Quantitative DNA hybridization in solution using magnetic/luminescent core–shell nanoparticles

Transrenal DNA detection of Mycobacterium tuberculosis in patients with pulmonary tuberculosis

Background

Multiple attempts have been made to use biological samples other than sputum to diagnose tuberculosis (TB). Sputum acid-fast bacillus (AFB) microscopy is the fastest, most straightforward, and most inexpensive method for diagnosing pulmonary TB. However, urine can be used in place of sputum owing to its various advantages, such as a noninvasive method of collection, convenient handling and storage, and minimal risk of infection in health-care workers involved in sample collection. In this study, we aimed to assess the suitability of urine as a sample to obtain transrenal DNA (trDNA) to diagnose TB. This study involved several patients with TB undergoing inpatient treatment, whose AFB microscopy showed negative inversion.

Methods

Here, 51 urine samples were collected from 40 patients with TB and examined to confirm the presence of trDNA. First, we compared the efficiency of two trDNA extraction methods.

An automated magnetic bead-based method and a more efficient anchoring extraction method. Statistical analyses were performed using Excel software (Microsoft Office Professional Plus 2019).

Results

Although molecular diagnosis using GeneXpert yielded negative results, a peculiarity was observed. There was no significant difference between GeneXpert findings and our results nor was there any difference in the sequential trDNA samples obtained. However, even when GeneXpert results were negative, trDNA was detected in seven out of ten samples using the anchor extraction method.

Conclusions

Further studies are needed to establish biomarkers for the progression of TB treatment.

The Implications of Fragmented Genomic DNA Size Range on the Hybridization Efficiency in NanoGene Assay

DNA hybridization-based assays are well known for their ability to detect and quantify specific bacteria. Assays that employ DNA hybridization include a NanoGene assay, fluorescence in situ hybridization, and microarrays. Involved in DNA hybridization, fragmentation of genomic DNA (gDNA) is necessary to increase the accessibility of the probe DNA to the target gDNA. However, there has been no thorough and systematic characterization of different fragmented gDNA sizes and their effects on hybridization efficiency. An optimum fragmented size range of gDNA for the NanoGene assay is hypothesized in this study. Bacterial gDNA is fragmented via sonication into different size ranges prior to the NanoGene assay. The optimum size range of gDNA is determined via the comparison of respective hybridization efficiencies (in the form of quantification capabilities). Different incubation durations are also investigated. Finally, the quantification capability of the fragmented (at optimum size range) and unfragmented gDNA is compared.

Quantitative and discriminative analysis of nucleic acid samples using luminometric nonspecific nanoparticle methods

Homogeneous simple assays utilizing luminescence quenching and time-resolved luminescence resonance energy transfer (TR-LRET) were developed for the quantification of nucleic acids without sequence information. Nucleic acids prevent the adsorption of a protein to europium nanoparticles which is detected as a luminescence quenching of europium nanoparticles with a soluble quencher or as a decrease of TR-LRET from europium nanoparticles to the acceptor dye. Contrary to the existing methods based on fluorescent dye binding to nucleic acids, equal sensitivities for both single- (ssDNA) and double-stranded DNA (dsDNA) were measured and a detection limit of 60 pg was calculated for the quenching assay. The average coefficient of variation was 5% for the quenching assay and 8% for the TR-LRET assay. The TR-LRET assay was also combined with a nucleic acid dye selective to dsDNA in a single tube assay to measure the total concentration of DNA and the ratio of ssDNA and dsDNA in the mixture. To our knowledge, such a multiplexed assay is not accomplished with commercially available assays.

Time-resolved luminescent biosensing based on inorganic lanthanide-doped nanoprobes

In this feature article, we review the latest advancements in lanthanide-doped luminescent nanocrystals as time-resolved luminescent nano-bioprobes, from their fundamental optical properties to their potential applications for ultrasensitive biodetection and high-resolution bioimaging.

Flexible Janus nanofibers: a feasible route to realize simultaneously tuned magnetism and enhanced color-tunable luminescence bifunctionality

Novel Janus nanofibers with magnetic and color-tunable bifunctionality have been fabricated by electrospinning technology using a specially designed parallel spinneret.

Magnetic quantum dots in biotechnology--synthesis and applications

Quantum dots (QDs) have great promise in biological imaging, and as this promise is realized, there has been increasing interest in combining the benefits of QDs with those of other materials to yield composites with multifunctional properties. One of the most common materials combined with QDs is magnetic materials, either as ions (e.g. gadolinium) or as nanoparticles (e.g. superparamagnetic iron oxide nanoparticles, SPIONs). The fluorescent property of the QDs permits visualization, whereas the magnetic property of the composite enables imaging, magnetic separation, and may even have therapeutic benefit. In this review, the synthesis of fluorescent-magnetic nanoparticles, including magnetic QDs is explored; and the applications of these materials in imaging, separations, and theranostics are discussed. As the properties of these materials continue to improve, QDs have the potential to greatly impact biological imaging, diagnostics, and treatment.

