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Digital PCR (dPCR) is a powerful method for highly sensitive and precise quantification of nucleic acids. However, designing and optimizing new multiplex dPCR assays using target sequence specific probes remains cumbersome, since fluorescent signals must be optimized for every new target panel. As a solution, we established a generic fluorogenic 6-plex reporter set, based on mediator probe technology, that decouples target detection from signal generation. This generic reporter set is compatible with different target panels and thus provides already optimized fluorescence signals from the start of new assay development. Generic reporters showed high population separability in a colorimetric 6-plex mediator probe dPCR, due to their tailored fluorophore and quencher selection. These reporters were further tested using different KRAS, NRAS and BRAF single-nucleotide polymorphisms (SNP), which are frequent point mutation targets in liquid biopsy. We specifically quantified SNP targets in our multiplex approach down to 0.4 copies per microliter (cp/µL) reaction mix, equaling 10 copies per reaction, on a wild-type background of 400 cp/µL for each, equaling 0.1% variant allele frequencies. We also demonstrated the design of an alternative generic reporter set from scratch in order to give detailed step-by-step guidance on how to systematically establish and optimize novel generic reporter sets. Those generic reporter sets can be customized for various digital PCR platforms or target panels with different degrees of multiplexing. [ABSTRACT FROM AUTHOR]

Digital PCRs (dPCRs) are widely used methods for the detection and quantification of rare abundant sequences relevant to fields such as liquid biopsy or oncology. In order to increase the information content and save valuable sample materials, there is a significant need for digital multiplexing methods that are easy to establish, analyse, and interpret, and ideally allow the usage of existing lab equipment. Herein, we present a novel reporter emission multiplexing approach for the digital PCR method (REM-dPCR), which meets these requirements. It further increases the multiplexing capacity of commercial dPCR devices. For example, we present a stepwise increase in multiplexing degrees from a monochrome two-plex assay in one detection channel to a six-plex REM-dPCR assay in a three-color dPCR device for KRAS/BRAF single nucleotide polymorphism (SNP) target sequences. The guidelines for the REM-dPCR design are presented, and the process from duplex to six-plex assay establishment, taking into account the target sequence-dependent effects on assay performance, is discussed. Furthermore, the assay-specific, sensitive and precise quantification of different fractions of KRAS mutant and wild-type DNA sequences in different ratios is demonstrated. To increase the device capacitance and the degree of multiplexing, the REM-dPCR uses the advantage of n target-independent reporter molecules in combination with target sequence-specific mediator probes. Different reporter types are labelled with fluorophores of different signal intensities but not necessarily different emission spectra. This leads to the generation of n independent single-positive populations in the dataspace, created by k detection channels, whereby n > k and n ≥ 2. By usage of target-independent but population-specific reporter types, a fixed set of six optimized signalling molecules could be defined. This reporter set enables the robust generation and precise differentiation of multiple fluorescence signals in dPCRs and can be transferred to new target panels. The set which enables stable signal generation and differentiation in a specified device would allow easy transfer to new target panels. [ABSTRACT FROM AUTHOR]

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RNA interference (RNAi) is a powerful therapeutic approach for messenger RNA (mRNA) level regulation in human cells. RNAi can be triggered by small interfering RNAs (siRNAs) which are delivered by non-viral carriers, e.g., dendriplexes. siRNA quantification inside carriers is essential in drug delivery system development. However, current siRNA measuring methods either are not very sensitive, only semi-quantitative or not specific towards intact target siRNA sequences. We present a novel reverse transcription real-time PCR (RT-qPCR)-based application for siRNA quantification in drug formulations. It enables specific and highly sensitive quantification of released, uncomplexed target siRNA and thus also indirect assessment of siRNA stability and concentration inside dendriplexes. We show that comparison with a dilution series allows for siRNA quantification, exclusively measuring intact target sequences. The limit of detection (LOD) was 4.2 pM (±0.2 pM) and the limit of quantification (LOQ) 77.8 pM (±13.4 pM) for uncomplexed siRNA. LOD and LOQ of dendriplex samples were 31.6 pM (±0 pM) and 44.4 pM (±9.0 pM), respectively. Unspecific non-target siRNA sequences did not decrease quantification accuracy when present in samples. As an example of use, we assessed siRNA complexation inside dendriplexes with varying nitrogen-to-phosphate ratios. Further, protection of siRNA inside dendriplexes from RNase A degradation was quantitatively compared to degradation of uncomplexed siRNA. This novel application for quantification of siRNA in drug delivery systems is an important tool for the development of new siRNA-based drugs and quality checks including drug stability measurements. [ABSTRACT FROM AUTHOR]

