Fluorescent cyanine dyes for the quantification of low amounts of dsDNA

PicoGreen assay for nucleic acid quantification - Applications, challenges, and solutions

Various analytical methods and reagents have been employed for nucleic acid analysis in cells, biological fluids, and formulations. Standard techniques like gel electrophoresis and qRT-PCR are widely used for qualitative and quantitative nucleic acid analysis. However, these methods can be time-consuming and labor-intensive, with limitations such as inapplicability to small RNA at low concentrations and high costs associated with qRT-PCR reagents and instruments. As an alternative, PicoGreen (PG) has emerged as a valuable method for the quantitative analysis of nucleic acids. PG, a fluorescent dye, enables the quantitation of double-stranded DNA (dsDNA) or double-stranded RNA, including miRNA mimic and siRNA, in solution. It is also applicable to DNA and RNA analysis within cells using techniques like FACS and fluorescence microscopy. Despite its advantages, PG's fluorescence intensity is affected by various experimental conditions, such as pH, salts, and chemical reagents. This review explores the recent applications of PG as a rapid, cost-effective, robust, and accurate assay tool for nucleic acid quantification. We also address the limitations of PG and discuss approaches to overcome these challenges, recognizing the expanding range of its applications.

A recombinase polymerase amplification-SYBR Green I assay for the rapid and visual detection of Brucella

Brucellosis is a zoonosis caused by Brucella, which poses a great threat to human health and animal husbandry. Pathogen surveillance is an important measure to prevent brucellosis, but the traditional method is time-consuming and not suitable for field applications. In this study, a recombinase polymerase amplification-SYBR Green I (RPAS) assay was developed for the rapid and visualized detection of Brucella in the field by targeting BCSP31 gene, a conserved marker. The method was highly specific without any cross-reactivity with other common bacteria and its detection limit was 2.14 × 104 CFU/mL or g of Brucella at 40 °C for 20 min. It obviates the need for costly instrumentation and exhibits robustness towards background interference in serum, meat, and milk samples. In summary, the RPAS assay is a rapid, visually intuitive, and user-friendly detection that is highly suitable for use in resource-limited settings. Its simplicity and ease of use enable swift on-site detection of Brucella, thereby facilitating timely implementation of preventive measures.

DNA Antiadhesive Layer for Reusable Plasmonic Sensors: Nanostructure Pitch Effect

A long-term reusable sensor that provides the opportunity to easily regenerate the active surface and minimize the occurrence of undesired absorption events is an appealing solution that helps to cut down the costs and improve the device performances. Impressive advances have been made in the past years concerning the development of novel cutting-edge sensors, but the reusability can currently represent a challenge. Direct shielding of the sensor surface is not always applicable, because it can impact the device performance. This study reports an antiadhesive layer (AAL) made of 90 mg/mL DNA sodium salt from salmon testes (ssstDNA) for passivating gold plasmonic sensor surfaces. Our gold two-dimensional (2D) nanostructured plasmonic metasurfaces modified with AAL were used for DNA quantification. AAL is thin enough that the plasmonic sensor remains sensitive to subsequent deposition of DNA, which serves as an analyte. AAL protects the gold surface from unwanted nonspecific adsorption by enabling wash-off of the deposited analyte after analysis and thus recovery of the LSPR peak position (rLSPR). The calibration curve obtained on a single nanostructure (Achiral Octupolar, 100 nm pitch) gave an LOD = 105 ng/mL and an extraordinary dynamic range, performances comparable or superior to those of commercial UV-vis spectrometers for acid nucleic dosage. Two different analytes were tested: ssstDNA (∼2000 bp) in deionized water and double-strand DNA (dsDNA) of 546-1614 bp in 100 mM Tris buffer and 10 mM MgCl₂. The two nanostructures (Achiral Octupolar 25 and 100) were found to have the same sensitivity to DNA in deionized water but different sensitivity to DNA in a salt/buffer solution, opening a potential for solute discrimination. To the best of our knowledge, this is the first report on the use of AAL made of several kilobase-pairs-long dsDNA to produce a reusable plasmonic sensor. The working principle and limitations are drawn based on the LSPR and SERS study.

