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Two soluble heme analogs of the insoluble malaria pigment hematin anhydride (HA, or ß-hematin), [Fe(III)(protoporphyrin)]2, with either mesoporphyrin (MHA) or deuteroporphyrin (DHA) are characterized by elemental analysis, SEM, IR spectroscopy, electronic spectroscopy, paramagnetic 1H NMR spectroscopy and solution magnetic susceptibility. While prior single crystal and X-ray powder diffraction results indicate all three have a common propionate linked dimer motif, there is considerable solid state variation in the conformation. This is associated with enhanced solubility of MHA and DHA. As with HA, DHA undergoes thermally promoted reversible hydration/dehydration in the solid state. Solution 1H NMR studies of DHA suggest a high spin dimeric structure with the porphyrin methyls distributed between two isomers which are also present in the solid state. These soluble iron(III)porphyrin dimers allow for the first direct solution studies by NMR and UV-Vis spectroscopies of these key species. Taken together the results illustrate the importance and utility of varying the substituents on the periphery of the porphyrin for studying heme aggregation and malaria pigment formation.

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G-quadruplexes (G4) are stable alternative secondary structures of nucleic acids. With increasing understanding of their roles in biological processes and their application in bio- and nanotechnology, the exploration of novel methods for the analysis of these structures is becoming important. In this work, N-methyl mesoporphyrin IX (NMM) was used as a voltammetric probe for an easy electrochemical detection of G4s. Cyclic voltammetry on a hanging mercury drop electrode (HMDE) was used to detect NMM with a limit of detection (LOD) of 40 nM. Characteristic reduction signal of NMM was found to be substantially higher in the presence of G4 oligodeoxynucleotides (ODNs) than in the presence of single- or double-stranded ODNs and even ODNs susceptible to form G4s but in their unfolded, single-stranded forms. Gradual transition from unstructured single strand to G4, induced by increasing concentrations of the G4 stabilizing K+ ions, was detected by an electrochemical method for the first time. All obtained results were supported by circular dichroism spectroscopy. This work expands on the concept of electrochemical probes utilization in DNA secondary structure recognition and offers a proof of principle that can be potentially employed in the development of novel electroanalytical methods for nucleic acid structure studies.

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DNA can fold into G-quadruplexes (GQs), non-canonical secondary structures formed by π-π stacking of G-tetrads. GQs are important in many biological processes, which makes them promising therapeutic targets. We identified a 42-nucleotide long, purine-only G-rich sequence from human genome, which contains eight G-stretches connected by A and AAAA loops. We divided this sequence into five unique segments, four guanine stretches each, named GA1-5. In order to investigate the role of adenines in GQ structure formation, we performed biophysical and X-ray crystallographic studies of GA1-5 and their complexes with a highly selective GQ ligand, N-methyl mesoporphyrin IX (NMM). Our data indicate that all variants form parallel GQs whose stability depends on the number of flexible AAAA loops. GA1-3 bind NMM with 1:1 stoichiometry. The Ka for GA1 and GA3 is modest, ∼0.3 µM -1, and that for GA2 is significantly higher, ∼1.2 µM -1. NMM stabilizes GA1-3 by 14.6, 13.1, and 7.0 °C, respectively, at 2 equivalents. We determined X-ray crystal structures of GA1-NMM (1.98 Å resolution) and GA3-NMM (2.01 Å). The structures confirm the parallel topology of GQs with all adenines forming loops and display NMM binding at the 3' G-tetrad. Both complexes dimerize through the 5' interface. We observe two novel structural features: 1) a 'symmetry tetrad' at the dimer interface, which is formed by two guanines from each GQ monomer and 2) a NMM dimer in GA1-NMM. Our structural work confirms great flexibility of adenines as structural elements in GQ formation and contributes greatly to our understanding of the structural diversity of GQs and their modes of interaction with small molecule ligands.

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BACKGROUND: Oncological analysis is important in tumor diagnosis. We constructed a dual-fluorescence and binary visual analysis system for circulating tumor cells (CTCs) using the folate receptor as a biomarker, combined with hybridization chain reaction and nanomaterial amplification. This strategy integrates terminal protection, selective recognition properties of N-methyl mesoporphyrin IX and CdTe quantum dots for Cu2+ and double-stranded templated copper nanoparticles, and inkjet printing technology. RESULTS: In fluorescence mode, folate receptor and A2780 ovarian cancer cells were specifically detected with a limit of detection of 0.1 fg mL-1, and 10 cells mL-1 were observed. The detection limits of both the color and distance reading modes were comparable to those obtained in fluorescence mode. The applicability of the method for quantifying CTCs was validated using 27 (6 negative and 21 positive) clinical ovarian cancer samples; the results agreed with those of both the clinical folate receptor-polymerase chain reaction kit and radiological and pathological results. SIGNIFICANCE: This dual-fluorescence and binary visual CTCs detection method provides multiple options for clinical tumor liquid biopsy.