We demonstrate detection and quantification of bacterial load with a novel microfluidic one-pot wash-free fluorescence in situ hybridization (FISH) assay in droplets. The method offers minimal manual workload by only requiring mixing of the sample with reagents and loading it into a microfluidic cartridge. By centrifugal microfluidic step emulsification, our method partitioned the sample into 210 pL (73 µm in diameter) droplets for bacterial encapsulation followed by in situ permeabilization, hybridization, and signal detection. Employing locked nucleic acid (LNA)/DNA molecular beacons (LNA/DNA MBs) and NaCl-urea based hybridization buffer, the assay was characterized with Escherichia coli, Klebsiella pneumonia, and Proteus mirabilis. The assay performed with single-cell sensitivity, a 4-log dynamic range from a lower limit of quantification (LLOQ) at ~3 × 103 bacteria/mL to an upper limit of quantification (ULOQ) at ~3 × 107 bacteria/mL, anda linearity R2 = 0.976. The total time-to-results for detection and quantification was around 1.5 hours. [ABSTRACT FROM AUTHOR]

We present a proof-of-principle study on automated, highly sensitive and multiplexed qPCR quantification by centrifugal microfluidics. The MRD disk can be used for standardisation of repetitive, longitudinal assays with high requirements on reproducibility and sensitivity, such as cancer monitoring. In contrast to high-throughput qPCR automation by bulky and expensive robotic workstations we employ a small centrifugal microfluidic instrument, addressing the need of low- to mid-throughput applications. As a potential application we demonstrate automated minimum residual disease (MRD) monitoring of prognostic markers in patients with acute lymphoblastic leukaemia (ALL). The disk-workflow covers all aspects of clinical gold standard MRD quantification: generation of standard curves, specificity controls, no template controls and quantification of the ALL patient sample. We integrated a highly sensitive, colorimetric 2-plex analysis of MRD targets, as well as a 2-plex analysis of reference genes, both in parallel and in a single LabDisk cartridge. For this purpose, a systematic procedure for crosstalk- and signal-to-noise-optimisation is introduced, providing a guideline for efficient multiplex readout inside microfluidic platforms. The qPCR standard curves (n = 12/12) generated on-disk reach clinically required linearity (R2 = 98.1% to R2 = 99.8%). In three consecutive MRD disk runs with an ALL patient sample containing the two representative MRD targets VH3D3D5JH3 and VkIkde, we observe high accordance between the on-disk quantifications (48 ± 6 copies/reaction and 69 ± 6 copies/reaction) and the expected concentrations (57 copies/reaction for both targets). In comparison to the clinical gold standard of manually pipetted, singleplex assays, the MRD disk yields comparable limit of quantification (1 × 10−4) in n = 6/6 analyses (vs. n = 4/4 in gold standard) and a limit of detection (1 × 10−5) in n = 6/6 analysis (vs. n = 2/4 in gold standard). The automation reduces the risk of manual liquid handling errors, making the MRD disk an attractive solution to assure reproducibility in moderate-throughput, longitudinal gene quantification applications. [ABSTRACT FROM AUTHOR]

We introduce a new concept for centrifugal microfluidics that enables fully automated serial dilution generation without any additional means besides temperature control. The key feature is time-independent, serial valving of mixing chambers by fill-level-coupled temperature change rate (FLC-TCR) actuated valving. The automated dilution is realized under continuous rotation which enables reliable control of wetting liquids without the need for any additional fabrication steps such as hydrophobic coating. All fluidic features are implemented in a monolithic fashion and disks are manufactured by foil thermoforming for scalable manufacturing. The new valving concept is demonstrated to reliably prevent valving if the diluted sample is not added to the mixing chamber (n = 30) and ensure valving if the dilution stage is completed (n = 15). The accuracy and precision of automated serial dilutions are verified by on-disk generation of qPCR standard curve dilutions and compared with manually generated reference dilutions. In a first step, the 5-log-stage standard curves are evaluated in a commercial qPCR thermocycler revealing a linearity of R2≥ 99.92% for the proposed LabDisk method vs. R2≥ 99.67% in manual reference dilutions. In a second step, the disk automated serial dilutions are combined with on-disk qPCR thermocycling and readout, both inside a LabDisk player. A 4-log-stage linearity of R2≥ 99.81% and a sensitivity of one leukemia associated ETV6-RUNX1 mutant DNA copy in a background of 100 000 wild-type DNA copies are achieved. [ABSTRACT FROM AUTHOR]

