Green Synthesis of Silver Nanoparticles Using Hypericum perforatum L. Aqueous Extract with the Evaluation of Its Antibacterial Activity against Clinical and Food Pathogens.

The rapid development of nanotechnology and its applications in medicine has provided the perfect solution against a wide range of different microbes, especially antibiotic-resistant ones. In this study, a one-step approach was used in preparing silver nanoparticles (AgNPs) by mixing silver nitrate with hot Hypericum perforatum (St. John's wort) aqueous extract under high stirring to prevent agglomeration. The formation of silver nanoparticles was monitored by continuous measurement of the surface plasma resonance spectra (UV-VIS). The effect of St. John's wort aqueous extract on the formation of silver nanoparticles was evaluated and fully characterized by using different physicochemical techniques. The obtained silver nanoparticles were spherical, monodisperse, face-centered cubic (fcc) crystal structures, and the size ranges between 20 to 40 nm. They were covered with a capping layer of organic compounds considered as a nano dimension protective layer that prevents agglomeration and sedimentation. AgNPs revealed antibacterial activity against both tested Gram-positive and Gram-negative bacterial strains causing the formation of 13-32 mm inhibition zones with MIC 6.25-12.5 µg/mL; Escherichia coli strains were resistant to tested AgNPs. The specific growth rate of S. aureus was significantly reduced due to tested AgNPs at concentrations ≥½ MIC. AgNPs did not affect wound migration in fibroblast cell lines compared to control. Our results highlighted the potential use of AgNPs capped with plant extracts in the pharmaceutical and food industries to control bacterial pathogens' growth; however, further studies are required to confirm their wound healing capability and their health impact must be critically evaluated.

Identification of Major Constituents of Hypericum perforatum L. Extracts in Syria by Development of a Rapid, Simple, and Reproducible HPLC-ESI-Q-TOF MS Analysis and Their Antioxidant Activities.

Hypericum perforatum Linn (St. John's wort) is a popular and widespread medicine in Syria, which is used for a wide range of conditions, including gastrointestinal diseases, heart disease, skin diseases, and psychological disorders. This widespread use prompted us to identify the main compounds of this plant from Syria that are responsible for its medicinal properties, especially since its components differ between countries according to the nature of the soil, climate, and altitude. This is, to the best of our knowledge, the first report in which St. John's wort, a plant native to Syria, is extracted using different solvents and its most important compounds are identified. In this study, the dried above-ground parts, i.e., leaves, stem, petals, and flowers, were extracted using different solvents (water, ethanol, methanol, and acetone) and extraction protocols. By increasing the polarity of the solvent, higher yields were obtained, indicating that mainly hydrophobic compounds were extracted. Therefore, we conclude that extraction using the tea method or using a mixture of water and organic solvents resulted in higher yields compared with pure organic solvents or continuous boiling with water for long periods. The obtained extracts were analyzed using high-performance liquid chromatography equipped with a diode array detector (HPLC-DAD), coupled with UV-visible spectrophotometry at a full spectrum (200-800 nm). The HPLC spectra of the extracts were almost identical at three wavelengths (260 nm for phloroglucinols (hyperforin and derivates), 590 nm for naphthodianthrones (hypericins), and 350 nm for other flavonols, flavones, and caffeoylquinic acids), with differences observed only in the intensity of the peaks. This indicates that the same compounds were obtained using different solvents, but in different amounts. Five standards (chlorogenic acid, quercetin, quercitrin hydrate, hyperoside, and hypericin) were used, and a comparison with retention times and ultraviolet (UV) spectra reported in the literature was performed to identify 10 compounds in these extracts: hyperforin, adhyperforin, hypericin, rutin, quercetin, quercitrin, quercitrin hydrate, hyperoside, biapigenin, and chlorogenic acid. Although the European Pharmacopoeia still describes ultraviolet spectroscopy as a method for determining the quantity of Hyperici herba, interference from other metabolites can occur. Combined HPLC-DAD and electrospray ionization-mass spectrometry (LC-ESI-MS) in the positive mode have therefore also been used to confirm the presence of these compounds in the extracts by correlating known masses with the identified masses or through characteristic fragmentation patterns. Total phenolic contents of the extracts were determined by the Folin-Ciocalteu assay, and antioxidant activity was evaluated as free radical scavenging capacity using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) assays. The results indicate that the aqueous extracts prepared by the tea method gave the highest total phenols, while the pure organic solvents gave very low phenols. Also, the extracts that contain the largest amount of phenols gave lower IC50 values or higher antioxidant activity than that of others.

