DNA Hybridization Assay Research Articles

Salt tolerance of potato genetically engineered with the Atriplex canescens BADH gene

Potato (Solanum tuberosum L.) is among the top staple foods in the world, and salinity adversely affects its yield and quality. To improve salt tolerance in potato, the present study is focused on the Agrobacterium-mediated transformation of potato by the Atriplex canescens betaine aldehyde dehydrogenase (BADH) gene driven by single, double, and triple CaMV 35S promoters. The study led first to the detection of seven lines containing the BADH gene followed by the identification of T-DNA insertions via DNA hybridization and enzyme-linked immunosorbent assays. The salt tolerance was found to be promoter dependent, as the lines with triple promoters showed a higher resistance than those tranformed with single and double promoters. The transgenic lines showed lower content of H2O2 and malondialdehyde and a lower relative electrical conductivity than wild-type plants. Furthermore, these lines also showed higher proline and chlorophyll content. In silico analysis confirmed that the A. canescens BADH protein had a remarkable tendency to interact with sodium ions and water molecules like other BADH proteins. Taken together, the overexpression of BADH under triple CaMV 35S promoters enhanced salt tolerance of potato.

Magnetosomes for bioassays by merging fluorescent liposomes and magnetic nanoparticles: encapsulation and bilayer insertion strategies

Magnetized liposome (magnetosomes) labels can overcome diffusion limitations in bioassays through fast and easy magnetic attraction. Our aim therefore was to advance the understanding of factors influencing their synthesis focusing on encapsulation strategies and synthesis parameters. Magnetosome synthesis is governed by the surface chemistry and the size of the magnetic nanoparticles used. We therefore studied the two possible magnetic labelling strategies, which are the incorporation of small, hydrophobic magnetic nanoparticles (MNPs) into the bilayer core (b-liposomes) and the entrapment of larger hydrophilic MNPs into the liposomes’ inner cavity (i-liposomes). Furthermore, they were optimized and compared for application in a DNA bioassay. The major obstacles observed for each of these strategies were on the one hand the need for highly concentrated hydrophilic MNPs, which is limited by their colloidal stability and costs, and on the other hand the balancing of magnetic strength vs. size for the hydrophobic MNPs. In the end, both strategies yielded magnetosomes with good performance, which improved the limit of detection of a non-magnetic DNA hybridization assay by a factor of 3–8-fold. Here, i-liposomes with a magnetization yield of 5% could be further improved through a simple magnetic pre-concentration step and provided in the end an 8-fold improvement of the limit of detection compared with non-magnetic conditions. In the case of b-liposomes, Janus-like particles were generated during the synthesis and yielded a fraction of 15% magnetosomes directly. Surprisingly, further magnetic pre-concentration did not improve their bioassay performance. It is thus assumed that magnetosomes pull normal liposomes through the magnetic field towards the surface and the presence of more magnetosomes is not needed. The overall stability of magnetosomes during storage and magnetic action, their superior bioassay performance, and their adaptability towards size and surface chemistry of MNPs makes them highly valuable signal enhancers in bioanalysis and potential tools for bioseparations.Graphical abstract

Fast enzyme-linked electrochemical sensing of DNA hybridization at pencil graphite electrodes. Application to detect gene deletion in a human cell culture

In this paper we present a rapid electrochemical enzyme-linked DNA hybridization assay using disposable pencil graphite electrodes (PeGE) to detect target DNA (tDNA) sequences in DNA fragments amplified by polymerase chain reaction. The procedure consists of several short (1–2 min) incubation steps, including adsorption of the tDNA at unpretreated PeGE from denaturing medium, surface blocking with milk proteins, hybridization with a biotinylated oligonucleotide probe and binding of streptavidin-alkaline phosphatase conjugate to the biotin tags. Then the PeGE is transferred into background electrolyte solution containing 1-naphthyl phosphate, which is enzymatically dephosphorylated to give electrochemically oxidizable indicator 1-naphthol. The assay, which can be performed within 7–8 min, offers a perfect discrimination between specific and nonspecific DNA amplicons and easy detection of about ~40 femtomoles of tDNA in large excesses of non-complementary DNA. An application on the detection of p53 gene deletion in a human cell culture, featuring a real biological model, is presented. The designed setup has a potential to be applied as one of simple, fast, robust ultralow cost “do-it-yourself “instruments recently introduced as diagnostic tools for third world countries.

