Mitochondria-Targeted DNA Nanoprobe for Real-Time Imaging and Simultaneous Quantification of Ca2+ and pH in Neurons

β-Naphthothiazolium-based ratiometric fluorescent probe with ideal pKa for pH imaging in mitochondria of living cells

The weakly alkaline microenvironment (pH ~8.0) in mitochondria plays a vital role in maintaining its morphology and function. Thus monitoring mitochondrial pH (pH_mito) is of great significance. Herein, a ratiometric fluorescent probe (ENBT) for pHmito imaging in mitochondria of living cells is reported. pH variation closely correlates to intramolecular charge transfer (ICT) from naphthol to β-naphthothiazolium. ENBT exhibits a remarkable decrease on ratiometric fluorescence at λ_em1/λ_em2 = F₅₉₅/F₇₀₀ in response to pH variation within 6.30-9.29. In addition, ENBT has an ideal pKa value of 7.94 ± 0.08, which is advantageous in accurate sensing of pH_mito. Moreover, ENBT has a Stokes shift of >150 nm, which effectively eliminates the potential interference from the excitation irradiation. ENBT shows excellent capability for specific staining of mitochondria with low cytotoxicity, which is most suitable for pH_mito imaging in live cells. The probe was applied for monitoring pH_mito variation in mitochondria of live cells caused by H₂O₂, NAC (N-Acetyl-l-cysteine), NH₄Cl, carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and lactate/pyruvate. The morphological alterations of mitochondria in living cells after treatment by CCCP were further evaluated.

pH- and miRNA-Responsive DNA-Tetrahedra/Metal-Organic Framework Conjugates: Functional Sense-and-Treat Carriers

The synthesis of stimuli-responsive hybrid structures composed of drug-loaded UiO-66 metal-organic framework nanoparticles, NMOFs, locked by DNA tetrahedra gates is presented. The hybrid systems combine the high loading capacity of drugs in the porous NMOFs and the effective cell permeation properties of the DNA tetrahedra. The nucleic acid-functionalized UiO-66 NMOFs are loaded with drugs (doxorubicin, DOX, or camptothecin, CPT) or with dyes as drug models (Rhodamine 6G or fluorescein) and used to prepare stimuli-responsive carriers. In this study, two different stimuli-responsive NMOFs are presented. One system introduces the drug-loaded NMOFs locked by pH-responsive DNA tetrahedra. At acidic pH values, the gating tetrahedra are dissociated from the NMOFs through the formation of i-motif structures, resulting in the unlocking of the NMOFs and the release of the drugs. In addition, the tetrahedra gates are modified with AS1411 aptamer tethers, and these target the drug-loaded NMOFs to nucleolin receptors overexpressed in certain malignant cells. A second system involves the preparation of NMOFs loaded with drugs/dyes and gated by the microRNA (miRNA)-responsive tetrahedra (miRNA-21 or miRNA-155). In the presence of miRNAs, the dissociation of miRNA-responsive tetrahedra from the NMOFs leads to the unlocking of the NMOFs and the release of the loads. Further developments of the miRNA-responsive tetrahedra-gated hybrid carriers include the following. (i) By appropriate engineering of the miRNA gating units, the exonuclease III (Exo III)-amplified unlocking of the carriers, through the regeneration of the miRNA triggers, and the enhanced release of the loaded drugs are demonstrated. (ii) By applying mixtures of miRNA-21-responsive DNA tetrahedra-gated DOX-loaded NMOFs and miRNA-155-responsive DNA tetrahedra-gated CPT-loaded NMOFs, the multiplexed miRNA-21/miRNA-155-dictated release of the drugs is demonstrated. As compared to the analog DNA duplex-modified NMOFs, DNA tetrahedra-gated, drug-loaded NMOFs permeation into malignant MDA-MB-231 breast cancer cells presents more effective cell permeation. Effective and selective cytotoxicity toward the malignant cells, as compared to nonmalignant epithelial MCF-10A breast cells, is demonstrated due to the acidic pH, present in cancer cells, or the miRNA-21, present in MDA-MB-231 malignant cells.