Magnetic and luminescent hybrid nanomaterial based on Fe(3)O(4) nanocrystals and GdPO(4):Eu(3+) nanoneedles

A bifunctional hybrid nanomaterial, which can show magnetic and luminescent properties, was obtained. A magnetic phase was synthesized as a core/shell type composite. Nanocrystalline magnetite, Fe(3)O(4) was used as the core and was encapsulated in a silica shell. The luminescent phase was GdPO(4) doped with Eu(3+) ions, as the emitter. The investigated materials were synthesized using a coprecipitation method. Encapsulated Fe(3)O(4) was "trapped" in a nano-scaffold composed of GdPO(4) crystalline nanoneedles. When an external magnetic field was applied, this hybrid composite was attracted in one direction. Also, the luminescent phase can move simultaneously with magnetite due to a "trapping" effect. The structure and morphology of the obtained nanocomposites were examined with the use of transmission electron microscopy and X-ray powder diffraction. Spectroscopic properties of the Eu(3+)-doped nanomaterials were studied by measuring their excitation and emission spectra as well as their luminescence decay times. GRAPHICAL ABSTRACT:

Quartz crystal microbalance detection of DNA single-base mutation based on monobase-coded cadmium tellurium nanoprobe

A new method for the detection of point mutation in DNA based on the monobase-coded cadmium tellurium nanoprobes and the quartz crystal microbalance (QCM) technique was reported. A point mutation (single-base, adenine, thymine, cytosine, and guanine, namely, A, T, C and G, mutation in DNA strand, respectively) DNA QCM sensor was fabricated by immobilizing single-base mutation DNA modified magnetic beads onto the electrode surface with an external magnetic field near the electrode. The DNA-modified magnetic beads were obtained from the biotin-avidin affinity reaction of biotinylated DNA and streptavidin-functionalized core/shell Fe(3)O(4)/Au magnetic nanoparticles, followed by a DNA hybridization reaction. Single-base coded CdTe nanoprobes (A-CdTe, T-CdTe, C-CdTe and G-CdTe, respectively) were used as the detection probes. The mutation site in DNA was distinguished by detecting the decreases of the resonance frequency of the piezoelectric quartz crystal when the coded nanoprobe was added to the test system. This proposed detection strategy for point mutation in DNA is proved to be sensitive, simple, repeatable and low-cost, consequently, it has a great potential for single nucleotide polymorphism (SNP) detection.

Biological applications of rare-earth based nanoparticles

Biomedicine and cell and molecular biology require powerful imaging techniques of the single molecule scale to the whole organism, either for fundamental science or diagnosis. These applications are however often limited by the optical properties of the available probes. Moreover, in cell biology, the measurement of the cell response with spatial and temporal resolution is a central instrumental problem. This has been one of the main motivations for the development of new probes and imaging techniques either for biomolecule labeling or detection of an intracellular signaling species. The weak photostability of genetically encoded probes or organic dyes has motivated the interest for different types of nanoparticles for imaging such as quantum dots, nanodiamonds, dye-doped silica particles, or metallic nanoparticles. One of the most active fields of research in the past decade has thus been the development of rare-earth based nanoparticles, whose optical properties and low cytotoxicity are promising for biological applications. Attractive properties of rare-earth based nanoparticles include high photostability, absence of blinking, extremely narrow emission lines, large Stokes shifts, long lifetimes that can be exploited for retarded detection schemes, and facile functionalization strategies. The use of specific ions in their compositions can be moreover exploited for oxidant detection or for implementing potent contrast agents for magnetic resonance imaging. In this review, we present these different applications of rare-earth nanoparticles for biomolecule detection and imaging in vitro, in living cells or in small animals. We highlight how chemical composition tuning and surface functionalization lead to specific properties, which can be used for different imaging modalities. We discuss their performances for imaging in comparison with other probes and to what extent they could constitute a central tool in the future of molecular and cell biology.

The synthesis and bio-applications of magnetic and fluorescent bifunctional composite nanoparticles

Magnetic-fluorescent composite nanoparticles as a new kind of nanoparticle have attracted much attention in recent years. The composite nanoparticles combine the fluorescent properties, magnetic properties and the physical properties of nano-size, so they can offer a range of potential applications, such as bioseparation and bio-imaging, tumor cell localization, and even cancer treatment. This Minireview will introduce the main synthesis strategies for the fabrication of magnetic-fluorescent composite nanoparticles, the current and potential bio-application of magnetic-fluorescent nanocomposites, including protein and DNA separation and detection, bio-imaging and sorting in vitro and in vivo, drug delivery and the cancer treatment.

