A highly selective and sensitive 1,8-naphthalimide-based fluorescent sensor for Zn2+ imaging in living cells

A new 4-amino-1,8-naphthalimide-based fluorescent sensor, with iminoacetic acid and iminoethoxyacetic acid as receptor, was developed. It was applied successfully to detect Zn²⁺ in aqueous solution and living cells. Under physiological pH conditions, it demonstrates high selectivity and sensitivity for sensing Zn²⁺ with about 7-fold enhancement in aqueous solution, with a characteristic emission band of 4-amino-1,8-naphthalimide with a green color centered at 550 nm.     

A highly selective aggregation‐induced emission fluorogen for sensitive detection of Al3+ in living cells

A Schiff's base derivative was synthesized using a condensation reaction between 8‐formyl‐7‐hydroxy‐4‐methylcoumarin and furan‐2‐carbohydrazide that produced marked aggregation‐induced emission and had excellent ability to specifically recognize aluminium ions (Al³⁺). This compound displayed faint fluorescence in the benign solvent dimethyl formamide, and exhibited obvious green fluorescence following addition of specific amounts of water. Moreover, it exhibited strong blue fluorescence after combination with Al³⁺ even in the presence of other interfering ions. These experimental results demonstrated that this derivative could be used as a fluorescence probe for Al³⁺. The advantages, including significant fluorescence change, high selectivity and sensitivity, and fast response, meant that this probe could be used both to detect Al³⁺ in water samples and for fluorescence imaging in living cells.     

Measuring zinc in living cells. A new generation of sensitive and selective fluorescent probes

New fluorescent indicators with nanomolar to micromolar affinities for Zn(2+) have been synthesized in wavelengths from UV to the far red. The UV light-excited indicators are ratiometric. The visible wavelength indicators are non-ratiometric and exhibit large and pH-independent fluorescence increases with increasing zinc concentrations, with little to no sensitivity to physiologically relevant Ca(2+) concentrations. Experiments in neuronal and non-neuronal cell cultures show the new indicators to retain their sensitivity to and selectivity for zinc after conversion to cell-permeable forms.     

Hemoglobin: A mechanism for the generation of hydroxyl radicals

Oxyhemoglobin (HbO₂) reduces Fe(III) NTA aerobically to become methemoglobin (metHb) and Fe(II)NTA. These conditions are favorable for the generation via Fenton chemistry of the hydroxyl radical that was measured by HPLC using salicylate as a probe. The levels of hydroxyl radicals generated are a function of both the percent metHb formed and the chemical nature of the buffer. The rates of formation of both metHb and hydroxyl radicals were dependent upon the concentration of Fe(III)NTA. Of the buffers tested, HEPES was the most effective scavenger of hydroxyl radicals while the other buffers scavenged in the order: HEPES > Tris > MOPS > NaCl ≈ unbuffered. The addition of catalase to remove H₂0₂ or bathophenanthroline to chelate Fe(II) inhibited virtually all hydroxyl radical formation. Carbonyl formation from free radical oxidation of amino acids was found to be 0.1 mol/mol of hemoglobin. These experiments demonstrate the ability of hemoglobin to participate directly in the generation of hydroxyl radicals mediated by redox metals, and provide insight into potential oxidative damage from metals released into the blood during some pathologic disorders including iron overload.     