Recent Advances of DNA Tetrahedra for Therapeutic Delivery and Biosensing

The chemical and self-assembly properties of nucleic acids make them ideal for the construction of discrete structures and stimuli-responsive devices for a diverse array of applications. Amongst the various three-dimensional assemblies, DNA tetrahedra are of particular interest, as these structures have been shown to be readily taken up by the cell, by the process of caveolin-mediated endocytosis, without the need for transfection agents. Moreover, these structures can be readily modified with a diverse range of pendant groups to confer greater functionality. This minireview highlights recent advances related to applications of this interesting DNA structure including the delivery of therapeutic agents ranging from small molecules to oligonucleotides in addition to its use for sensing and imaging various species within the cell.

Role of protons in calcium signaling

Thirty-six years after the publication of the important article by Busa and Nuccitelli on the variability of intracellular pH (pHi) and the interdependence of pHi and intracellular Ca2+ concentration ([Ca2+]i), little research has been carried out on pHi and calcium signaling. Moreover, the results appear to be contradictory. Some authors claim that the increase in [Ca2+]i is due to a reduction in pHi, others that it is caused by an increase in pHi. The reasons for these conflicting results have not yet been discussed and clarified in an exhaustive manner. The idea that variations in pHi are insignificant, because cellular buffers quickly stabilize the pHi, may be a limiting and fundamentally wrong concept. In fact, it has been shown that protons can move and react in the cell before they are neutralized. Variations in pHi have a remarkable impact on [Ca2+]i and hence on some of the basic biochemical mechanisms of calcium signaling. This paper focuses on the possible triggering role of protons during their short cellular cycle and it suggests a new hypothesis for an IP3 proton dependent mechanism of action.

mRNA-Activated Multifunctional DNAzyme Nanotweezer for Intracellular mRNA Sensing and Gene Therapy

Deoxyribozyme (DNAzyme) is regarded as a promising gene therapy drug. However, poor cellular uptake efficacy and low biological stability limit the utilization of DNAzyme in gene therapy. Here, we report a well-known programmable DNAzyme-based nanotweezer (DZNT) that provides a new strategy for the detection of TK1 mRNA and survivin mRNA-targeted gene silencing therapy. At the end of the DZNT arm, there are two functionalized single-stranded DNA and each consists of two parts: the segment complementary to TK1 mRNA and the split-DNAzyme segment. The hybridization with intracellular TK1 mRNA enables the imaging of TK1 mRNA. Meanwhile, the hybridization draws the split-DNAzyme close to each other and activates DNAzyme to cleave the survivin mRNA to realize gene silencing therapy. The results demonstrate that the DZNT nanocarrier has excellent cell penetration, good biocompatibility, and noncytotoxicity. DZNT can image intracellular biomolecule TK1 mRNA with a high contrast. Furthermore, the split-DNAzyme can efficiently cleave the survivin mRNA with the aid of TK1 mRNA commonly present in cancer cells, accordingly can selectively kill cancer cells, and has no harm to normal cells. Taken together, the multifunctional programmable DZNT provides a promising platform for the early diagnosis of tumors and gene therapy.

Triggered Dimerization and Trimerization of DNA Tetrahedra for Multiplexed miRNA Detection and Imaging of Cancer Cells

The reversible and switchable triggered reconfiguration of tetrahedra nanostructures from monomer tetrahedra structures into dimer or trimer structures is introduced. The triggered bridging of monomer tetrahedra by K⁺ -ion-stabilized G-quadruplexes or T-A•T triplexes leads to dimer or trimer tetrahedra structures that are separated by crown ether or basic pH conditions, respectively. The signal-triggered dimerization/trimerization of DNA tetrahedra structures is used to develop multiplexed miRNA-sensing platforms, and the tetrahedra mixture is used for intracellular sensing and imaging of miRNAs.