Development of a Directly Visualized Recombinase Polymerase Amplification-SYBR Green I Method for the Rapid Detection of African Swine Fever Virus

African swine fever (ASF) is a lethal disease in swine caused by etiologic African swine fever virus (ASFV). The global spread of ASFV has resulted in huge economic losses globally. In the absence of effective vaccines or drugs, pathogen surveillance has been the most important first-line intervention to prevent ASF outbreaks. Among numerous diagnostic methods, recombinase polymerase amplification (RPA)-based detection is capable of producing sensitive and specific results without relying on the use of expensive instruments. However, currently used gene-specific, probe-based RPA for ASFV detection is expensive and time-consuming. To improve the efficiency of ASFV surveillance, a novel directly visualized SYBR Green I-staining RPA (RPAS) method was developed to detect the ASFV genome. SYBR Green I was added to the amplified RPA products for direct visualization by the naked eye. The sensitivity and specificity of this method were confirmed using standard plasmid and inactivated field samples. This method was shown to be highly specific with a detection limit of 10³ copies/μl of ASFV in 15 min at 35°C without any cross-reactions with other important porcine viruses selected. In summary, this method enables direct sample visualization with reproducible results for ASFV detection and hence has the potential to be used as a robust tool for ASF prevention and control.

Investigation of a cyanine dye assay for the evaluation of the biocompatibility of magnesium alloys by direct and indirect methods

Magnesium and its alloys are promising candidates for a new generation of biodegradable metals in orthopaedic applications due to their excellent biocompatibility, biodegradability, and mechanical properties that are similar to natural bone. However, direct in vitro assessment of these materials in the presence of cells is complicated by degradation products from the alloy that lead to a false positive for the most commonly used cell adhesion and cell proliferation assays. In this paper, a cyanine dye was used to quantitatively evaluate the in vitro biocompatibility of a Mg AZ31 alloy by both direct and indirect methods. The cytotoxicity of the corrosion products was evaluated via an indirect method; a 25% decrease in cell viability compared to control samples was observed. Moreover, direct assessment of cell adhesion and proliferation showed a statistically significant increase in cell number at the surface after 72 h. In addition, the degradation rate and surface characteristics of the Mg AZ31 alloy were evaluated for both direct and indirect tests. The degradation rate was unaffected by the presence of cells while evidence of an increase in calcium phosphate deposition on the magnesium alloy surface in the presence of cells was observed. This study demonstrates that a cyanine dye based assay provides a more accurate assessment of the overall in vitro biocompatibility of biodegradable metals than the more commonly used assays reported in the literature to date.

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Quantitative analysis of cell numbers on the surface of magnesium has been performed.

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No false positive was observed.

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Cyanine dye assays are an excellent alternative to tetrazolium salts for in vitro evaluation of bioabsorbable implants.

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.

Sensitive determination of DNA based on phosphate-dye interaction using photothermal lens technique

Photothermal lens spectrometry is a powerful optical detection technique that can be used to investigate biomolecules. In this work, for the first time to our knowledge, photothermal lens spectrometry was used for determination of nanomolar concentrations of three distinct deoxyribonucleic acid (DNA) strands using methylene blue as a labeling dye. Methylene blue interacts with phosphate groups of the DNA in lower DNA concentrations. It was observed that phosphate-methylene blue interaction had no obvious effect on methylene blue absorption and fluorescence spectra, but the photothermal lens spectrometry signal of methylene blue increased with DNA concentration. For this purpose, to evaluate the performance of the presented method, herring sperm DNA, Escherichia coli bacteria DNA, and partial 16S rRNA genes were examined. Under optimum conditions, photothermal lens spectrometry intensity of methylene blue increased linearly with DNA concentration when herring sperm DNA, Escherichia coli DNA, and 16S rRNA gene concentrations increased in the ranges of 0.1-250, 1-700, and 1-800  nmol L^-1, respectively. The corresponding detection limits were found to be 0.07, 0.71, and 0.56  nmol L^-1, respectively, and relative standard deviations for 50  nmol L^-1 of the tested samples were 2.59%, 4.95%, and 4.57%, respectively.

Integrated Optoelectronic Device for Detection of Fluorescent Molecules

This paper presents the development of a compact optoelectronic device suitable for on-chip detection of fluorescent molecules. In order to obtain a highly integrated device, a long-pass multi-dielectric filter has been integrated with thin-film amorphous silicon photosensors on a single glass substrate. Filter rejects the excitation light, allowing the reduction of the distance between the source and the fluorescent site and avoiding the use of external optical component. The compatibility of the technological processes determined the materials and the temporal sequence of the device fabrication. The developed device has been designed for the fluorescence detection of ruthenium complex based molecules and tested, as a proof of concept, for the detection of double-stranded DNA down to 0.5 ng. Results demonstrate the correct operation of the integrated system in both rejecting the excitation light and in detecting the fluorescent signal, demonstrating the suitability of this optoelectronic platform in practical biomedical applications.