New highly sensitive and selective catalytic DNA biosensors for metal ions

While remarkable progress has been made in developing sensors for metal ions such as Ca(II) and Zn(II), designing and synthesizing sensitive and selective metal ion sensors remains a significant challenge. Perhaps the biggest challenge is the design and synthesis of a sensor capable of specific and strong metal binding. Since our knowledge about the construction of metal-binding sites in general is limited, searching for sensors in a combinatorial way is of significant value. Therefore, we have been able to use a combinatorial method called in vitro selection to obtain catalytic DNA that can bind a metal ion of choice strongly and specifically. The metal ion selectivity of the catalytic DNA was further improved using a 'negative selection' strategy where catalytic DNA that are selective for competing metal ions are discarded in the in vitro selection processes. By labeling the resulting catalytic DNA with a fluorophore/quencher pair, we have made a new class of metal ion fluorescent sensors that are the first examples of catalytic DNA biosensors for metal ions. The sensors combine the high selectivity of catalytic DNA with the high sensitivity of fluorescent detection, and can be applied to the quantitative detection of metal ions over a wide concentration range and with high selectivity. The use of DNA sensors in detection and quantification of lead ions in environmental samples such as water from Lake Michigan has been demonstrated. DNA is stable, cost-effective, environmentally benign, and easily adaptable to optical fiber and microarray technology for device manufacture. Thus, the DNA sensors explained here hold great promise for on-site and real-time monitoring of metal ions in the fields of environmental monitoring, developmental biology, clinical toxicology, wastewater treatment, and industrial process monitoring.     

Differential formation of hydroxyl radicals by adriamycin in sensitive and resistant MCF-7 human breast tumor cells: implications for the mechanism of action

Adriamycin-stimulated formation of .OH in sensitive and resistant subline of human breast tumor cells (MCF-7) has been examined by electron spin resonance spectroscopy. It was shown that adriamycin significantly stimulated the formation of .OH spin adducts [5,5-dimethyl-1-pyrroline N-oxide (DMPO)-OH] in the sensitive cells but not in the resistant cells. By use of spin-broadening techniques and inhibition of .OH with high molecular weight poly(ethylene glycol), which does not enter intact cells, it was shown that 60-65% of adriamycin-induced .OH were located extracellularly and were metal ion dependent since they were decreased in the presence of desferal. Furthermore, superoxide dismutase and catalase, enzymes that detoxify superoxide and hydrogen peroxide, also significantly inhibited adriamycin-induced .OH formation and protected against the cytotoxicity of adriamycin. The differential .OH formation in these two cell lines is not due to diminished activities of flavin-dependent activating enzymes nor decreased accumulation of the drug in the cells but appears to be related to enhanced activities of detoxifying enzymes, particularly, glutathione peroxidases in the resistant cells.     

A highly sensitive and selective fluorescent probe for fluoride anions based on intramolecular charge transfer

Currently, there is a great need to develop methods for the selective detection of fluoride anions (F^–) owing to their toxicity in the environment and biological function in living systems. In this study, we developed a new fluorescent probe (probe 1) employing a Si–O bond as a highly selective recognition receptor for detecting F^– via intramolecular charge transfer. Probe 1 could detect F^– quantitatively using the turn‐on fluorescence spectroscopy method with excellent sensitivity in the range of 4–38 μM and a detection limit of 0.26 μM; the detection time was < 17 min. We anticipate that probe 1 would be used widely to monitor F^– in the environment. Copyright © 2015 John Wiley & Sons, Ltd.     

A highly parallel strategy for storage of digital information in living cells

Background

Encoding arbitrary digital information in DNA has attracted attention as a potential avenue for large scale and long term data storage. However, in order to enable DNA data storage technologies there needs to be improvements in data storage fidelity (tolerance to mutation), the facility of writing and reading the data (biases and systematic error arising from synthesis and sequencing), and overall scalability.

Results

To this end, we have developed and implemented an encoding scheme that is suitable for detecting and correcting errors that may arise during storage, writing, and reading, such as those arising from nucleotide substitutions, insertions, and deletions. We propose a scheme for parallelized long term storage of encoded sequences that relies on overlaps rather than the address blocks found in previously published work. Using computer simulations, we illustrate the encoding, sequencing, decoding, and recovery of encoded information, ultimately demonstrating the possibility of a successful round-trip read/write. These demonstrations show that in theory a precise control over error tolerance is possible. Even after simulated degradation of DNA, recovery of original data is possible owing to the error correction capabilities built into the encoding strategy. A secondary advantage of our method is that the statistical characteristics (such as repetitiveness and GC-composition) of encoded sequences can also be tailored without sacrificing the overall ability to store large amounts of data. Finally, the combination of the overlap-based partitioning of data with the LZMA compression that is integral to encoding means that the entire sequence must be present for successful decoding. This feature enables inordinately strong encryptions. As a potential application, an encrypted pathogen genome could be distributed and carried by cells without danger of being expressed, and could not even be read out in the absence of the entire DNA consortium.

