ir(III)-1 and the pesticide concentration in the range of 0.5-25 μg/L ( R² = 0.994), and the limit of detection for the pesticide was as low as 0.37 μg/L when using aldicarb as the model pesticide. Moreover, this strategy demonstrates good applicability for the pesticide detection in real samples. It is also versatile for the detection of other organophosphate or carbamate pesticides, which have the inhibition ability toward AChE. Therefore, the proposed approach is scalable for practical application in food safety and environmental monitoring fields and will provide promising solutions for the assay of pesticide residues.

A Non-Label and Enzyme-Free Sensitive Detection Method for Thrombin Based on Simulation-Assisted DNA Assembly

Taking advantage of the high selectivity of aptamers and enzyme-free catalyzed hairpin assembly (CHA) amplification strategy, we herein describe a label-free and enzyme-free sensitive fluorescent and colorimetric strategy for thrombin detection in this paper. In the presence of target, the corresponding aptamer of the partial dsDNA probes will bind to the target and liberate the initiation strand, which is artfully designed as the “on” switch for hairpin assembly. Moreover, the displaced initiation strand partakes in a multi-cycle process and produces numerous G-quadruplexes, which have a remarkable enhancement in fluorescent/colorimetric signal from NMM (N-methyl-mesoporphyrin IX) and TMB (3,3′,5,5′-tetramethylbenzidine), respectively. The proposed amplification strategy for thrombin detection is of high sensitivity, down to 2.4 pM, and also achieves colorimetric signals that are able to be distinguished by naked eye. More importantly, the thermodynamics of interacting DNA strands used in our work, and the process of toehold strand displacement-driven assembly are simulated before biological testing, verifying the feasibility theoretically, and simplifying the subsequent actual experiments. Therefore, our approach and simulation have a certain potential application in biomarker detection and quantitatively monitor for disease diagnosis.

Ethyl-substitutive Thioflavin T as a highly-specific fluorescence probe for detecting G-quadruplex structure

G-quadruplex has attracted considerable attention due to their prevalent distribution in functional genomic regions and transcripts, which can importantly influence biological processes such as regulation of telomere maintenance, gene transcription and gene translation. Artificial receptor study has been developed for accurate identification of G-quadruplex from DNA species, since it is important for the G-quadruplex related basic research, clinical diagnosis, and therapy. Herein, fluorescent dye ThT-E, a derivative of the known fluorescence probe Thioflavin T (ThT), was designed and synthesized to effectively differentiate various G-quadruplex structures from other nucleic acid forms. Compared with methyl groups in ThT, three ethyl groups were introduced to ThT-E, which leads to strengthened affinity, selectivity and little inducing effect on the G-quadruplex formation. More importantly, ThT-E could be served as a visual tool to directly differentiate G-quadruplex solution even with naked eyes under illumination of ultraviolet light. Thus, this probe reported herein may hold great promise for high-throughput assay to screen G-quadruplex, which may widely apply to G-quadruplex-based potential diagnosis and therapy.

Label-free and nicking enzyme-assisted fluorescence signal amplification for RNase H determination based on a G-quadruplexe/thioflavin T complex

In this paper, we describe a novel, label-free and nicking enzyme-assisted fluorescence signal amplification strategy that demonstrates to be cost efficient, sensitive, and unique for assaying the RNase H activity and inhibition based on G-quadruplex formation using a thioflavin T (ThT) dye. This novel assay method is able to detect RNase H with a detection limit of 0.03 U /mL and further exhibits a good linearity R² = 0.9923 at a concentration range of 0.03-1 U/mL under optimized conditions. Moreover, the inhibition effect of gentamycin on the RNase H activity is also studied. This strategy provides a potential tool for the biochemical enzyme analysis and inhibitor screening.

A dual-cycling biosensor for target DNA detection based on the toehold-mediated strand displacement reaction and exonuclease III assisted amplification

Based on the toehold-mediated strand displacement reaction and exonuclease III assisted amplification, a sensitive and simple target DNA biosensor was established.