Application of multiple response optimization design to quantum dot-encoded microsphere bioconjugates hybridization assay

The optimization of DNA hybridization for genotyping assays is a complex experimental problem that depends on multiple factors such as assay formats, fluorescent probes, target sequence, experimental conditions, and data analysis. Quantum dot-doped particle bioconjugates have been previously described as fluorescent probes to identify single nucleotide polymorphisms even though this advanced fluorescent material has shown structural instability in aqueous environments. To achieve the optimization of DNA hybridization to quantum dot-doped particle bioconjugates in suspension while maximizing the stability of the probe materials, a nonsequential optimization approach was evaluated. The design of experiment with response surface methodology and multiple optimization response was used to maximize the recovery of fluorescent probe at the end of the assay simultaneously with the optimization of target-probe binding. Hybridization efficiency was evaluated by the attachment of fluorescent oligonucleotides to the fluorescent probe through continuous flow cytometry detection. Optimal conditions were predicted with the model and tested for the identification of single nucleotide polymorphisms. The design of experiment has been shown to significantly improve biochemistry and biotechnology optimization processes. Here we demonstrate the potential of this statistical approach to facilitate the optimization of experimental protocol that involves material science and molecular biology.

Multifunctional nanocomposites of superparamagnetic (Fe3O4) and NIR-responsive rare earth-doped up-conversion fluorescent (NaYF4 : Yb,Er) nanoparticles and their applications in biolabeling and fluorescent imaging of cancer cells

A new kind of magnetic/luminescent multifunctional nanoparticles was synthesized by covalently linking multiple carboxyl-functionalized superparamagnetic Fe(3)O(4) nanoparticles and individual amino-functionalized silica-coated fluorescent NaYF(4) : Yb,Er up-conversion nanoparticles (UCNPs). The resultant nanocomposites bear active carboxylic and amino groups on the surface that were proved to be chemically active and useful for further facile bioconjugation with biomolecules. The UCNPs in the nanocomposite particles can emit visible light in response to the irradiation by near infrared (NIR) light, enabling the application of the nanocomposites in bioimaging. X-Ray diffraction, infrared spectroscopy, transmission electron microscopy, luminescence spectroscopy, and magnetometry were applied to characterize the multifunctional nanocomposites. The nanocomposites exhibited good superparamagnetic and excellent green up-conversion photoluminescent properties that can be exploited in magnetic separation and guiding as well as bioimaging. Due to the presence of active functional groups on the nanocomposite surface, the Fe(3)O(4)/NaYF(4) : Yb,Er magnetic/luminescent nanocomposites were successfully conjugated with a protein called transferrin, which specifically recognizes the transferrin receptors overexpressed on HeLa cells, and can be employed for biolabeling and fluorescent imaging of HeLa cells. Because NIR light can penetrate biological samples with good depth without damaging them and can avoid autofluorescence from them, the presence of both NIR-responsive UCNPs and superparamagnetic nanoparticles in the nanocomposite particles will enable the practical application of the nanocomposites in bioimaging and separation.

Quantitative gene monitoring of microbial tetracycline resistance using magnetic luminescent nanoparticles

A magnetic/luminescent nanoparticles (MLNPs) based DNA hybridization method was developed for quantitative monitoring of antibiotic resistance genes and gene-expression in environmental samples. Manipulation of magnetic field enabled the separation of the MLNPs-DNA hybrids from the solution and the fluorescence of MLNPs normalized the quantity of target DNA. In our newly developed MLNPs-DNA assay, linear standard curves (R(2) = 0.99) of target gene was determined with the detection limit of 620 gene copies. The potential risk of increased bacterial antibiotic resistance was assessed by quantitative monitoring of tetracycline resistance (i.e., tetQ gene) in wastewater microcosms. The gene abundance and its expression showed a significant increase of tetQ gene copies with the addition of tetracycline, triclosan (TCS), or triclocarban (TCC). A real-time PCR assay was employed to verify the quantification capability of the MLNPs-DNA assay and accordingly both assays have shown strong correlation (R(2) = 0.93). This non-PCR based MLNPs-DNA assay has demonstrated its potential for gene quantification via a rapid, simple, and high throughput platform and its novel use of internal calibration standards.

Synthesis and characterization of multifunctional silica core-shell nanocomposites with magnetic and fluorescent functionalities

Multifunctional core-shell nanocomposites with a magnetic core and a silica shell doped with lanthanide chelate have been prepared by a simple method. First, citric acid-modified magnetite nanoparticles were synthesized by a chemical coprecipitation method. Then the magnetite nanoparticles were coated with silica shells doped with terbium (Tb(3+)) complex by a modified Stöber method based on hydrolyzing and condensation of tetraethyl orthosilicate (TEOS) and a silane precursor. These multifunctional nanocomposites are potentially useful in a variety of biological areas such as bio-imaging, bio-labeling and bioassays because they can be simultaneously manipulated with an external magnetic field and exhibit unique phosphorescence properties.

Synthesis and bio-functionalization of multifunctional magnetic Fe(3)O(4)@Y(2)O(3):Eu nanocomposites

A facile homogenous precipitation method has been developed for the synthesis of multifunctional, magnetic, luminescent nanocomposites with Fe(3)O(4) nanoparticles as the core and europium-doped yttrium oxide (Y(2)O(3):Eu) as the shell. The nanocomposites showed both super-paramagnetic behavior and unique europium fluorescence properties with high emission intensity. Their surface has been modified with a bifunctional ligand, p-aminobenzoic acid (PABA), and further biofunctionalized with biotin; the nanocomposites showed specific targeting for avidin-coupled polystyrene beads.