Are other fluorescent tags used instead of ethidium bromide safer?

Staining Properties of Selected Commercial Fluorescent Dyes Toward B- and Z-DNA

The properties of six commonly used, commercially available, fluorescent dyes were compared in staining right-handed B-DNA and left-handed Z-DNA. All showed different degree of fluorescence turn-on in the presence of B-DNA, but very little in the presence of Z-DNA. The optimal range of dye-DNA ratios of DNA was determined. While these dyes do not provide a turn-on type probe for Z-DNA, staining between B- and Z-DNA using dyes such as SYBR Green I was shown to be useful in tracking the kinetics of conformational changes between these two forms of DNA. Finally, SYBR Green I showed unique circular dichroism patterns in 4 M NaCl that change in the presence of double stranded DNA, both in the visible and UV range.

3, 5-Dihydroxy 4', 7-dimethoxyflavone-DNA interaction study for nucleic acid detection and differential cell staining

The present study is focused on application of a natural compound, 3, 5-dihydroxy 4', 7-dimethoxyflavone (DHDM) from a medicinal plant Alpinia nigra for nucleic acid detection and differential cell staining. DHDM was found to interact with nucleic acid and forms complex, which was investigated for various applications. It was successfully utilized to visualize plasmid, genomic, and ds-linear DNA in agarose gel electrophoresis without affecting the DNA mobility in the gel. Fluorescence of DHDM increased several fold upon binding to dsDNA. Photostability of the compound was assessed and showed photobleaching effect that decreased gradually over time. Application of the compound was further extended to differential cell staining. When observed in fluorescence microscope, DHDM stained the dead cells and differentiated them from live cells in the case of bacterial, yeast, and mammalian cells. Higher concentration of the compound was found to be less cytotoxic to cancerous cells. Nucleic acid staining dyes like Ethidium bromide (EtBr), Propidium iodide (PI), etc. are carcinogens and environmental pollutants and therefore DHDM a natural compound, is a major benefit and thus can serve as an alternative to the current dyes.

Efficient removal of ethidium bromide from aqueous solutions using chromatin-loaded chitosan polyvinyl alcohol composites

In this work, a novel chromatin-loaded chitosan polyvinyl alcohol composite was developed as a simple, efficient and environmentally friendly adsorbent for the efficient removal of ethidium bromide (EtBr). SEM images showed that the composites were characterized by dense porous and uniformly distributed morphology. The BET analysis showed the presence of mesopores and macropores in the composites. FTIR and XRD results showed that the chromatin was uniformly dispersed in the chitosan-polyvinyl alcohol carrier through hydrogen bonding. The fluorescence microscopy images showed the change of fluorescence effect before and after the adsorption of the material, which indicated that the chromatin was uniformly distributed in the composites and had a good adsorption effect. The optimal experimental conditions were T = 30℃, t = 120 min, pH = 7.4, m = 0.2 g when the composite with only 5% chromatin content had the ability to adsorb EtBr efficiently (minimum concentration 2 mg·L-1: adsorption rate 99%; maximum concentration 20 mg·L-1: adsorption rate 90%).The adsorption kinetics and thermodynamics showed that the EtBr adsorption kinetics of the composite conformed to the pseudo-second-order kinetic model (0.995 < R2 < 0.999) and the Freundlich isothermal model, and was a spontaneous process (ΔH < 0). This study on the immobilization of chromatin will provide a new way and reference for the application of chromatin in the treatment of EtBr pollutants.

A Novel and Quantitative Detection Assay (effluxR) for Identifying Efflux-Associated Resistance Genes Using Multiplex Digital PCR in Clinical Isolates of Pseudomonas aeruginosa