Combining bacteriophage engineering and linear dichroism spectroscopy to produce a DNA hybridisation assay.

Nucleic acid detection is an important part of our bio-detection arsenal, with the COVID-19 pandemic clearly demonstrating the importance to healthcare of rapid and efficient detection of specific pathogenic sequences. As part of the drive to establish new DNA detection methodologies and signal read-outs, here we show how linear dichroism (LD) spectroscopy can be used to produce a rapid and modular detection system for detecting quantities of DNA from both bacterial and viral pathogens. The LD sensing method exploits changes in fluid alignment of bionanoparticles (bacteriophage M13) engineered with DNA stands covalently attached to their surfaces, with the read-out signal induced by the formation of complementary duplexes between DNA targets and two M13 bionanoparticles. This new sandwich assay can detect pathogenic material down to picomolar levels in under 1 minute without amplification, as demonstrated by the successful sensing of DNA sequences from a plant virus (Potato virus Y) and an ampicillin resistance gene, ampR.

Smartphone-based chemiluminometric hybridization assays and quantitative competitive polymerase chain reaction

The present report introduces the smartphone as a simple, low-cost detector/imager for chemiluminometric hybridization assays and quantitative competitive polymerase chain reaction (QCPCR). In QCPCR the amplification products from the target and the competitor DNA have identical sizes but differ in a short sequence flanked by the primers. The products are hybridized with their cognate oligonucleotide probes, captured on microtiter wells and detected via an enzyme-catalyzed chemiluminogenic reaction using the smartphone as a detector/imager. We provide, for the first time, data on: (a) the detectability, analytical range and reproducibility of smartphone-based chemiluminometric hybridization assays of double stranded amplification products, (b) the comparison of smartphone-based detection with a conventional digital camera and a luminometer, and (c) the detectability, analytical range and reproducibility of smartphone-based QCPCR in terms of the number of copies of input target sequences in the sample prior to amplification. The limits of detection of the DNA hybridization assay based on the smartphone, digital camera and luminometer were 1.6, 2.4 and 1 pmol L−1. Smartphone-based QCPCR showed an analytical range from 137 to 9 × 105 copies of target DNA.

Microfluidic chip-photothermal lens microscopy for DNA hybridization assay using gold nanoparticles

A new approach employing a microchip in combination with photothermal lens microscopy has been described for a DNA hybridization assay using gold nanoparticles. The difference in adsorption propensities of single- and double-stranded DNAs on gold nanoparticles was used for a highly sensitive DNA hybridization assay through a photothermal lens effect in a femtoliter scale of detection volume. Under the optimized conditions, the results showed that the variation of photothermal lens signal in the focal volume of 105fL (10-15L) was linearly proportional to the target DNA concentration over the range of 50-500nM with detection limits of 30.7nM and 27.3nM for target DNA I and II, respectively. The lowest amount of target DNA that was measured using gold nanoparticles was 2.6 zepto mole. The assay was completed within 5min and the relative standard deviations (n = 8) for both target DNAs were about 2.34%. The hybridization process was proved by two different common methods including gel electrophoresis and in situ fluorescence monitoring of DNA hybridization. The performance of this detection method was investigated in diluted human serum sample as a complex sample. The recovery values were between 98 and 104.9%. Graphical abstract.

Preparation of graphene oxide quantum dots from waste toner, and their application to a fluorometric DNA hybridization assay.