Aptamer-Modified Hydrogels.

Hydrogels have attracted much attention especially due to their biocompatibility and their potential for stimulus responsiveness. By combining hydrogels with aptamers, biological recognition and responsiveness can be added to hydrogels, thereby opening path to advanced applications in biosensing and biomedicine. Within this chapter aptamers will be introduced and their contributions to biological responsiveness of hydrogels will be described. Especially the aptamer-based mechanisms that result in biological responsiveness will be explained and examples for the application of these mechanisms will be given ranging from rather simple sensing approaches to advanced materials for tissue engineering and drug delivery. Since aptamers are not only highly specific bioreceptors, but represent switchable structures that can be easily manipulated using well-known DNA techniques, the combination of aptamers and hydrogels facilitates the rational design of well-programmable and target-responsive smart hydrogels.

Hypericum perforatum L.-Mediated Green Synthesis of Silver Nanoparticles Exhibiting Antioxidant and Anticancer Activities.

This contribution focuses on the green synthesis of silver nanoparticles (AgNPs) with a size < 100 nm for potential medical applications by using silver nitrate solution and Hypericum Perforatum L. (St John's wort) aqueous extracts. Various synthesis methods were used and compared with regard to their yield and quality of obtained AgNPs. Monodisperse spherical nanoparticles were generated with a size of approximately 20 to 50 nm as elucidated by different techniques (SEM, TEM). XRD measurements showed that metallic silver was formed and the particles possess a face-centered cubic structure (fcc). SEM images and FTIR spectra revealed that the AgNPs are covered by a protective surface layer composed of organic components originating from the plant extract. Ultraviolet-visible spectroscopy, dynamic light scattering, and zeta potential were also measured for biologically synthesized AgNPs. A potential mechanism of reducing silver ions to silver metal and protecting it in the nanoscale form has been proposed based on the obtained results. Moreover, the AgNPs prepared in the present study have been shown to exhibit a high antioxidant activity for 2, 2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) radical cation, and super oxide anion radical and 2,2-diphenyl-1-picrylhydrazyl. Synthesized AgNPs showed high cytotoxicity by inhibiting cell viability for Hela, Hep G2, and A549 cells.

All-Optical Planar Polymer Waveguide-Based Biosensor Chip Designed for Smartphone-Assisted Detection of Vitamin D.

An all-optical plasmonic sensor platform designed for smartphones based on planar-optical waveguide structures integrated in a polymer chip is reported for the first time. To demonstrate the applicability of the sensor system for biosensing purposes, the detection of 25-hydroxyvitamin D (25OHD) in human serum samples using an AuNP-enhanced aptamer-based assay was demonstrated. With the aid of the developed assay sensitivity of 0.752 pixel/nM was achieved for 25OHD concentrations ranging from 0-100 nM. The waveguide structure of the sensor enables miniaturisation and parallelisation, thus, demonstrates the potential for simultaneous detection of various analytes including biomarkers. The entire optical arrangement can be integrated into a single polymer chip which allows for large scale and cost-efficient sensor fabrication. The broad utilization and access of smartphone electronics make the proposed design most attractive for its wider use in lab-on-chip applications.

Aptamers vs. antibodies as capture probes in optical porous silicon biosensors.

Over the past decade aptamers have emerged as a promising class of bioreceptors for biosensing applications with significant advantages over conventional antibodies. However, experimental studies comparing aptasensors and immunosensors, under equivalent conditions, are limited and the results are inconclusive, in terms of benefits and limitations of each bioreceptor type. In the present work, the performance of aptamer and antibody bioreceptors for the detection of a his-tagged protein, used as a model target, is compared. The bioreceptors are immobilized onto a nanostructured porous silicon (PSi) thin film, used as the optical transducer, and the target protein is detected in a real-time and label-free format by reflective interferometric Fourier transform spectroscopy. For the antibodies, random-oriented immobilization onto the PSi nanostructure results in a poor biosensing performance. Contrary, Fc-oriented immobilization of the antibodies shows a similar biosensing performance to that exhibited by the aptamer-based biosensor, in terms of binding rate, dynamic detection range, limit of detection and selectivity. The aptasensor outperforms in terms of its reusability and storability, while the immunosensor could not be regenerated for subsequent experiments.