The rise of multidrug resistance of Pseudomonas aeruginosa highlights an increased need for selective and precise antimicrobial treatment. Drug efflux pumps are one of the major mechanisms of antimicrobial resistance found in many bacteria, including P. aeruginosa. Detection of efflux genes using a polymerase chain reaction (PCR)-based system would enable resistance detection and aid clinical decision making. Therefore, we aimed to develop and optimize a novel method herein referred to as "effluxR detection assay" using multiplex digital PCR (mdPCR) for detection of mex efflux pump genes in P. aeruginosa strains. The annealing/extension temperatures and gDNA concentrations were optimized to amplify mexB, mexD, and mexY using the multiplex quantitative PCR (mqPCR) system. We established the optimal mqPCR conditions for the assay (Ta of 59 °C with gDNA concentrations at or above 0.5 ng/µL). Using these conditions, we were able to successfully detect the presence of these genes in a quantity-dependent manner. The limit of detection for mex genes using the effluxR detection assay with mdPCR was 0.001 ng/µL (7.04-34.81 copies/µL). Moreover, using blind sample testing, we show that effluxR detection assay had 100% sensitivity and specificity for detecting mex genes in P. aeruginosa. In conclusion, the effluxR detection assay, using mdPCR, is able to identify the presence of multiple mex genes in P. aeruginosa that may aid clinical laboratory decisions and further epidemiological studies.

Chromatin extracted from common carp testis as an economical and easily available adsorbent for ethidium bromide decontamination

The waste of ethidium bromide (EtBr) used in the laboratory will bring a great burden to the environment, which need to be solved urgently. In the present paper, an efficient and inexpensive method for EtBr removal using chromatin extracted from common carp testis was investigated. The observation of fluorescence microscopy showed that chromatin had similar property to DNA for selective adsorption of EtBr. The results of batch adsorption showed that the removal efficiency of EtBr by chromatin exceeded 99% at pH 7.4 and 30 °C for 3 min with the EtBr concentration of 2 mg L⁻¹ and the chromatin dosage of 0.5 g L⁻¹, and the maximum adsorption amount of chromatin was 45.73 mg g⁻¹. Further, the analysis of kinetic and isotherm suggested that the adsorption followed Pseudo-second-order kinetics and Langmuir isotherm model, and the calculated maximum theoretical adsorption amount of chromatin to EtBr was 48.08 mg g⁻¹. According to thermodynamic analysis, chromatin adsorption of EtBr was a spontaneous process dominated by hydrogen bonding and van der Waals forces. This work will not only offer an adsorbent for EtBr decontamination, also provide a possibility for EtBr analogs removal.

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The inexpensive bio-adsorbent was prepared from common carp testis by-production.

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The bio-adsorbent was applied in EtBr decontamination.

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The maximum adsorption amount of EtBr by chromatin was up to 45.73 mg g⁻¹, while the maximum adsorption amount of EtBr by activated carbon was only 0.46 mg g⁻¹.

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The adsorption of EtBr by chromatin followed Pseudo-second-order kinetics and Langmuir isotherm model.

"Technical Note:" Optimisation of Diamond™ Nucleic Acid Dye preparation, application, and visualisation, for latent DNA detection

A targeted sampling approach of latent DNA, deposited when a person makes contact with a surface, can prove challenging during crime scene or evidence processing, with the sampling of latent DNA often relying on the expert judgement from crime scene officers and forensic examiners. As such, the ability to use the quick and robust screening tool Diamond™ Nucleic Acid Dye (DD) was explored, with a focus on the visualisation of latent DNA on non-porous substrates, namely polypropylene, acrylic, aluminium, PVC composite material, glass, and crystalline silicon. The application of DD was performed according to methods reported in literature, where 10 µL of the dye solution (20-fold dilution of DD in 75% EtOH) was applied onto a variety of non-porous substrates via a micropipette and then subsequently visualised using a portable fluorescence microscope. It was discovered that there was scope for improvement in the reported methods due to the observation of crystal formations on all test substrates upon drying of the DD, resulting in the impaired visualisation of latent DNA and fingerprint detail. Thus, changes to the EtOH water ratio of the dye solution, and changes to the mode of dye application from a micropipette to a spray application, were explored to improve the drying time of the dye and mitigate the formation of crystals. While changes to the EtOH water ratio did not improve the overall drying time, the mode of dye application enhanced visualisation, with a spray application eliminating the formation of crystals no matter the EtOH water ratio. Visualisation with a portable Dino-Lite and Zeiss Widefield fluorescence microscope were also explored, with the Zeiss Widefield fluorescence microscope proving to be useful in whole print imaging and a more efficient imaging tool in a laboratory setting.