Conclusions

We have developed a method for DNA encoding, using a significantly different fundamental approach from existing work, which often performs better than alternatives and allows for a great deal of freedom and flexibility of application.

     

A simple and sensitive method for monitoring drug-induced cell injury in cultured cells

A simple, sensitive method has been developed for evaluating cell injury noninvasively in monolayer cells in culture. The cell ATP pool was radiolabeled by incubating the cells with [14C]adenine. The uptake and incorporation of [14C]adenine was shown to proportional to the number of cells. As determined by HPLC, about 65-70% of the incorporated 14C label was in the ATP pool, 15-20% was in the ADP pool, and the rest was in the 5'-AMP pool. When prelabeled cells were exposed to toxic drugs (acetaminophen, calcium ionophore A-23187, or daunomycin) there was a marked decrease in cell ATP with a concomitant increase in leakage of labeled nucleotides, mainly 5'-AMP and 5'IMP. We have shown that leakage of 14C label into the medium from the prelabeled cells may be employed for quantitation of cell injury. This new measure of toxicity was shown to correlate very well with LDH leakage from the cells, which is a well accepted measure of cell injury. The leakage of 5'-[14C]AMP also correlated very well with the reduction of cell ATP in cardiac myocytes. This method has been used for monitoring drug-induced toxicity in liver cells, cardiac myocytes, and LB cells.     

Terephthalic acid: A dosimeter for the detection of hydroxyl radicals in vitro

Hydroxylation reactions of aromatic compounds have been used to detect hydroxyl radicals produced by gamma irradiation and ultrasound. The present study investigated the suitability of terephthalic acid (THA) as a hydroxyl radical dosimeter for general use in biologically relevant reactions. Hydroxyl radicals were generated by: (1) irradiating, THA with a 254 nm ultraviolet; (2) irradiating with gamma rays from a cesium source; and (3) generating hydroxyl radicals with 1 mM H₂O₂ and 10 μM Cu⁺². In each of the three experiments, a fluorescent product was generated which exhibited identical fluorescent excitation and emission spectra. THA is non-fluorescent, eliminating the problem of a high initial background. Because THA has four ring hydrogens, only one mon-hydroxylated isomer was formed. The hydrogen peroxide reaction was dependent on the presence of a metal and cupric ions were effective in enhancing the reaction. With a Cu⁺² concentration of 10 μM, the reation was linear between 0–30 mM H₂O₂. Catalase abolished the reaction at a concentration of 100 μg/ml and the effects could still be observed at 10 ng/ml, consistent with the very high rate at which catalase destroys hydrogen peroxide. Tertbutyl- hydroperoxide did not generate any fluorescence in this system which makes THA a very specific detector of hydroxyl radicals.     

DNA degradation and protein peroxidation in cells exposed to hydroxyl free radicals

The kinetics of DNA and protein damage in two lines of cultured cells exposed to radiation-generated hydroxyl free radicals were measured. The results show that DNA damage is a relatively late event, preceded by the formation of protein hydroperoxides which may play a role in the degradation of the DNA.     

A highly sensitive, mixed-phase assay for chloramphenicol acetyltransferase activity in transfected cells

We describe a simple, rapid yet extremely sensitive assay for chloramphenicol acetyltransferase (CAT) activity in extracts from transfected eukaryotic cells. Using our modified reaction conditions and the mixed-phase assay, less than 0.000010 unit of CAT activity in transfected cells can be reliably detected. The mixed-phase assay is based on the inability of the polar [3H]-acetyl-Coenzyme A (CoA) substrate to partition out of a urea containing aqueous phase into the nonpolar scintillation fluor, while the [3H]chloramphenicol reaction products partition into the toluene scintillation fluor and are quantitated by scintillation counting. The increased sensitivity of this assay is due to the optimization of the acetyl-CoA concentration, to a urea-containing aqueous phase which lowers the assay background, and to the use of extract blanks. The mixed-phase assay is simpler, is quantitative, uses less costly substrates, and is far more sensitive than the most widely used CAT assays, which require solvent extraction followed by thin-layer chromatography to separate the unreacted substrate from product.     