Synthesis of fluorescent nanoprobe with simultaneous response to intracellular pH and Zn2+ for tumor cell distinguishment

A novel dual-functional nanoprobe was designed and synthesized by facile assembly of quinoline derivative (PEIQ) and meso-tetra (4-carboxyphenyl) porphine (TCPP) via electrostatic interaction for simultaneous sensing of fluorescence of Zn²⁺ and pH. Under the single-wavelength excitation at 400 nm, this nanoprobe not only exhibits "OFF-ON" green fluorescence at 512 nm by specific PEIQ-Zn²⁺ chelation, but also presents red fluorescence enhancement at 654 nm by H⁺-triggered TCPP release. The nanoprobe demonstrated excellent sensing performance with a good linear range (Zn²⁺, 1-40 μM; pH, 5.0-8.0), low detection limit (Zn²⁺, 0.88 μM), and simultaneous response towards Zn²⁺ and pH in pure aqueous solution within 2 min. More importantly, this dual-functional nanoprobe demonstrates the capability of discerning cancerous cells from normal cells, as evidenced by the fact that cancerous HepG2 cells in tumor microenvironment exhibit substantially higher red fluorescence and significantly lower green fluorescence than normal HL-7702 cells. The simultaneous, real-time fluorescence imaging of multiple analytes in a living system could be significant for cell analysis and tracking, cancer diagnosis, and even fluorescence-guided surgery of tumors.

The interaction of ASIC1a and ERS mediates nerve cell apoptosis induced by insulin deficiency

Diabetes-related brain complications are the most serious complications of terminal diabetes. The increasing evidence have showed that the predisposing factor is not only hyperglycemia, but also insulin deficiency. In this study, we demonstrated that insulin deficiency was involved in the apoptosis of nerve cells, and it was related to the interaction between acid-sensitive ion channel 1a (ASIC1a) and endoplasmic reticulum stress (ERS). By silencing C/EBP homologous protein (CHOP) and ASIC1a, the pro-apoptotic effect of insulin deficiency on NS20y cells was relieved. Further research found that the binding of CHOP and C/EBPα was increased in the nucleus of cells cultured without insulin, and C/EBPα was competitively inhibited as a negative regulator of ASIC1a, which further increased the ERS and lead to neuronal apoptosis. In summary, ERS and ASIC1a play an important role in neurological damage caused by insulin deficiency. Our finding may lead to new ideas and treatment of diabetes-related brain complications.

Simultaneous detection and speciation of mono- and di-valent copper ions with a dual-channel fluorescent nanoprobe

Redox cyclings between mono-/di-valent copper oxidation states occur in electron transfer reactions that underlie their biological functions. We report herein a dual channel fluorescent nanoprobe for the detection of mono- and di-valent copper ions. The probe, BSA-CDs@RBH/BCS, is designed by decorating carbon dots (CDs) on BSA encapsulated rhodamine hydrazide (RBH) and conjugating with bathocuproine disulfonate (BCS). Cu²⁺ catalyzes the hydrolysis of RBH, and the formed rhodamine B (RhB) shows emission at λ_ex/λ_em = 360/575 nm which ensures Cu²⁺ detection. BSA reduces Cu²⁺ to Cu⁺ and the BCS-Cu⁺ chelate shows emission at λ_ex/λ_em 360/450 nm which ensures Cu⁺ assay. Thus, the dual-channel fluorescence enables speciation of Cu²⁺ and Cu⁺.

The applications of functionalized DNA nanostructures in bioimaging and cancer therapy

Deoxyribonucleic acid (DNA) is a molecular carrier of genetic information that can be fabricated into functional nanomaterials in biochemistry and engineering fields. Those DNA nanostructures, synthesized via Watson-Crick base pairing, show a wide range of attributes along with excellent applicability, precise programmability, and extremely low cytotoxicity in vitro and in vivo. In this review, the applications of functionalized DNA nanostructures in bioimaging and tumor therapy are summarized. We focused on approaches involving DNA origami nanostructures due to their widespread use in previous and current reports. Non-DNA origami nanostructures such as DNA tetrahedrons are also covered. Finally, the remaining challenges and perspectives regarding DNA nanostructures in the biomedical arena are discussed.

Surface functionalized red fluorescent dual-metallic Au/Ag nanoclusters for endoplasmic reticulum imaging

An efficient method is reported to prepare endoplasmic reticulum-targetable dual-metallic gold-silver nanoclusters, denoted as ER-Au/Ag nanoclusters (NCs), by virtue of a rationally designed molecular ligand. The prepared ER-Au/Ag NCs possesses red-emitting fluorescence with a strong emission at 622 nm and a high fluorescence quantum yield of 5.1%, which could avoid the influence of biological auto-fluorescence. Further investigation results showed that ER-Au/Ag NCs exhibited superior photostability, minimal cytotoxicity, and ER-targeting capability. Enabled by these meritorious features, ER-Au/Ag NCs have been successfully employed for long-term bioimaging of ER in living cells.Graphical abstract A sensitive non-enzymatic fluorescent glucose probe-based ZnO nanorod decorated with Au nanoparticles.