A perspective review on impact and molecular mechanism of environmental carcinogens on human health

Cancer is one of the leading causes of death all around the world. It is a group of diseases characterized by abnormal and uncontrollable division of cells leading to severe health conditions and fatality if remains undiagnosed till later stages. Cancer can be caused due to mutation or sudden alterations by effect of certain external agents. Agents that can cause sudden alterations in the genetic content of an individual are known as mutagens. Mutations can lead to permanent changes in the genetic constituency of an individual and possibly lead to cancer. Mutagenic agents that possess the capacity to induce cancer in humans are called carcinogens. Carcinogens may be naturally present in the environment or generated by anthropogenic activities. However, with the progress in molecular techniques, genetic and/or epigenetic mechanisms of carcinogenesis of a wide range of carcinogens have been elucidated. Present review aims to discuss different types of environmental carcinogens and their respective mechanisms responsible for inducing cancer in humans.

Hydrogen sulfide in longevity and pathologies: Inconsistency is malodorous

Hydrogen sulfide (H₂S) is one of the biologically active gases (gasotransmitters), which plays an important role in various physiological processes and aging. Its production in the course of methionine and cysteine catabolism and its degradation are finely balanced, and impairment of H₂S homeostasis is associated with various pathologies. Despite the strong geroprotective action of exogenous H₂S in C. elegans, there are controversial effects of hydrogen sulfide and its donors on longevity in other models, as well as on stress resistance, age-related pathologies and aging processes, including regulation of senescence-associated secretory phenotype (SASP) and senescent cell anti-apoptotic pathways (SCAPs). Here we discuss that the translation potential of H₂S as a geroprotective compound is influenced by a multiplicity of its molecular targets, pleiotropic biological effects, and the overlapping ranges of toxic and beneficial doses. We also consider the challenges of the targeted delivery of H₂S at the required dose. Along with this, the complexity of determining the natural levels of H₂S in animal and human organs and their ambiguous correlations with longevity are reviewed.

In vivo comet assay in rabbit corneal epithelial cells following ocular instillation with genotoxic compounds

Background

The in vivo comet assay is used to evaluate the genotoxic potential of compounds by detecting DNA strand breaks in cells isolated from animal tissue. The comet assay of hepatocytes is well established; however, the levels of systemic drug exposure following systemic administration are often insufficient to evaluate the genotoxic potential of compounds on the ocular surface following ocular instillation. To investigate the possibility of using the comet assay as a genotoxic evaluation tool for the ocular surface, we performed this assay on the corneal epithelial cells of rabbit eyes 2 h after the single ocular instillation of five genotoxic compounds, namely ethidium bromide, 1,1′-dimethyl-4,4′-bipyridinium dichloride (paraquat), methyl methanesulfonate (MMS), acrylamide, and 4-nitroquinoline 1-oxide (4-NQO).

Results

The mean % tail DNA, as an indicator of DNA damage, in the corneal epithelial cells treated with ethidium bromide, MMS, and 4-NQO exhibited statistically significant increases compared with those in the negative controls (saline or 5 % dimethyl sulfoxide in saline). However, paraquat and acrylamide did not increase the mean % tail DNA, presumably because of the high antioxidant levels and low cytochrome P450 levels present in the corneal epithelium, respectively.

Conclusions

The comet assay was able to detect genotoxic potential on the ocular surface following ocular instillation with genotoxic compounds. The study findings indicate that the in vivo comet assay may provide a useful tool for assessing the genotoxicity of compounds topically administrated on the ocular surface under mimicking clinical condition.

Trisaminocyclopropenium Cations as Small-Molecule Organic Fluorophores: Design Guidelines and Bioimaging Applications

The discovery of fluorescence two centuries ago ushered in, what is today, an illuminating field of science rooted in the rational design of photochromic molecules for task-specific bio-, material-, and medical-driven applications. Today, this includes applications in bioimaging and diagnosis, photodynamic therapy regimes, in addition to photovoltaic devices and solar cells, among a vast multitude of other usages. In furthering this indispensable area of daily life and modern-day scientific research, we report herein the synthesis of a class of trisaminocyclopropenium fluorophores along with a systematic investigation of their unique molecular and electronic dependent photophysical properties. Among these fluorophores, tris[N(naphthalen-2-ylmethyl)phenylamino] cyclopropenium chloride (TNTPC) displayed a strong photophysical profile including a 0.92 quantum yield ascribed to intramolecular charge transfer and intramolecular through-space conjugation. Moreover, this cyclopropenium-based fluorophore functions as a competent imaging agent for DNA visualization and nuclear counterstaining in cell culture. To facilitate the broader use of these compounds, design principles supported by density functional theory calculations for engineering analogs of this class of fluorophores are offered. Collectively, this study adds to the burgeoning interest in cyclopropenium compounds and their unique properties as fluorophores with uses in bioimaging applications.