Non-fouling TiO2 surfaces are attractive for a wide range of applications such as biosensors and medical devices, where biologically inert surfaces are needed. Typically, this is achieved by controlled surface modifications which prevent protein adsorption. For example, polyethylene glycol (PEG) or PEG-derived polymers have been widely applied to render TiO2 surfaces biologically inert. These surfaces have been further modified in order to achieve specific bio-activation. Therefore, there have been efforts to specifically functionalize TiO2 surfaces with polymers with embedded biotin motives, which can be used to couple streptavidin for further functionalization. As an alternative, here a streptavidin layer was immobilized by self-assembly directly on a biotinylated TiO2 surface, thus forming an anti-adhesive matrix, which can be selectively bio-activated. The anti-adhesive properties of these substrates were analyzed by studying the interaction of the surface coating with fibronectin, lysozym, and osteoblast cells using surface plasmon resonance spectroscopy, atomic force microscopy, and light microscopy. In contrast to non-modified TiO2 surfaces, streptavidin-coated TiO2 surfaces led to a very biologically inert substrate, making this type of surface coating a promising alternative to polymer coatings of TiO2 surfaces. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2012. [ABSTRACT FROM AUTHOR]

Simple Summary: Cancer treatment strategies and their follow-up monitoring are changing to personalized therapies, based on molecular genetic information from the individual person. Liquid biopsy, where this molecular information is derived from body fluids such as blood, has the potential to provide a systemic fingerprint of cancer dynamics, and, compared to tissue biopsy, is much less invasive for the patient. We used the previously published mediator probe PCR technology for liquid biopsy detection of several mutations in one reaction, so-called digital multiplex PCR. Quantification of point mutations in plasma eluates from follow-up patients using 4-plex digital assays showed a comparable performance to reference 2-plex assays. As a key feature, the presented multiplex assays require no laborious optimization as they use the same concentrations and cycling conditions for all targets. This allows for flexible design and interchangeable target panels, thus the assay is easily adaptable for individual patient monitoring and reduces sample consumption. There is an increasing demand for optimization-free multiplex assays to rapidly establish comprehensive target panels for cancer monitoring by liquid biopsy. We present the mediator probe (MP) PCR for the quantification of the seven most frequent point mutations and corresponding wild types (KRAS and BRAF) in colorectal carcinoma. Standardized parameters for the digital assay were derived using design of experiments. Without further optimization, the limit of detection (LoD) was determined through spiking experiments with synthetic mutant DNA in human genomic DNA. The limit of blank (LoB) was measured in cfDNA plasma eluates from healthy volunteers. The 2-plex and 4-plex MP ddPCR assays showed a LoB of 0 copies/mL except for 4-plex KRAS G13D (9.82 copies/mL) and 4-plex BRAF V600E (16.29 copies/mL) and allele frequencies of 0.004% ≤ LoD ≤ 0.38% with R2 ≥ 0.98. The quantification of point mutations in patient plasma eluates (18 patients) during follow-up using the 4-plex MP ddPCR showed a comparable performance to the reference assays. The presented multiplex assays need no laborious optimization, as they use the same concentrations and cycling conditions for all targets. This facilitates assay certification, allows a fast and flexible design process, and is thus easily adaptable for individual patient monitoring. [ABSTRACT FROM AUTHOR]

Increasing cell adhesion on implant surfaces is an issue of high biomedical importance. Early colonization with endogenous cells reduces the risk of bacterial contamination and enhances the integration of an implant into the diverse cellular tissues surrounding it. In vivo integration of implants is controlled by a complex spatial and temporal interplay of cytokines and adhesive molecules. The concept of a multi-biofunctionalized TiO 2 surface for stimulating bone and soft tissue growth is presented here. All supramolecular architectures were built with a biotin-streptavidin coupling system. Biofunctionalization of TiO 2 with immobilized FGF-2 and heparin could be shown to selectively increase the proliferation of fibroblasts while immobilized BMP-2 only stimulated the growth of osteoblasts. Furthermore, TiO 2 surfaces biofunctionalized with either the BMP-2 or BMP-2/6 growth factor and the cell adhesion-enhancing protein fibronectin showed higher osteoblast adhesion than a TiO 2 surface functionalized with only one of these proteins. In conclusion, the presented immobilization strategy is applicable in vivo for a selective surface coating of implants in both hard and connective tissue. The combined immobilization of different extracellular proteins on implants has the potential to further influence cell-specific reactions. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 2910-2922, 2018., (© 2018 Wiley Periodicals, Inc.)