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Guanine quadruplexes (G4s) serve as regulators of replication, recombination and gene expression. G4 motifs have been recently identified in LTR retrotransposons, but their role in the retrotransposon life-cycle is yet to be understood. Therefore, we inserted G4s into the 3'UTR of Ty1his3-AI retrotransposon and measured the frequency of retrotransposition in yeast strains BY4741, Y00509 (without Pif1 helicase) and with G4-stabilization by N-methyl mesoporphyrin IX (NMM) treatment. We evaluated the impact of G4s on mRNA levels by RT-qPCR and products of reverse transcription by Southern blot analysis. We found that the presence of G4 inhibited Ty1his3-AI retrotransposition. The effect was stronger when G4s were on a transcription template strand which leads to reverse transcription interruption. Both NMM and Pif1p deficiency reduced the retrotransposition irrespective of the presence of a G4 motif in the Ty1his3-AI element. Quantity of mRNA and products of reverse transcription did not fully explain the impact of G4s on Ty1his3-AI retrotransposition indicating that G4s probably affect some other steps of the retrotransposon life-cycle (e.g., translation, VLP formation, integration). Our results suggest that G4 DNA conformation can tune the activity of mobile genetic elements that in turn contribute to shaping the eukaryotic genomes.

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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.

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To develop a novel light-up probe and DNAzyme, we selected aptamers for N-methyl mesoporphyrin IX (NMM), a common fluorogenic analogue of coenzyme hemin, by a modified affinity chromatography-based systematic evolution of ligands by exponential enrichment (SELEX). Two truncated aptamers Nm1 and Nm2 with low micromolar dissociation constants (0.75 and 13.27 µM) were obtained after 11 rounds of selection and the final minimized 39-mer aptamer Nm2.1 showed 24-fold fluorescence enhancement for NMM at saturated concentration. Study of the interactions between aptamers and other porphyrin compounds by circular dichroism (CD) and absorption spectroscopy showed that Nm1 mainly assembled as a stem-loop structure, which exhibited a catalytic activity for the metal insertion reaction of mesoporphyrin IX with 3.3-fold rate enhancement. In contrast, the G-rich Nm2 and Nm2.1 were likely to form G-quadruplexes in the presence of alkali metal cations (K+ and Na+), which displayed excellent peroxidase activity exhibiting 19-fold higher catalytic efficiency than hemin alone. The selected aptamers could therefore be used as novel light-up fluorescent probes and DNAzymes by pairing with porphyrin compounds that have potential to construct sensors for various applications.

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N-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect - high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules (e.g. ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.

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Paper-based analytics allows building portable and disposable devices for point-of-care (POC) diagnosis. Conventional methods for quantifying proteins exhibit substantial disadvantages related to costs and difficulty of the technique when used in settings where fast and cost-effective assays are needed. We report the successful application of a simple, rapid, easy to use, and label-free aptasensor strategy based on the selective fluorescence of the NMM IX dye. For the probe design, the three-dimensional (3-D) structures of the DNA components were carefully analyzed using software for the 3-D visualization of crystallographic structures. The chimeric aptafluorescence molecule consists of two modules, a detection aptamer and a transduction sequence that induces the specific fluorescence of NMM IX. In the presence of thrombin, a fluorescent spot visible to the naked eye can be observed. The fluorescent response is directly proportional to protein concentration and can be easily quantified colorimetrically using a low-cost microscopy system. The recognition probe design might be adaptable to other relevant biological analytes by changing the sequence of the aptamer. This proof of principle represents a contribution to the development of useful, cheap, reliable, and simple protein quantification assays for POC testing.

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As one of the most toxic mycotoxins, aflatoxin B1 (AFB1) is a major food pollutant which can pose a high risk to human health. In this work, an accurate fluorescent sensing method was proposed for AFB1 determination, based on hairpin structure of G-quadruplex oligonucleotide-Aptamer chimera, silica nanoparticles coated with streptavidin (SNPs-Streptavidin) and N-methyl mesoporphyrin IX (NMM). The hairpin structure of chimera and SNPs-Streptavidin allowed AFB1 detection with high sensitivity and specificity. Moreover, the developed sensor could detect AFB1 in 30 min. The relative fluorescence intensity increased as AFB1 concentrations increased with a linear range of 30-900 pg/mL and a limit of detection (LOD) of 8 pg/mL. The constructed aptasensor was successfully employed to assess AFB1 spiked grape juice and human serum samples. The analytical recovery of AFB1 in the grape juice samples ranged from 95 to 106%, implying the great potential of the presented aptasensor in food product analysis.