Luminescent Strategies for Label-Free G-Quadruplex-Based Enzyme Activity Sensing

By catalyzing highly specific and tightly controlled chemical reactions, enzymes are essential to maintaining normal cellular physiology. However, aberrant enzymatic activity can be linked to the pathogenesis of various diseases. Therefore, the unusual activity of particular enzymes can represent testable biomarkers for the diagnosis or screening of certain diseases. In recent years, G-quadruplex-based platforms have attracted wide attention for the monitoring of enzymatic activities. In this Personal Account, we discuss our group's works on the development of G-quadruplex-based sensing system for enzyme activities by using mainly iridium(III) complexes as luminescent label-free probes. These studies showcase the versatility of the G-quadruplex for developing assays for a variety of different enzymes.

Synthesis of hydrophilic and conductive molecularly imprinted polyaniline particles for the sensitive and selective protein detection

In this work, a novel kind of water-dispersible molecular imprinted conductive polyaniline particles was prepared through a facile and efficient macromolecular co-assembly of polyaniline with amphiphilic copolymer, and applied as the molecular recognition element to construct protein electrochemical sensor. In our strategy, an amphiphilic copolymer P(AMPS-co-St) was first synthesized using 2-acrylamido-2-methyl-1-propanesulfonic acid (AMPS) and styrene (St) as monomer, which could co-assemble with PANI in aqueous solution to generate PANI particles driven by the electrostatic interaction. During this process, ovalbumin (OVA) as template protein was added and trapped into the PANI NPs particles owing to their interactions, resulting in the formation of molecular imprinted polyaniline (MIP-PANI) particles. When utilizing the MIP-PANI particles as recognition element, the resultant imprinted PANI sensor not only exhibited good selectivity toward template protein (the imprinting factor α is 5.31), but also a wide linear range over OVA concentration from 10^-11 to 10^-6mgmL^-1 with a significantly lower detection limit of 10^-12mgmL^-1, which outperformed most of reported OVA detecting methods. In addition, an ultrafast response time of less than 3min has also been demonstrated. The superior performance is ascribed to the water compatibility, large specific surface area of PANI particles and the electrical conductivity of PANI which provides a direct path for the conduction of electrons from the imprinting sites to the electrode surface. The outstanding sensing performance combined with its facile, quick, green preparation procedure as well as low production cost makes the MIP-PANI particles attractive in specific protein recognition and sensing.

Two-photon photodynamic ablation of tumor cells by mitochondria-targeted iridium(iii) complexes in aggregate states

Two iridium(iii) complexes with a rotary phenyl substituent ligand were used as mitochondria-targeted photosensitizers for two-photon photodynamic therapy in aggregate states.

Novel hybrid probe based on double recognition of aptamer-molecularly imprinted polymer grafted on upconversion nanoparticles for enrofloxacin sensing

A novel luminescent "double recognition" method for the detection of enrofloxacin (ENR) is developed to overcome some of the challenges faced by conventional molecularly imprinting. Biotinylated ENR aptamers immobilised on upconversion nanoparticles (UCNPs) surface are implemented to capture and concentrate ENR as the first imprinting recognition safeguard. After correct folding of the aptamer upon the existing targets, polymerization of methacrylic acid monomers around the ENR-aptamer complexes to interact with the residual functional groups of ENR by using molecularly imprinting techniques is the second imprinting recognition safeguard. The "double recognition" imprinting cavities are formed after removal of ENR, displaying recognition properties superior to that of aptamer or traditional molecularly imprinting alone. Another interest of this method is simultaneous molecular recognition and signal conversion by fabricating the "double recognition" receptor on to the surface of UCNPs to form a hybrid sensing system of apta-MIP/UCNPs. The proposed sensing method is applied to measure ENR in different fish samples. Good recoveries between 87.05% and 96.24%, and relative standard deviation (RSD) values in the range of 1.19-4.83% are obtained, with the limits of detection and quantification of 0.04 and 0.12ng/mL, respectively. It indicates that the sensing method is feasible for the quantification of target ENRs in real samples, and show great potential for wide-ranging application in bioassays.

Iridium(iii) complexes with 1,10-phenanthroline-based N^N ligands as highly selective luminescent G-quadruplex probes and application for switch-on ribonuclease H detection

A study was performed to investigate the relationship between molecular structure and G4 sensing ability for a series of iridium(iii) complexes. The complex7was used to construct a G4-based assay for RNase H.