Characterization of the binding interactions between EvaGreen dye and dsDNA

Understanding the dsDNA·EG binding interaction is important because the EvaGreen (EG) dye is increasingly used in real-time quantitative polymerase chain reaction, high resolution melting analysis, and routine quantification of DNA. In this work, a binding isotherm for the interactions of EG with duplex DNA (poly-dA₁₇·poly-dT₁₇) has been determined from the absorption and fluorescence spectra of the EG and dsDNA·EG complex. The isotherm has a sigmoidal shape and can be modeled with the Hill equation, indicating positive cooperativity for the binding interaction. A Scatchard plot of the binding data yields a concave-down curve in agreement with the Hill analysis of the binding isotherm for a positive cooperative binding interaction. Analysis of the Scatchard plot with the modified McGhee and von Hippel model for a finite one-dimensional homogeneous lattice and nonspecific binding of ligands to duplex DNA yields the intrinsic binding constant, the number of lattice sites occluded by a bound ligand, and the cooperativity parameter of 3.6 × 10⁵ M^-1, 4.0, and 8.1, respectively. The occluded site size of 4 indicates that moieties of the EG intercalate into the adjacent base pairs of the duplex DNA with a gap of 1 intercalation site between EG binding sites, as expected for a bifunctional molecule. Interestingly, at high [EG]/[base pair], the intercalation is disrupted. A model is proposed based on the fluorescence spectrum where the formation of anti-parallel stacked chains of EGs bound externally to the duplex DNA occur at these high ratios.

Relationship between blastocoel cell-free DNA and day-5 blastocyst morphology

PURPOSE

Cell-free DNA (cfDNA) which is present in the blastocoel cavity of embryos is believed to result from physiological apoptosis during development. This study assessed cfDNA content and caspase-3 protease activity in day-5 IVF blastocysts to determine if there was a correlation with embryo morphology.

METHODS

Day-5 IVF blastocysts were scored according to the Gardner and Schoolcraft system (modified to generate a numerical value) and cfDNA was collected following laser-induced blastocoel collapsing prior to cryopreservation in 25 μL of media. cfDNA was quantified via fluorospectrometry and apoptotic activity was assessed via a caspase-3 protease assay using a fluorescent peptide substrate. Data were compared by linear regression.

RESULTS

A total of 32 embryos were evaluated. There was a significant (p < 0.01) and positive correlation (cfDNA = 104.753 + (11.281 × score); R² = 0.200) between embryo score and cfDNA content. A significant (p < 0.05) and positive correlation (cfDNA = 115.9 + (0.05 × caspase-3); R²= 0.128) was observed between caspase-3 activity and cfDNA levels. There was no significant relationship between caspase-3 activity and embryo morphology score.

CONCLUSIONS

This study provides further evidence that cfDNA is present in blastocoel fluid, can be quantified, and positively correlates with embryonic morphology. There is also evidence that at least a portion of the cfDNA present is from intracellular contents of embryonic cells that underwent apoptosis. Additional studies are warranted to determine other physiological sources of the cfDNA in blastocyst fluid and to determine the relationship with cfDNA content, embryo morphology, and chromosomal ploidy status plus implantation potential.

Stressful Surfaces: Cell Metabolism on a Poorly Adhesive Substrate

The adhesion and proliferation of cells are exquisitely sensitive to the nature of the surface to which they attach. Aside from cell counting, cell "health" on surfaces is typically established by measuring the metabolic rate with dyes that participate in the metabolic pathway or using "live/dead" assays with combinations of membrane permeable/impermeable dyes. The binary information gleaned from these tests-whether cells are attached or not, and whether they are living or dead-provides an incomplete picture of cell health. In the present work, proliferation rates and net metabolism of 3T3 fibroblasts seeded on "biocompatible" ultrathin polyelectrolyte multilayer films and on control tissue culture plastic were compared. Cells adhered to, and proliferated on, both surfaces, which were shown to be nontoxic according to live/dead assays. However, adhesion was poorer on the multilayer surface, illustrated by diffuse organization of the actin cytoskeleton and less-developed focal adhesions. Proliferation was also slower on the multilayer. When normalized for the total number of cells, it was shown that cells on multilayers experienced a five-day burst of metabolic stress, after which the metabolic rate approached that of the control surface. This initial state of high stress has not been reported or appreciated in studies of cell growth on multilayers, although the observation period for this system is usually a few days.

Dataset of the absorption, emission and excitation spectra and fluorescence intensity graphs of fluorescent cyanine dyes for the quantification of low amounts of dsDNA

This article describes data related to a research article entitled “Fluorescent cyanine dyes for the quantification of low amounts of dsDNA” (B. Bruijns, R. Tiggelaar, J. Gardeniers, 2016) [1]. Six cyanine dsDNA dyes - EvaGreen, SYBR Green, PicoGreen, AccuClear, AccuBlue NextGen and YOYO-1 – are investigated and in this article the absorption spectra, as well as excitation and emission spectra, for all six researched cyanine dyes are given, all recorded under exactly identical experimental conditions. The intensity graphs, with the relative fluorescence in the presence of low amounts of dsDNA, are also provided.