A one-pot hydrothermal method was developed for the synthesis of graphene oxide quantum dots (GOQDs). It is making use of toner waste as the precursor and H2O2 as the oxidant. Synthesis takes 4h and does not require strong acids or complex purification steps and does not produce environmentally harmful metal ions. The GOQDs display blue fluorescence with excitation/emission maxima at 340/445nm. The feasibility of detecting specific DNA sequence was promoted using polyethyleneimine to modify the GOQDs surface. A method was developed to recognized a specific DNA sequence. This is based on electrostatic aggregation of GOQDs and ssDNA labeled with Dabcyl at the 3' end, which promotes fluorescence quenching of GOQDs. The possible fluorescence quenching mechanism (which is mainly dynamic) was investigated using the Stern-Volmer equation. When a target sequence was added, which is complementary to the ssDNA, the dabcyl-labeled ssDNA is released due to strict complementary base pairing. This promotes fluorescence recovery of GOQDs. The assay has a 0.17nM detection limit and a linear range of 0.5-30nM. The method was used to quantify specific DNA sequences from extracts of genetically modified plant tissues. Graphical abstract Graphene oxide quantum dots (GOQDs) were synthesized by one-pot hydrothermal method using waste toner, and the surface was modified by polyethyleneimine (PEI). Through the interaction of PEI-GOQDs with Dabcyl-DNA single strands to dynamically quench the fluorescence of GOQDs. Based on DNA hybridization technology, we established specific DNA sequence detection nanoprobe.

Scanometric Detection of Tomato Leaf Curl New Delhi Viral DNA Using Mono- and Bifunctional AuNP-Conjugated Oligonucleotide Probes.

Scanometric detection of tomato leaf curl New Delhi viral DNA using AuNP-conjugated mono- and bifunctional oligo probes through direct DNA hybridization assay (DDH assay) and sandwich DNA hybridization assay (SDH assay) with silver enhancement was developed. Tomato leaf curl New Delhi virus (ToLCNDV) coat protein gene-specific thiol-modified ssoligo probes were used for the preparation of mono- and bifunctional AuNP-ssoligo probe conjugates (signal probes). ssDNA arrays were prepared using polymerase chain reaction (PCR), rolling circle amplification (RCA), genomic DNAs fragments, and phosphate-modified positive control/capture probes through 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide/1-methylimidazole conjugation on the amine-modified glass slide (GS) surface. In the DDH assay, signal probes were directly hybridized with ssDNA array of positive control and ToLCNDV DNA samples and the detection signals were amplified by silver enhancement. Dark black/gray colors were developed on the GS by the result of Ag enhancement, which can be visualized and discriminated by the naked eye. The images were captured using a simple flatbed scanner, and the determined amounts of signal probes were hybridized with their target DNA. Similarly, the SDH assay also performed through two rounds of hybridization between capture probes and target DNA; target DNA and signal probes followed by silver enhancement. The detection signals were found higher in the PCR sample than the RCA and genomic DNA samples because of the presence of increased copy numbers of complementary DNAs in PCR samples. Further, bifunctional AuNP-ssoligo probe shows higher intensity of detection signal than monofunctional probes because it can be hybridized with both strands of dsDNA targets. Moreover, the DDH-based scanometric method showed higher detection sensitivity than the SDH assay-based scanometric method. Overall, bifunctional signal probes showed more detection sensitivity than monofunctional probes in scanometric methods based on both DDH and SDH assays. The limit of detection of this developed scanometric method was optimized (100 zM to 100 pM concentration). Further, DDH assay-based scanometric method shows significant advantages over the SDH assay method, such as cost-effectiveness, because it requires only single probes (signal probes), less time-consuming by the need of only single-step hybridization, and higher detection sensitivity (up to zM). To the best of our knowledge, this is the first attempt made to develop a scanometric-based nanoassay method for the detection of plant viral DNA. This approach will be a remarkable milestone for the application of nanotechnology in the development of nanobiosensor for plant pathogen detection.

Conformational Details of Quantum Dot-DNA Resolved by Förster Resonance Energy Transfer Lifetime Nanoruler.

DNA-nanoparticle conjugates are important tools in nanobiotechnology. Knowing the orientation, function, and length of DNA on nanoparticle surfaces at low nanomolar concentrations under physiological conditions is therefore of great interest. Here, we investigate the conformation of a 31 nucleotides (nt) long DNA attached to a semiconductor quantum dot (QD) via Förster resonance energy transfer (FRET) from Tb-DNA probes hybridized to different positions on the QD-DNA. Precise Tb-to-QD distance determination from 7 to 14 nm along 26 nt of the peptide-appended QD-DNA was realized by time-resolved FRET spectroscopy. The FRET nanoruler measured linear single-stranded (ssDNA) and double-stranded (dsDNA) extensions of ∼0.15 and ∼0.31 nm per base, reflecting the different conformations. Comparison with biomolecular modeling confirmed the denser conformation of ssDNA and a possibly more flexible orientation on the QD surface, whereas the dsDNA was fully extended with radial orientation. The temporally distinct photoluminescence decays of the different DNA-FRET configurations were used for prototypical DNA hybridization assays that demonstrated the large potential for extended temporal multiplexing. The extensive experimental and theoretical analysis of 11 different distances/configurations of the same QD-DNA conjugate provided important information on DNA conformation on nanoparticle surfaces and will be an important benchmark for the development and optimization of DNA-nanobiosensors.