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To meet the severe water pollution status, multi-target biosensor becomes one of research focus. We herein report a novel duplex functional fluorescent biosensor for the label-free and separate detection of Pb2+ and Hg2+ with high sensitivity and selectivity. A K+-induced fluorescent G-quadruplex probe was assembled by a guanine-rich sequence (AGRO100) and N-methyl mesoporphyrin IX(NMM). It changed into a more stably non-fluorescent G-quadruplex structure and a hairpin-like structure upon binding Pb2+ and Hg2+ ions, respectively. As a result, the fluorescence decreased with relation to the addition of targets, allowing the separate detection of Pb2+ and Hg2+ ions at concentrations as low as 5 nM and 18.6 nM. The linear correlation existed between the fluorescence intensity and the concentration of Pb2+ and Hg2+ over the range of 10-200 nM (R2 = 0.98) and 20-1000 nM (R2 = 0.99), respectively. All real lake samples, even containing Pb2+ or Hg2+ at 50 nM, could be determined by the duplex functional fluorescent probe with recovery rates 96% and 104%, respectively. Considering that this sensor is label-free, simple, time-saving, cost-effective and easy-to-handle, it is possible to pave its way for Pb2+ and Hg2+ detection in various application fields.

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Herein, we are presenting an approach that utilizes the λ exonuclease (λ exo) cleavage reaction in combination with the formation of G-quadruplex, thereby providing a label-free fluorometric tool for simply and accurately determining alkaline phosphatase (ALP) activity and inhibition. A hairpin probe (HP) with 5'-phosphoryl termini and 3'-end containing a G-rich region, is designed. Taking advantage of the efficient enzyme reactions, namely the λ exo cleavage reaction, the G-rich DNA fragment is released from HP and folds into a stable G-quadruplex in the presence of potassium ions, thus greatly enhance the fluorescence of N-methyl mesoporphyrin IX (NMM) (a specific G-quadruplex binder). However, in the presence of ALP, the 5'-phosphoryl of the HP is dephosphorylated. The yielding 5'-hydroxyl end product hampers the λ exo cleavage reaction. HP maintains its stem-loop structure. Thus the formation of the G-quadruplex is prohibited, and this results in weak fluorescence of NMM. The fluorescence intensity exhibits a linear correlation to ALP concentration in the range of 1-50 U/L with a detection limit of 0.75 U/L. Additionally, inhibition effect of sodium orthovanadate has also been investigated. This study offers a simple yet sensitive method for ALP activity assay.

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Formation of amyloid fibrils by amyloid-ß peptide (Aß) is an important step in Alzheimer's disease (AD) progression. Screening and designing of new molecules which can monitor the amyloidosis process especially in cells are diagnostically and therapeutically important. Utilizing Thioflavin T (ThT), the commonly used amyloid dye, is the most standardized way to monitor amyloid. However, with the green fluorescence emission and small Stokes shift, the fluorescence of ThT can overlap with that arising from other intrinsic fluorescent components in the cells, making it not suitable for detection of protein aggregates in vivo. Therefore, it is urgent for developing amyloid probes with large Stokes shifts and red-shifted fluorescence emission to detect Aß aggregates in cells. In this report, we found that N-methyl mesoporphyrin IX (NMM), a widely used G-quadruplex DNA specific fluorescent binder, can be an efficient probe for monitoring Aß fibrillation in living cells. NMM is nonfluorescent in aqueous solution or monomeric Aß environments. However, through stacking with the Aß assemblies, NMM emits strong fluorescence. Furthermore, the large Stokes shift and stable photoluminescence make it an ideal probe for detecting Aß aggregates in highly fluorescent environments and cell culture. Our results provide a new sight to design and screen new reagents for monitoring the diseases associated with protein conformational disorders.