A Robust Au-C≡C Functionalized Surface: Toward Real-Time Mapping and Accurate Quantification of Fe2+ in the Brains of Live AD Mouse Models

Described here is that Au-C≡C bonds showed the highest stability under biological conditions, with abundant thiols, and the best electrochemical performance compared to Au-S and Au-Se bonds. The new finding was also confirmed by theorical calculations. Based on this finding, a specific molecule for recognition of Fe²⁺ was designed and synthesized, and used to create a selective and accurate electrochemical sensor for the quantification of Fe²⁺ . The present ratiometric strategy demonstrates high spatial resolution for real-time tracking of Fe²⁺ in a dynamic range of 0.2-120 μM. Finally, a microelectrode array with good biocompatibility was applied in imaging and biosensing of Fe²⁺ in the different regions of live mouse brains. Using this tool, it was discovered that the uptake of extracellular Fe²⁺ into the cortex and striatum was largely mediated by cyclic adenosine monophosphate (cAMP) through the CREB-related pathway in the brain of a mouse with Alzheimer's disease.

Full-color fluorescent carbon quantum dots

Quantum dots have innate advantages as the key component of optoelectronic devices. For white light-emitting diodes (WLEDs), the modulation of the spectrum and color of the device often involves various quantum dots of different emission wavelengths. Here, we fabricate a series of carbon quantum dots (CQDs) through a scalable acid reagent engineering strategy. The growing electron-withdrawing groups on the surface of CQDs that originated from acid reagents boost their photoluminescence wavelength red shift and raise their particle sizes, elucidating the quantum size effect. These CQDs emit bright and remarkably stable full-color fluorescence ranging from blue to red light and even white light. Full-color emissive polymer films and all types of high-color rendering index WLEDs are synthesized by mixing multiple kinds of CQDs in appropriate ratios. The universal electron-donating/withdrawing group engineering approach for synthesizing tunable emissive CQDs will facilitate the progress of carbon-based luminescent materials for manufacturing forward-looking films and devices.

Hairpin DNA assisted dual-ratiometric electrochemical aptasensor with high reliability and anti-interference ability for simultaneous detection of aflatoxin B1 and ochratoxin A

The simultaneous detection of multiple mycotoxins in grains is significant due to the enhanced toxicity induced by their synergistic effects. In this work, a dual-ratiometric electrochemical aptasensing strategy for the simultaneous detection of aflatoxin B1 (AFB1) and ochratoxin A (OTA) was developed. Here, an anthraquinone-2-carboxylic acid (AQ)-labelled complementary DNA (cDNA) was used to provide separate and specific binding sites to assemble the ferrocene-labelled AFB1 aptamer (Fc-Apt1) and methylene blue-labelled OTA aptamer (MB-Apt2). The target-induced current ratios of I_Fc/I_AQ and I_MB/I_AQ were then used to quantitatively relate to AFB1 and OTA, respectively. Following this principle, two types of aptasensors involving the hairpin DNA (hDNA) and linear single-stranded DNA (ssDNA) as the cDNA were fabricated for performance comparisons. The results revealed that hairpin DNA with a rigid 2D structure can greatly improve the assembly and recognition efficiency of the sensing interface, which makes the hDNA-based aptasensor possess high sensitivity, reliability and anti-interference ability. The hDNA-based aptasensor exhibited a detection range of 10-3000 pg mL^-1 for AFB1 and 30-10000 pg mL^-1 for OTA, respectively, with no observable cross-reactivity. Furthermore, the aptasensor was applied to analyze corn and wheat samples, and the reliability was validated by HPLC-MS/MS. Our work has presented a novel way for fabricating a high-performance aptasensor for simultaneous detection of multiple mycotoxins.