Antigen Capture Enzyme-Linked Immunosorbent Assay for Detecting Middle East Respiratory Syndrome Coronavirus in Humans

The Middle East respiratory syndrome (MERS) is the second novel zoonotic disease infecting humans caused by coronavirus (CoV) in this century. To date, more than 2200 laboratory-confirmed human cases have been identified in 27 countries, and more than 800 MERS-CoV associated deaths have been reported since its outbreak in 2012. Rapid laboratory diagnosis of MERS-CoV is the key to successful containment and prevention of the spread of infection. Though the gold standard for diagnosing MERS-CoV infection in humans is still nucleic acid amplification test (NAAT) of the up-E region, an antigen capture enzyme-linked immunosorbent assay (ELISA) could also be of use for early diagnosis in less developed locations. In the present method, a step-by-step guide to perform a MERS-CoV nucleocapsid protein (NP) capture ELISA using two NP-specific monoclonal antibodies is provided for readers to develop their in-house workflow or diagnostic kit for clinical use and for mass-screening project of animals (e.g., dromedaries and bats) to better understand the spread and evolution of the virus.

Analysis of deoxyribonuclease activity by conjugation-free fluorescence polarisation in sub-nanolitre droplets

We report the analysis of deoxyribonuclease (DNase) activity by conjugation-free fluorescence polarisation in a droplet-based microfluidic chip. DNase is a DNA cleaving enzyme and its activity is important in the maintenance of normal cellular functions. Alterations in DNase activity have been implicated as the cause of various cancers and autoimmune diseases. To date, various methods for the analysis of DNase activity have been reported. However, they are not cost effective due to the requirement of large sample volumes and the need for the conjugation of fluorescent dyes. In this study, we have used ethidium bromide (EtBr), a DNA intercalating reagent, as a fluorescent reporter without any prior conjugation or modification of DNA. Degradation of DNA by DNase 1 was monitored at a steady state by making changes in the fluorescence polarisation of EtBr in droplets with a volume of 330 picolitre at a 40 hertz frequency under visible light. Using this technique, we successfully determined the half-maximal inhibitory concentration (IC₅₀) of ethylenediaminetetraacetic acid (EDTA) for the inhibition of DNase 1 activity to be 1.56 ± 0.91 mM.

Enhanced removal of ethidium bromide (EtBr) from aqueous solution using rectorite

Ethidium bromide (EtBr) is an intercalating agent commonly used as nucleic acid fluorescent tag in various techniques of life science field. It is considered as a serious biohazard due to its mutagenicity and carcinogenicity. As such, developing high efficiency and low cost materials as cleanup kits is in urgent need although many methods have already been developed. In this study we take use of the affinity of organic cations for clay minerals of high cation exchange capacity (CEC) and large specific surface area (SSA) and tested the removal of EtBr using rectorite, a type of clay mineral made of 1:1 regularly mixed layers of illite and montmorillonite. Our results showed that the uptake of Et⁺ on rectorite could be as high as 400 mmol/kg and the removal of Et⁺ was extremely fast. Desorption of inorganic cation Ca²⁺ and sorption of counterion Br^- revealed that cation exchange was the dominating mechanism of Et⁺ removal using rectorite. Thermal analyses revealed that the EtBr could be thermally destructed inside the interlayer of rectorite and the material could be thermally regenerated. Thus, clay minerals could have a great potential to be fabricated into cleanup kits for the removal of EtBr in case of spill.

DNA binding fluorescent proteins as single-molecule probes

DNA binding fluorescent proteins are useful probes for a broad range of biological applications.