Highly sensitive detection of DNA hypermethylation in melanoma cancer cells

Aberrant hypermethylation of CpG islands in the promoter region of tumor suppressor genes is a promising biomarker for early cancer detection. This methylation status is reflected in the methylation pattern of ctDNA shed from the primary tumor; however, to realize the full clinical utility of ctDNA methylation detection via liquid biopsy for early cancer diagnosis, improvements in the sensitivity and multiplexability of existing technologies must be improved. Additionally, the assay must be cheap and easy to perform in a clinical setting. We report the integration of methylation specific PCR (MSP) to melt curve analysis on giant magnetoresistive (GMR) biosensors to greatly enhance the sensitivity of our DNA hybridization assay for methylation detection. Our GMR sensor is functionalized with synthetic DNA probes that target methylated or unmethylated CpG sites in the MSP amplicon, and measures the difference in melting temperature (Tm) between the two probes (ΔTm), giving an analytical limit of detection down to 0.1% methylated DNA in solution. Additionally, linear regression of ΔTm's for serial dilutions of methylated:unmethylated mixtures allows for quantification of methylation percentage, which could have diagnostic and prognostic utility. Lastly, we performed multiplexed MSP on two different genes, and show the ability of our GMR assay to resolve this mixture, despite their amplicons’ overlapping Tm's in standard EvaGreen melt analysis. The multiplexing ability of our assay and its enhanced sensitivity, without necessitating deep sequencing, represent important steps toward realizing an assay for the detection of methylated ctDNA in plasma for early cancer detection in a clinical setting.

Application of LATE-PCR to Detect Candida and Aspergillus Fungal Pathogens by a DNA Hybridization Assay

Application of LATE-PCR to Detect Candida and Aspergillus Fungal Pathogens by a DNA Hybridization Assay

An integrated all foil based micro device for point of care diagnostic applications

Point-of-Care (POC) diagnostics often fail to meet the market requirements of low cost and advanced functionality, and are often limited to lateral flow based serological diagnostics with reduced sensitivity and specificity. We report here on an integrated microfluidic absorbance measurement device fabricated by roll-to-roll (R2R) compatible manufacturing processes, suitable for low cost POC systems. It is a device exclusively made of foils and takes external light from a low cost LED and converts the point light source to a homogeneous light via a foil based optical filter at the bottom of the device. The light is converted to an electrical signal by an amorphous organic semiconductor (OSC) material, integrated with screen-printed carbon finger on top of the device for electrical measurement. As a proof of principle, we demonstrate DNA hybridization assay, where the target DNA is coupled to magnetic beads for absorbance measurement. The device successfully distinguishes between matched and mismatched DNA hybridization and can differentiate between 1 μM, 50 nM and 2.5 nM DNA target concentrations. The inherent characteristics of the substrates and R2R fabrication concept significantly reduce the cost, making it suitable for POC applications at resource-limited settings.

DNA Hybridization Assay Using Gold Nanoparticles and Electrophoresis Separation Provides 1 pM Sensitivity.

The efficiency of gold nanoparticle (AuNP) dimerization mediated by hybridization between two probe DNA molecules and a complementary target DNA molecule was maximized by examining several possible hybridization combinations. The uniformity of the size of the AuNPs, the use of surface modification appropriate for high hybridization efficiency, together with efficient blocking of nonspecific binding, all contributed to achieving a 1 pM detection limit following conventional gel electrophoresis separation of the DNA-modified AuNP multimers. This practical homogeneous DNA hybridization assay methodology will provide a rapid, cost-effective, and field-portable tool for clinical diagnosis.

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization.

Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution.