Programming Biomimetically Confined Aptamers with DNA Frameworks

Active sites of proteins are generally encapsulated within three-dimensional peptide scaffolds that provide the molecular-scale confinement microenvironment. Nevertheless, the ability to tune thermodynamic stability in biomimetic molecular confinement relies on the macromolecular crowding effect of lack of stoichiometry and reconfigurability. Here, we report a framework nucleic acid (FNA)-based strategy to increase thermodynamic stability of aptamers. We demonstrate that the molecular-scale confinement increases the thermodynamic stability of aptamers via facilitated folding kinetics, which is confirmed by the single-molecule FRET (smFRET). Unfavorable conformations of aptamers are restricted as revealed by the Monte Carlo simulation. The binding affinity of the DNA framework-confined aptamer is improved by ∼3-fold. With a similar strategy we improve the catalytic activity of hemin-binding aptamer. Our approach thus shows high potential for designing protein-mimicking DNA nanostructures with enhanced binding affinity and catalytic activity for biosensing and biomedical engineering.

A DNA-Based FLIM Reporter for Simultaneous Quantification of Lysosomal pH and Ca2+ during Autophagy Regulation

pH and Ca²⁺ play important roles in regulating lysosomal activity and lysosome-mediated physiological and pathological processes. However, effective methods for simultaneous determination of pH and Ca²⁺ is the bottleneck. Herein, a single DNA-based FLIM reporter was developed for real-time imaging and simultaneous quantification of pH and Ca²⁺ in lysosomes with high affinity, in which a specific probe for recognition of Ca²⁺ was assembled onto a DNA nanostructure together with pH-responsive and lysosome-targeted molecules. The developed DNA reporter showed excellent biocompatibility and long-term stability up to ∼56 h in lysosomes. Using this powerful tool, it was discovered that pH was closely related to Ca²⁺ concentration in lysosome, whereas autophagy can be regulated by lysosomal pH and Ca²⁺. Furthermore, Aβ-induced neuronal death resulted from autophagy abnormal through lysosomal pH and Ca²⁺ changes. In addition, lysosomal pH and Ca²⁺ were found to regulate the transformation of NSCs, resulting in Rapamycin-induced antiaging.

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A DNA-based FLIM reporter was developed for tracking lysosomal pH and Ca²⁺

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It was found that autophagy could be induced by lysosomal pH and Ca²⁺

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Aβ-induced neuronal death was due to pH_ly- and [Ca²⁺]_ly-mediated autophagy abnormal

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Antiaging-related transformation of qNSCs can be regulated by pH_ly and [Ca²⁺]_ly

An enzyme-free amplification strategy based on two-photon fluorescent carbon dots for monitoring miR-9 in live neurons and brain tissues of Alzheimer's disease mice

An enzyme-free amplification strategy based on two-photon fluorescent carbon dots for monitoring miR-9 in live neurons and brain tissues of Alzheimer's disease (AD) mice. Notably, using our developed probe, miR-9 was found to be up-regulated in early onset AD, while it was found to be down regulated to lower than the normal level in late onset AD.

Rapid and Targeted Photoactivation of Ca2+ Channels Mediated by Squaraine To Regulate Intracellular and Intercellular Signaling Processes

As an important cellular signal transduction messenger, Ca²⁺ has the capability to regulate cell function and control many biochemical processes, including metabolism, gene expression, and cell survival and death. Here, we introduce an accessible method for the photoactivation of Ca²⁺ channels mediated by squaraine (SQ) to rapidly induce cellular Ca²⁺ release and activate signal transduction. With a short preparation time, the maximum Ca²⁺ concentration increase could reach approximately 450% in 30 s, resulting from marked Ca²⁺ release channel opening in the endoplasmic reticulum (ER). This release was enhanced by another target location of SQ, that is, the outer mitochondrial-associated membrane where Ca²⁺ channels accumulate, and by the consequent large amounts of reactive oxygen species resulting from the respiratory chain activity stimulated by Ca²⁺ load. We used this method to investigate cellular signal transduction in different cancer cells and revealed rapid intracellular Ca²⁺ flow, unidirectional intercellular signaling processes, and neuronal signaling activity, which demonstrated the potential and convenience of the method for routine Ca²⁺ research.