A highly sensitive fluorogenic probe for cytochrome P450 activity in live cells

A derivative of rhodamine 110 has been designed and assessed as a probe for cytochrome P450 activity. This probe is the first to utilize a 'trimethyl lock' that is triggered by cleavage of an ether bond. In vitro, fluorescence was manifested by the CYP1A1 isozyme with k(cat)/K(M)=8.8x10(3)M(-1)s(-1) and K(M)=0.09microM. In cellulo, the probe revealed the induction of cytochrome P450 activity by the carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin, and its repression by the chemoprotectant resveratrol.     

The production of hydroxyl radicals by adriamycin in red blood cells

Spin trapping of the free radicals formed from the interaction between adriamycin and red blood cells resulted in the formation of a hydroxyl spin adduct. The formation of hydroxyl radicals was found to be inhibited by mannitol. Hemoglobin was found not to be obligatory for the formation of hydroxyl radicals which probably result from the reduction of hydrogen peroxide by adriamycin semiquinone.     

A highly selective and sensitive boronic acid-based sensor for detecting Pd2+ ion under mild conditions

Herein, a boronic acid-based sensor was reported selectively to recognize Pd²⁺ ion. The fluorescence intensity increased 36-fold after sensor binding with 2.47 × 10⁻⁵ M of Pd²⁺ ion. It was carried out in the 99% aqueous solution for binding tests, indicating sensor having good water solubility. In addition, it is discernible that Pd²⁺ ion turned on the blue fluorescence of sensor under a UV–lamp (365 nm), while other ions (Ag⁺, Al³⁺, Ba²⁺, Ca²⁺, Cr²⁺, Cd²⁺, Co²⁺, Cs²⁺, Cu²⁺, Fe²⁺, Fe³⁺, K⁺, Li⁺, Mg²⁺, Mn²⁺, Na⁺, Ni²⁺ and Zn²⁺) did not show the similar change. Furthermore, sensor has a low limit of detection (38 nM) and high selectivity, which exhibits the potential for the development of Pd²⁺ recognition in practical environments.     

DNA-based biosensor for monitoring pH in vitro and in living cells

DNA is a promising material for the construction of a biosensor or bioindicator because its structure is sensitive to the binding of cofactors. In the current studies, we found that a combination of two DNA oligonucleotides, 5'-TCTTTCTCTTCT-3' and 5'-AGAAAGAGAAGA-3', exhibit a novel structural transition from a Watson-Crick antiparallel duplex to a parallel Hoogsteen duplex as the pH changes from pH 7.0 to 5.0. By labeling this DNA for fluorescence resonance energy transfer, we were able to develop a sensitive pH indicator that can detect changes between pH 7.0 and 5.0. Moreover, using DNA-based hairpin parallel-stranded duplex in conjunction with fluorescence microscopy, we were able to observe the pH changes in living cells during apoptosis as an easily detected change in color. These results indicate that the DNA-based pH indicator should be useful for detecting pH changes between pH 7.0 and 5.0 in living cells.     

Induction of apoptosis in HL-60 cells by photochemically generated hydroxyl radicals

Reactive oxygen species (ROS), especially hydroxyl radicals are postulated to mediate apoptosis of the cell. Here we demonstrate that hydroxyl radicals generated selectively by photolysis of a photo-Fenton reagent, N,N'-bis(2-hydroperoxy-2-methoxyethyl)-1,4,5,8-naphthaldiimide (NP-III), induce apoptosis in HL-60 (human promyelocytic leukemia) cells involving the activation of caspase-3.