Controlling wettability of PECVD-deposited dual organosilicon/carboxylic acid films to influence DNA hybridisation assay efficiency.

Herein, plasma polymerisation of a dual-layer tetraethyl orthosilicate (TEOS) and acrylic acid (AA) film under a specific recipe is performed. Newly deposited films are found to retain a weakly-bound soft layer of partially polymerised acrylic acid (wbAA), which can be ultimately removed by washing. However, when on the surface, this soft layer is shown to be influential in manipulating the properties of a robust covalently-bound AA (cbAA) underlayer when treated appropriately. Specifically, treatment of the as-deposited dual-layer TEOS/AA films via timed incubation in a humidity-controlled environment results in changes in the water contact angle (WCA) of the cbAA, and ultimately the surface of the TEOS/AA, enabling tuning of the wettability of the acrylic acid layer. Through the use of a controlled incubation environment of the TEOS/AA, followed by washing, we have demonstrated that carboxylic-acid containing surfaces with a WCA between 85° and 10° can be routinely generated, using basic apparatus and simple methodology. Moreover, these surfaces not only retain their AA functionality, demonstrated by covalent-linking of amine-terminated single-stranded DNA, but also strongly inhibit non-specific binding of the DNA strands. The efficiency of these surfaces to be used in DNA direct-binding hybridisation assays has been demonstrated, with limits of detection of 1.11 and 1.66 nM being measured.

A Luminex-based single DNA fragment amplification assay as a practical tool for detecting and serotyping dengue virus

Dengue is a mosquito-borne viral infection that can evolve from subclinical to severe forms of disease. Early recognition during initial primary and secondary infections correlates with a reduced case-fatality rate in susceptible groups. The aim of this study was to standardize a DNA hybridization assay based on the Luminex technology for detecting and serotyping dengue virus (DENV). Reference DENVs representing the four different serotypes were used as controls to standardize the test. For validation, 16 DENV isolates obtained from a reference laboratory were analyzed in a double-blind manner to validate the test. Sixty blood samples from patients suspected of having dengue fever were used to evaluate the methodology after the validation step, and the results were compared with the reference semi-nested RT-PCR. Additionally, five human samples of each Zika and Chikungunya confirmed patients were used for specificity analysis. The Luminex-based assay correctly identified all 16 DENV isolates. In the evaluation step, the results of the RT-PCR/Luminex assay showed a concordance of 86.7% with those of the semi-nested RT-PCR. None of other virus infection samples was amplified. This is the first description of a hybridization assay that can discriminate the four DENV serotypes using probes against a single DENV sequence. The results indicated that the RT-PCR/Luminex DENV assay designed and evaluated in this study is a valuable additional tool for the early and rapid detection and serotyping of DENV, which could, in the future, be applied to new targets such as the Zika and Chikungunya viruses.

Fluorescence coupled in-capillary DNA hybridization assay and its application to identification of DNA point mutation

We have developed a fluorescence coupled in-capillary DNA hybridization assay and applied it to the detection of DNA base pair mutation(s). A 15-mer thrombin-binding single-stranded DNA oligonucleotide labeled with 6-carboxyfluorescein (DNA1-FAM) was mixed and hybridized with its complementary DNA (cDNA1) via the in-capillary approach. A fluorescence coupled capillary electrophoresis (CE-FL) was used to measure the status and reaction rate of DNA double strands hybridization under different reaction conditions, and the results were recorded on the electrophoretograms. Recorded electrophoretograms have shown that the in-capillary assay has different DNA hybridization patterns compared to the post-capillary assay. The DNA hybridization efficiency of the in-capillary assay was affected by the molar ratio, the time interval of injection and the volume of DNA oligos. Interestingly, this assay could be used to detect one or two base pair mutation(s) in the target DNA. The in-capillary assay, characterized by an easy operation, reproducible results, and a low instrumental requirement, can be coupled to an online base pair mutation-based detection system, which would facilitate the related small-scale research analysis at non-major research centers.

Important hemoprotozoan diseases of livestock: Challenges in current diagnostics and therapeutics: An update.