Real-Time Imaging and Simultaneous Quantification of Mitochondrial H2O2 and ATP in Neurons with a Single Two-Photon Fluorescence-Lifetime-Based Probe

Mitochondrial oxidative stress and energy metabolism are vital biological events and are involved in various physiological and pathological processes such as apoptosis and necrosis. However, it remains unclear how the dynamic patterns of mitochondrial hydrogen peroxide (H₂O₂) and adenosine-5'-triphosphate (ATP) change in these events and, more importantly, how they affect each other. Herein, we developed a single two-photon fluorescence-lifetime-based probe (TFP), which offered real-time imaging and the simultaneous determination of mitochondrial H₂O₂ and ATP changes in two well-separated fluorescence channels without spectral crosstalk. The fluorescence lifetime of TFP exhibited good responses and selectivity in the detection ranges of 0.4-10 μM H₂O₂ and 0.5-15 mM ATP, taking advantage of accuracy and the quantitative ability of fluorescence lifetime imaging. Using this useful probe, we studied the relationship between H₂O₂ and ATP in mitochondria and visualized the dynamic level changes of mitochondrial H₂O₂ and ATP induced by the superoxide anion (O₂^•-). It was discovered that O₂^•- stimulation in a short period of time (8 min) temporarily changes the levels of H₂O₂ and ATP in mitochondria, and neurons were capable of recovering to the initial state in a short time. However, increasing time of up to 50 min of O₂^•- stimulation led to permanent oxidative damage and an energy deficiency. Meanwhile, it was first found that the exogenous stimulation of O₂^•- and H₂O₂ had different impacts on the levels of mitochondrial H₂O₂ and ATP, in which O₂^•- demonstrated more severe and negative consequences. As a matter of fact, this work not only has provided a general molecular design methodology for multiple species imaging but also has revealed oxidative-stress-induced intracellular functions related to H₂O₂ and ATP in mitochondria based on this developed TFP probe.

Complementary Oligonucleotide Conjugated Multicolor Carbon Dots for Intracellular Recognition of Biological Events

By using complementary DNA sequences as surface ligands, we selectively allow two individual diffusing "dual-color" carbon dots to interact in situ and in vitro. Spontaneous nanoscale oxidation of surface-abundant nitroso-/nitro-functionalities leads to two distinctly colored carbon dots (CD) which are isolated by polarity driven chromatographic separation. Green- and red-emitting carbon dots (gCD and rCD) were decorated by complementary single-stranded DNAs which produce a marked increase in the fluorescence emission of the respective carbon dots. Mutual colloidal interactions are achieved through hybridization of complementary DNA base pairs attached to the respective particles, resulting in quenching of their photoluminescence. The observed post-hybridization quenching is presumably due to a combined effect from an aggregation of CDs post duplex DNA formation and close proximity of multicolored CDs, having overlapped spectral regions leading to a nonradiative energy transfer process possibly released as heat. This strategy may contribute to the rational design of mutually interacting carbon dots for a better control over the resulting assembly structure for studying different biological phenomenon including molecular cytogenetics. One of the newly synthesized CDs was successfully used to image intracellular location of GAPDH mRNA using an event of change in fluorescence intensity (FI) of CDs. This selectivity was introduced by conjugating an oligonucleotide harboring complementary sequence to GAPDH mRNA. FI of this conjugated carbon dot, rCD-GAPDH, was also found to decrease in the presence of Ca2+, varied in relation to H+ concentrations, and could serve as a tool to quantify the intracellular concentrations of Ca2+ and pH value (H+) which can give important information about cell survival. Therefore, CD-oligonucleotide conjugates could serve as efficient probes for cellular events and interventions.

An endoplasmic reticulum-targeted two-photon fluorescent probe for bioimaging of HClO generated during sleep deprivation

With the development of social society, sleep deprivation has become a serious and common issue. Previous studies documented that there is a correlation between sleep deprivation and oxidative stress. However, the information of sleep deprivation related ROS has rarely been obtained. Also, it has been demonstrated that sleep deprivation can induce endoplasmic reticulum (ER) stress. As such, for a better understanding of sleep deprivation as well as its related diseases, it is important to develop probes with ER-targeting ability for detecting ROS generated in this process. Herein, a novel two-photon fluorescent molecular probe, JX-1, was designed for sensing HClO in live cells and zebrafish. The investigation data showed that in addition to real-time response (about 150 s), the probe also exhibited high sensitivity and selectivity. Moreover, the probe JX-1 demonstrated two-photon fluorescence, low cytotoxicity and ER targeting ability. These prominent properties enabled the utilization of the probe for monitoring exogenous and endogenous HClO in both live cells and zebrafish. Using this useful tool, it was found that sleep deprivation can induce the generation of HClO in zebrafish.