Mediator probe (MP) PCR is a real-time PCR approach that uses standardized universal fluorogenic reporter oligonucleotides (UR) in conjunction with label-free sequence-specific probes. To enable multiplex real-time MP PCR, we designed a set of five optimized URs with different fluorescent labels. Performance of the optimized URs was verified in multiplex real-time MP PCR for the detection of a pentaplex food panel and a quadruplex methicillin-resistant Staphylococcus aureus (MRSA) panel. Results were comparable to corresponding multiplex hydrolysis probe (HP) PCR, also designated as TaqMan PCR. Analyses of MRSA DNA standards and DNA extracted from patient swab samples showed improved lower limits of detection (LoDs) by a factor of 2-5 when using quadruplex real-time MP PCR instead of HP PCR. The novel set of standardized URs we present here simplifies development of multiplex real-time PCR assays by requiring only the design of label-free probes. In the future, real-time PCR master mixes could be augmented with up to five standardized fluorogenic URs, each emitting light at a different wavelength.

Mediator probe PCR (MP PCR) is a novel detection format for real-time nucleic acid analysis. Label-free mediator probes (MP) and fluorogenic universal reporter (UR) oligonucleotides are combined to accomplish signal generation. Compared to conventional hydrolysis probe PCRs costs can thus be saved by using the same fluorogenic UR for signal generation in different assays. This tutorial provides a practical guideline to MP and UR design. MP design rules are very similar to those of hydrolysis probes. The major difference is in the replacement of the fluorophore and quencher by one UR-specific sequence tag, the mediator. Further protocols for the setup of reactions, to detect either DNA or RNA targets with clinical diagnostic target detection as models, are explained. Ready to use designs for URs are suggested and guidelines for their de novo design are provided as well, including a protocol for UR signal generation characterization.

The biomodification of surfaces, especially titanium, is an important issue in current biomedical research. Regarding titanium, it is also important to ensure a specific protein modification of its surface because here protein binding that is too random can be observed. Specific nanoscale architectures can be applied to overcome this problem. As recently shown, streptavidin can be used as a coupling agent to immobilize biotinylated fibronectin (bFn) on a TiO(X) surface. Because of the conformation of adsorbed biotinylated fibronectin on a streptavidin monolayer, it is possible to adsorb more streptavidin and biotinylated fibronectin layers. On this basis, an alternating protein multilayer can be built up. In contrast to common layer-by-layer technology, in this procedure the mechanism of layer adsorption is very specific because of the interaction of biotin and streptavidin. In addition, we showed that the assembly of this multilayer system and its stability are dependent on the degree of labeling of biotinylated fibronectin. Hence we conclude that it is possible to build up well-defined nanoscale protein architectures by varying the degree of labeling of biotinylated fibronectin.

It is well-known that protein-modified implant surfaces such as TiO(2) show a higher bioconductivity. Fibronectin is a glycoprotein from the extracellular matrix (ECM) with a major role in cell adhesion. It can be applied on titanium oxide surfaces to accelerate implant integration. Not only the surface concentration but also the presentation of the protein plays an important role for the cellular response. We were able to show that TiO(X) surfaces modified with biotinylated fibronectin adsorbed on a streptavidin-silane self-assembly multilayer system are more effective regarding osteoblast adhesion than surfaces modified with nonspecifically bound fibronectin. The adsorption and conformation behavior of biotinylated and nonbiotinylated (native) fibronectin was studied by surface plasmon resonance (SPR) spectroscopy and atomic force microscopy (AFM). Imaging of the protein modification revealed that fibronectin adopts different conformations on nonmodified compared to streptavidin-modified TiO(X) surfaces. This conformational change of biotinylated fibronectin on the streptavidin monolayer delivers a fibronectin structure similar to the conformation inside the ECM and therefore explains the higher cell affinity for these surfaces., (© 2011 American Chemical Society)