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For many decades, the world scientific literature has accounted for a number of works on the biological effects of bilirubin-IXalpha (BR). The first studies focused on the neurotoxic effects of the excessive production of BR, in particular regarding both physiological neonatal jaundice and the more severe ones, typically as consequences of severe hemolysis or other underlying diseases. Only since 1987, has significant evidence, however, underlined the neuroprotective role of BR linked to the scavenging effect of free radicals as reactive oxygen species and nitric oxide and its congeners. Despite the presence in the literature of many excellent papers dealing with the multiple roles played by BR in health and disease, there were very few and somewhat dated reviews that summarize the key findings related to the neuroprotective and neurotoxic effects of the bile pigment and underlying mechanisms. In light of the previous statements, the aim of this review is to provide a summary of the main discoveries in the last years on the effects of BR on the central nervous system. An analytical description about the synthesis of BR, its distribution in the systemic circulation, liver metabolism and elimination through feces and urine will be provided, together with the main mechanisms claimed to describe the neurotoxicity and neuroprotection by the bile pigment. Finally, the possible translational aspects of pharmacological modulation in the production of BR in order to prevent or counteract toxic effects or enhance the protective actions, will be discussed.

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A gender difference in stroke is observed throughout epidemiologic studies, pathophysiology, treatment and outcomes. We investigated the neuroprotective role of hemeoxygenase (HO) enzyme, which catabolizes free heme to bilirubin, carbon monoxide and biliverdin in the female brain after permanent ischemia. We have previously reported in male mice that genetic deletion of HO1 exacerbates the brain damage after permanent ischemia, and the mechanism of neuroprotection is dependent on the HO1/Wnt pathway; however, the role of HO1/Wnt mediated neuroprotection in the female brain is yet to be investigated. We subjected ovary intact female mice, HO1-/- intact, HO1 inhibitor tin mesoporphyrin (SnMP) treated intact and/or ovariectomized female mice to permanent ischemia (pMCAO), and the animals were sacrificed after 7days. The SnMP treatment for 7days significantly reduced the HO1 enzyme activity as compared to that of vehicle treated group. Infarct volume analysis showed significantly lower infarct in intact, HO1-/- intact, and SnMP treated group as compared to the OVX group, suggesting the role of estrogen in neuroprotection. However, there were no differences in infarct volume observed between the intact, HO1-/- and SnMP treated group, suggesting a sexually dimorphic role of HO1 neuroprotection. Western blot analysis on intact and SnMP-treated groups subjected to pMCAO suggested no significant differences in Wnt expression. Together, these results suggest that HO1 neuroprotection is sexually dimorphic and Wnt expression is independently regulated in the female brain following permanent ischemia.

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PURPOSE: Anterior ischemic optic neuropathy (AION) is the most common cause of non-glaucomatous optic nerve head (ONH) injury among older adults. AION results from a sudden ischemic insult to the proximal portion of the optic nerve, typically leading to visual impairment. Here, we present an experimental model of photodynamically induced ONH injury that can be used to study neuroprotective modalities. METHODS: Intraperitoneal injection of mesoporphyrin IX was followed by photodynamic treatment of the ONH in one eye of Brown-Norway rats; the fellow eye received the reverse sequence as a sham control. Fluorescein angiography (FA), spectral domain optical coherence tomography (SD-OCT), and visual evoked potential (VEP) recordings were performed at different time points following laser treatment. Immunohistochemistry was used to monitor apoptotic cell death (TUNEL) and macrophage infiltration (CD68). Cytokine levels were evaluated using enzyme-linked immunosorbent assay (ELISA). RESULTS: FA showed early hyperfluorescence and late leakage of the ONH, while SD-OCT revealed optic nerve edema. No leakage or other abnormalities were detected in control eyes. VEPs were significantly reduced in amplitude and showed prolonged responses compared to sham eyes. The number of apoptotic retinal ganglion cells was elevated one day after laser treatment (13.77 ± 4.49, p < 0.01) and peaked on day 7 (57.22 ± 11.34, p < 0.01). ONH macrophage infiltration also peaked on day 7 (101.8 ± 9.8, p < 0.05). ELISAs performed showed upregulation of macrophage chemoattractant protein-1 and macrophage inflammatory protein-2 on days 3 and 1, respectively. CONCLUSIONS: Photodynamic treatment of the ONH after administration of mesoporphyrin IX leads to macroscopic, histologic, and physiologic evidence of ONH injury. Given the long half-life of mesoporphyrin IX and the ease of intraperitoneal injections, this new model of photodynamically induced ONH injury may be a useful tool for studying optic nerve injury and possible neuroprotective treatments.