Trichromatic-emission and dual-ratio semiconducting polymer dots as fluorescent probe for simultaneous quantification of Cu2+ and pH in vitro and in vivo

Polymer dots emitting in the red, green and blue color regions, have been successfully applied as lysosome-targeting nanoprobes for the simultaneous detection and multicolor imaging of pH and Cu²⁺ in HeLa cells and zebrafish.

Aptamer-Functionalized Activatable DNA Tetrahedron Nanoprobe for PIWI-Interacting RNA Imaging and Regulating in Cancer Cells

It has been reported that PIWI-interacting RNAs (piRNAs) play critical roles in activating invasion and metastasis, evading growth suppressors, and sustaining proliferative signaling of cancer and can be regarded as a novel biomarker candidate. Thus, it is necessary to develop an effective method for imaging and regulating cancer-related piRNAs to diagnose and treat cancers. Herein, we designed aptamer-functionalized activatable DNA tetrahedron nanoprobes (apt-ADTNs) to image and regulate endogenous piRNAs in cancer cells. As proof of concept, overexpressed piRNA-36026 in MCF-7 cells was used for this study. In brief, aptamer AS1411 and piRNA-36026 antisequence with Cy5 fluorescent dye are appended from the DNA tetrahedron; then, a short oligonucleotide with black hole quencher 2 (Q-oligo) is complementary with piRNA-36026 antisequence to quench the fluorescence of Cy5. The apt-ADTNs can recognize the MCF-7 cells through aptamer AS1411, and then enter the cells. Q-oligo is detached from the apt-ADTNs because of the binding between apt-ADTNs and piRNA-36026, leading to the recovery of the Cy5 fluorescence signal. Meanwhile, the hybridization of apt-ADTNs and piRNA-36026 results in down-regulating of dissociative piRNA-36026 in cytoplasm and the subsequent apoptosis of MCF-7 cells. As the achievement of synchronously imaging and regulating piRNA-36026 in MCF-7 cells, we believe that this design holds great promise in application of diagnosis and therapy for cancer.

Three-dimensional DNA nanostructures to improve the hyperbranched hybridization chain reaction

Nonenzymatic nucleic acid amplification techniques (e.g. the hybridization chain reaction, HCR) have shown promising potential for amplified detection of biomarkers.

Nonenzymatic nucleic acid amplification techniques (e.g. the hybridization chain reaction, HCR) have shown promising potential for amplified detection of biomarkers. However, the traditional HCR occurs through random diffusion of DNA hairpins, making the kinetics and efficiency quite low. By assembling DNA hairpins at the vertexes of tetrahedral DNA nanostructures (TDNs), the reaction kinetics of the HCR is greatly accelerated due to the synergetic contributions of multiple reaction orientations, increased collision probability and enhanced local concentrations. The proposed quadrivalent TDN (qTDN)-mediated hyperbranched HCR has a ∼70-fold faster reaction rate than the traditional HCR. The approximately 76% fluorescence resonance energy transfer (FRET) efficiency obtained is the highest in the reported DNA-based FRET sensing systems as far as we know. Moreover, qTDNs modified by hairpins can easily load drugs, freely traverse plasma membranes and be rapidly cross-linked via the target-triggered HCR in live cells. The reduced freedom of movement as a result of the large crosslinked structure might constrain the hyperbranched HCR in a confined environment, thus making it a promising candidate for in situ imaging and photodynamic therapy. Hence, we present a paradigm of perfect integration of DNA nanotechnology with nucleic acid amplification, thus paving a promising way to the improved performance of nucleic acid amplification techniques and their wider application.

A ratiometric fluorescent DNA nanoprobe for cerebral adenosine triphosphate assay

A silver nanocluster-based ratiometric fluorescent nanosensor was developed for the determination of ATP in the cerebrospinal fluid of a mouse brain. Using this useful tool with good stability and high selectivity as well as a wide linear detection range, it was found that the ATP concentration in a mouse brain with Alzheimer's disease was 2300-fold higher than that in a normal one.