The staining efficiency of cyanine dyes for single-stranded DNA is enormously dependent on nucleotide composition

The staining of nucleic acids with fluorescent dyes is one of the most fundamental technologies in relevant areas of science. For reliable and quantitative analysis, the staining efficiency of the dyes should not be very dependent on the sequences of the specimens. However, this assumption has not necessarily been confirmed by experimental results, especially in the staining of ssDNA (and RNA). In this study, we found that both SYBR Green II and SYBR Gold did not stain either homopyrimidines or ssDNA composed of only adenine (A) and cytosine (C). However, these two dyes emit strong fluorescence when the ssDNA contains both guanine (G) and C (and/or both A and thymine (T)) and form potential Watson-Crick base pairs. Interestingly, SYBR Gold, but not SYBR Green II, strongly stains ssDNA consisting of G and A (or G and T). Additionally, we found that the secondary structure of ssDNA may play an important role in DNA staining. To obtain reliable results for practical applications, sufficient care must be paid to the composition and sequence of ssDNA.

Mutagen-induced phytotoxicity in maize seed germination is dependent on ROS scavenging capacity

Ethidium bromide (EB) and acridine orange (AO) bind to nucleic acids and are thus considered as potential mutagens. In this study, the effects of EB and AO on the germination behaviours of white, yellow, red, and purple maize seeds were investigated. The results indicate that low concentrations of EB (50 μg mL⁻¹) and AO (500 μg mL⁻¹) promote germination, particularly for the white and yellow seeds. However, high concentrations of EB (0.5 mg mL⁻¹) and AO (5 mg mL⁻¹) significantly inhibit germination, with the level of inhibition decreasing in the following order: white > yellow > red > purple. In addition, EB and AO induce H₂O₂ production in a concentration-dependent manner. The effects of these mutagens on seed germination were partly reversed by dimethyl thiourea, a scavenger of reactive oxygen species (ROS), and diphenylene iodonium (DPI), an inhibitor of NADPH oxidase, while the effects were enhanced by treatment with H₂O₂ and 3-amino-1,2,4-triazole, a specific inhibitor of catalase. In addition, AO and EB profoundly increased NADPH oxidase activities in germinating seeds. The treatment of seeds with EB and AO did not affect the growth or drought tolerance of the resultant seedlings. The findings suggest that the mechanism of mutagen toxicity is related to the induction of ROS production.

Manipulating Metallogel Properties by Luminogens and Their Applications in Cell Imaging

Manipulating gelation properties of the isomeric zinc-terpyridine complexes C-1 (nongelator) and C-2 (gelator) using three different luminescent dyes, viz., acridine yellow (AY), ethidium bromide (EB), and azido-boron dipyrromethene, have been described. Hybrid gels created by the combination of C-1, C-2, and above-mentioned dyes have been termed complex-luminogen mixed gels (CLMGs). Ensuing CLMGs have been thoroughly characterized by spectral, morphological, and rheological studies. Cytotoxicity measurements and imaging against breast cancer cell line MDA-MB-231 unveiled that three out of the five CLMGs can be effectively used for cell imaging. Interestingly, direct use of the metal-containing hybrid gels for live cell imaging which is a distinctive approach, has been successfully achieved with significantly encouraging results.

Analysis of ribonuclease activity in sub-nanoliter droplets by label-free fluorescence measurements

We report the results of a label-free analysis of ribonuclease activity using droplet-based microfluidics.

DNA binding fluorescent proteins for the direct visualization of large DNA molecules

Fluorescent proteins that also bind DNA molecules are useful reagents for a broad range of biological applications because they can be optically localized and tracked within cells, or provide versatile labels for in vitro experiments. We report a novel design for a fluorescent, DNA-binding protein (FP-DBP) that completely 'paints' entire DNA molecules, whereby sequence-independent DNA binding is accomplished by linking a fluorescent protein to two small peptides (KWKWKKA) using lysine for binding to the DNA phosphates, and tryptophan for intercalating between DNA bases. Importantly, this ubiquitous binding motif enables fluorescent proteins (Kd = 14.7 μM) to confluently stain DNA molecules and such binding is reversible via pH shifts. These proteins offer useful robust advantages for single DNA molecule studies: lack of fluorophore mediated photocleavage and staining that does not perturb polymer contour lengths. Accordingly, we demonstrate confluent staining of naked DNA molecules presented within microfluidic devices, or localized within live bacterial cells.