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Acinetobacter baumannii is a challenging pathogen due to antimicrobial resistance and biofilm development. The role of iron in bacterial physiology has prompted the evaluation of iron-modulation as an antimicrobial strategy. The non-reducible iron analog gallium(III) nitrate, Ga(NO3)3, has been shown to inhibit A. baumannii planktonic growth; however, utilization of heme-iron by clinical isolates has been associated with development of tolerance. These observations prompted the evaluation of iron-heme sources on planktonic and biofilm growth, as well as antimicrobial activities of gallium meso- and protoporphyrin IX (Ga-MPIX and Ga-PPIX), metal heme derivatives against planktonic and biofilm bacteria of multidrug-resistant (MDR) clinical isolates of A. baumannii in vitro. Ga(NO3)3 was moderately effective at reducing planktonic bacteria (64 to 128 µM) with little activity against biofilms (≥512 µM). In contrast, Ga-MPIX and Ga-PPIX were highly active against planktonic bacteria (0.25 to 8 µM). Cytotoxic effects in human fibroblasts were observed following exposure to concentrations exceeding 128 µM of Ga-MPIX and Ga-PPIX. We observed that the gallium metal heme conjugates were more active against planktonic and biofilm bacteria, possibly due to utilization of heme-iron as demonstrated by the enhanced effects on bacterial growth and biofilm formation.

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A sensitive, lable-free and low cost fluorescence aptasensor was developed for detecting 8-hydroxy-2'-deoxyguanosine (8-OHdG) by using 8-OHdG aptamer (Apt) as a recognition probe and N-methyl mesoporphyrin IX (NMM) as a reporter. The method is based on the conformational switching of a K(+)-stabilized G-quadruplex to a 8-OHdG-stabilized one. NMM can selectively bind to K(+)-stabilized G-quadruplex instead of 8-OHdG-stabilized one. The addition of 8-OHdG in the solution of Apt - K(+) ions leads to a sharp change in fluorescence intensity, which showed a good linear response toward 8-OHdG concentration ranging from 3.96 nM to 211 nM with a detection limit of 1.19 nM. The relative standard deviation and the recovery were 1.23-3.26% (n=11) and 94.8-106.7%, respectively. The proposed aptasensor consists of only an aptamer probe and a specific dye NMM, avoiding the complex and expensive labeling procedure. Thus it is much cheaper and more applicable.

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Lin28 is an evolutionarily conserved RNA-binding protein that inhibits processing of pre-let-7 microRNAs (miRNAs) and regulates translation of mRNAs that control developmental timing, pluripotency, metabolism, and tumorigenesis. The RNA features that mediate Lin28 binding to the terminal loops of let-7 pre-miRNAs and to Lin28-responsive elements (LREs) in mRNAs are not well defined. Here we show that Lin28 target datasets are enriched for RNA sequences predicted to contain stable planar structures of 4 guanines known as G-quartets (G4s). The imino NMR spectra of pre-let-7 loops and LREs contain resonances characteristic of G4 hydrogen bonds. These sequences bind to a G4-binding fluorescent dye, N-methyl-mesoporphyrin IX (NMM). Mutations and truncations in the RNA sequence that prevent G4 formation also prevent Lin28 binding. The addition of Lin28 to a pre-let-7 loop or an LRE reduces G4 resonance intensity and NMM binding, suggesting that Lin28 may function to remodel G4s. Further, we show that NMM inhibits Lin28 binding. Incubation of a human embryonal carcinoma cell line with NMM reduces its stem cell traits. In particular it increases mature let-7 levels, decreases OCT4, HMGA1, CCNB1, CDK4, and Lin28A protein, decreases sphere formation, and inhibits colony formation. Our results suggest a previously unknown structural feature of Lin28 targets and a new strategy for manipulating Lin28 function.

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We proposed a novel strategy which combines graphene oxide-based background reduction with RCDzyme-based enzyme strand recycling amplification for ultrahigh sensitive detection of uranyl. The RCDzyme is designed to contain a guanine (G)-rich sequence that replaces the partial sequence in an uranyl-specific DNAzyme. This multifunctional probe can act as the target recognition element, DNAzyme and the primer of signal amplification. The presence of UO2(2+) can induce the cleavage of the substrate strands in RCDzyme. Then, each released enzyme strand can hybridize with another substrate strands to trigger many cycles of the cleavage by binding uranyl, leading to the formation of more G-quadruplexes by split guanine-rich oligonucleotide fragments. The resulting G-quadruplexes could bind to N-methyl-mesoporphyrin IX (NMM), causing an amplified detection signal for the target uranyl. Next, graphene oxide-based background reduction strategy was further employed for adsorbing free ssDNA and NMM, thereby providing a proximalis zero-background signal. The combination of RCDzyme signal amplification and proximalis zero-background signal remarkably improves the sensitivity of this method, achieving a dynamic range of two orders of magnitude and giving a detection limit down to 86 pM, which is much lower than those of related literature reports. These achievements might be helpful in the design of highly sensitive analytical platform for wide applications in environmental and biomedical fields.

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