Ratiometric fluorescent nanoprobes for visual detection: Design principles and recent advances - A review

Signal generation techniques for visual detection of analytes have received a great deal of attention in various sensing fields. These approaches are considered to be advantageous when instrumentation cannot be employed, such as for on-site assays, point-of-care tests, and he althcare diagnostics in resource-constrained areas. Amongst various visual detection approaches explored for non-invasive quantitative measurements, ratiometric fluorescence sensing has received particular attention as a potential method to overcome the limitations of intensity-based probes. This technique relies on changes in the intensity of two or more emission bands (induced by an analyte), resulting in an effective internal referencing which improves the sensitivity of the detection. The self-calibration, together with the unique optophysical properties of nanoparticles (NPs) have made the ratiometric fluorescent nanoprobes more sensitive and reliable, which in turn, can result in more precise visual detection of the analytes. Over the past few years, a vast number of ratiometric sensing probes using nanostructured fluorophores have been designed and reported for a wide variety of sensing, imaging, and biomedical applications. In this work, a review on the NP-based ratiometric fluorescent sensors has been presented to meticulously elucidate their development, advances and challenges. With a special emphasis on visual detection, the most important steps in the design of fluorescent ratiometric nanoprobes have been given and based on different classes of analytes, recent applications of fluorescent ratiometric nanoprobes have been summarized. The challenges for the future use of the technique investigated in this review have been also discussed.

Fluorescent probes for organelle-targeted bioactive species imaging

The dynamic fluctuations of bioactive species in living cells are associated with numerous physiological and pathological phenomena. The emergence of organelle-targeted fluorescent probes has significantly facilitated our understanding on the biological functions of these species. This review describes the design, applications, challenges and potential directions of organelle-targeted bioactive species probes.

Bioactive species, including reactive oxygen species (ROS, including O₂˙^–, H₂O₂, HOCl, ¹O₂, ˙OH, HOBr, etc.), reactive nitrogen species (RNS, including ONOO^–, NO, NO₂, HNO, etc.), reactive sulfur species (RSS, including GSH, Hcy, Cys, H₂S, H₂S_n, SO₂ derivatives, etc.), ATP, HCHO, CO and so on, are a highly important category of molecules in living cells. The dynamic fluctuations of these molecules in subcellular microenvironments determine cellular homeostasis, signal conduction, immunity and metabolism. However, their abnormal expressions can cause disorders which are associated with diverse major diseases. Monitoring bioactive molecules in subcellular structures is therefore critical for bioanalysis and related drug discovery. With the emergence of organelle-targeted fluorescent probes, significant progress has been made in subcellular imaging. Among the developed subcellular localization fluorescent tools, ROS, RNS and RSS (RONSS) probes are highly attractive, owing to their potential for revealing the physiological and pathological functions of these highly reactive, interactive and interconvertible molecules during diverse biological events, which are rather significant for advancing our understanding of different life phenomena and exploring new technologies for life regulation. This review mainly illustrates the design principles, detection mechanisms, current challenges, and potential future directions of organelle-targeted fluorescent probes toward RONSS.

A SERS Optophysiological Probe for the Real-Time Mapping and Simultaneous Determination of the Carbonate Concentration and pH Value in a Live Mouse Brain

To have a profound understanding of the physiological and pathological processes in a brain, both chemical and electrical signals need to be recorded, but this is still very challenging. Herein, micrometer- to nanometer-sized SERS optophysiological probes were created to determine both the CO₃ ^2- concentration and the pH in live brains and neurons because both species play important roles in regulating the acid-base balance in the brain. A ratiometric SERS microarray of eight microprobes with tip sizes of 5 μm was established and used for the first time for real-time mapping and simultaneous quantification of CO₃ ^2- and pH in a live brain. We found that both the CO₃ ^2- concentration and the pH value dramatically decreased under ischemic conditions. The present SERS technique can be combined with electrophysiology without cross-talk to record both electrical and chemical signals in brains. To deepen our understanding of the mechanism of ischemia on the single-cell level, a SERS nanoprobe with a tip size of 200 nm was developed for use in a single neuron.

A yellow-emissive carbon nanodot-based ratiometric fluorescent nanosensor for visualization of exogenous and endogenous hydroxyl radicals in the mitochondria of live cells

A ratiometric fluorescent nanosensor with high sensitivity was developed for visualization of hydroxyl radicals in the mitochondria of live cells.