Hemoprotozoan parasites pose a serious threat to the livestock population in terms of mortality, reduced milk yield and lowered draft power. Diagnosis of these diseases often poses a challenging task. Needless to say that impact of disease in health and productivity is huge though a fair economic assessment on the quantum of economic loss associated is yet to be worked out from India. The diagnosis of hemoprotozoan infections largely depends on various laboratory-based diagnostic methods as the clinical manifestations are often inconspicuous and non-specific. Traditional diagnostic methods rely on microscopical demonstration of infective stages in blood or tissue fluids. However, it is laborious, lesser sensitive, and cannot differentiate between morphologically similar organisms. Recent development in the technologies has opened new avenues for improvement in the accurate diagnosis of parasitic infections. Serological tests are simple, fast but lack specificity. With advent of molecular techniques, as DNA hybridization assays, polymerase chain reaction and its modifications ensure the detection of infection in the latent phase of the disease. Nucleic acid-based assays are highly sensitive, free from immunocompetence and can differentiate between morphologically similar parasites. With the advent of newer diagnostics complemented with traditional ones will be of huge help for targeted selective treatment with better chemotherapeutic agents.

Description of Variovorax humicola sp. nov., isolated from a forest topsoil.

Employing a modified cultivation method, we studied two bacterial strains, UC10 and UC38T, found on the Kyonggi University campus, Suwon in Gyeonggi-Do province, South Korea. These strains were non-spore-forming, Gram-stain-negative, motile and rod-shaped. Growth occurred in the presence of 0-2 % (w/v) NaCl, at pH 4-9 and a temperature range of 4-35 °C. On an R2A agar plate incubated for 5 days at 28 °C, irregular, raised and pale-yellowish colonies were observed. Comparative analysis of nearly full-length 16S rRNA gene sequences indicated that these strains were closely related to Variovorax guangxiensis GXGD002T, with 98.6 % similarity. Strains UC10 and UC38T were 98.0 % similar to V.ariovorax soli GH9-3T; 97.8 % to V.ariovorax dokdonensis DS-43T; 97.3-97.7 % to V.ariovorax ginsengisoli Gsoil 3165T; 97.7-98.0 % to V.ariovorax paradoxus IAM 12373T; 97.4-97.6 % to V.ariovorax defluvii 2C1-bT; and 97.3-97.4 % to V.ariovorax boronicumulans BAM-48T. The predominant ubiquinone was Q-8. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 0 cyclo. DNA-DNA hybridization assays indicated 89.2-91.4 % genomic DNA similarity between strains UC10 and UC38T. Moreover, genomic DNA similarity between these novel strains and reference strains of the genus Variovoraxwas less than the 70 %. Based on these results, strain UC38T was designated a representative of a novel species of the genus Variovorax, with the proposed name Variovorax humicola sp. nov. The type strain is UC38T (=KACC 18501T=NBRC 111520T).

Polystyrene Core–Silica Shell Particles with Defined Nanoarchitectures as a Versatile Platform for Suspension Array Technology

The need for rapid and high-throughput screening in analytical laboratories has led to significant growth in interest in suspension array technologies (SATs), especially with regard to cytometric assays targeting a low to medium number of analytes. Such SAT or bead-based assays rely on spherical objects that constitute the analytical platform. Usually, functionalized polymer or silica (SiO2) microbeads are used which each have distinct advantages and drawbacks. In this paper, we present a straightforward synthetic route to highly monodisperse SiO2-coated polystyrene core-shell (CS) beads for SAT with controllable architectures from smooth to raspberry- and multilayer-like shells by varying the molecular weight of poly(vinylpyrrolidone) (PVP), which was used as the stabilizer of the cores. The combination of both organic polymer core and a structurally controlled inorganic SiO2 shell in one hybrid particle holds great promises for flexible next-generation design of the spherical platform. The particles were characterized by electron microscopy (SEM, T-SEM, and TEM), thermogravimetry, flow cytometry, and nitrogen adsorption/desorption, offering comprehensive information on the composition, size, structure, and surface area. All particles show ideal cytometric detection patterns and facile handling due to the hybrid structure. The beads are endowed with straightforward modification possibilities through the defined SiO2 shells. We successfully implemented the particles in fluorometric SAT model assays, illustrating the benefits of tailored surface area which is readily available for small-molecule anchoring. Very promising assay performance was shown for DNA hybridization assays with quantification limits down to 8 fmol.