SPR Biosensor Based on Polymer Multi-Mode Optical Waveguide and Nanoparticle Signal Enhancement.

We present a surface plasmon resonance (SPR) biosensor that is based on a planar-optical multi-mode (MM) polymer waveguide structure applied for the detection of biomolecules in the lower nano-molar (nM) range. The basic sensor shows a sensitivity of 608.6 nm/RIU when exposed to refractive index changes with a measurement resolution of 4.3 × 10-3 RIU. By combining the SPR sensor with an aptamer-functionalized, gold-nanoparticle (AuNP)-enhanced sandwich assay, the detection of C-reactive protein (CRP) in a buffer solution was achieved with a response of 0.118 nm/nM. Due to the multi-mode polymer waveguide structure and the simple concept, the reported biosensor is well suited for low-cost disposable lab-on-a-chip applications and can be used with rather simple and economic devices. In particular, the sensor offers the potential for fast and multiplexed detection of several biomarkers on a single integrated platform.

Aptazymes: Expanding the Specificity of Natural Catalytic Nucleic Acids by Application of In Vitro Selected Oligonucleotides.

Aptazymes are synthetic molecules composed of an aptamer domain and a catalytic active nucleic acid unit, which may be a ribozyme or a DNAzyme. In these constructs the aptamer domain serves as a molecular switch that can regulate the catalytic activity of the ribozyme or DNAzyme subunit. This regulation is triggered by binding of the aptamers target molecule, which causes significant structural changes in the aptamer and thus in the entire aptazyme. Therefore, aptazymes function similar to allosteric enzymes, whose catalytic activity is regulated by binding of ligands (effectors) to allosteric sites due to alteration of the three-dimensional structure of the active site of the enzyme. In case of aptazymes, the allosteric site is composed of an aptamer. Aptazymes can be designed for different applications and have already been used in analytical assays as well as for the regulation of gene expression.

Development of Aptamer-Based TID Assays Using Thermophoresis and Microarrays.

Aptamers are single-stranded oligonucleotides which can be used as alternative recognition elements for protein detection, because aptamers bind their targets with a high affinity similar to antibodies. Due to the targetinduced conformational changes of aptamers, these oligonucleotides can be applied in various biosensing platforms. In this work, aptamers directed against the vascular endothelial growth factor (VEGF) were used as a model system. VEGF plays a key role in physiological angiogenesis and vasculogenesis. Furthermore, VEGF is involved in the development and growth of cancer and other diseases like agerelated macular degeneration, rheumatoid arthritis, diabetes mellitus, and neurodegenerative disorders. Detecting the protein biomarker VEGF is therefore of great importance for medical research and diagnostics. In this research, VEGFbinding aptamers were investigated for the systematic development of a targetinduced dissociation (TID) assay utilizing thermophoresis and microarrays. The established aptamer-microarray allowed for the detection of 0.1 nM of VEGF. Furthermore, the systematic development of the TID method using the VEGF model protein could help to develop further TID assays for the detection of various protein biomarkers.

Production of polycaprolactone nanoparticles with hydrodynamic diameters below 100 nm.

Cancer is a worldwide increasing burden and its therapy is often challenging and causes severe side effects in healthy tissue. If drugs are loaded into nanoparticles, side effects can be reduced, and efficiency can be increased via the enhanced permeability and retention effect. This effect is based on the fact that nanoparticles with sizes from 10 to 200 nm can accumulate in tumor tissue due to their leaky vasculature. In this work, we produced polycaprolactone (PCL) in the sizes 1.8, 5.4, and 13.6 kDa and were able to produce spherical shaped nanoparticles with mean diameters of 64 ± 19 nm out of the PCL5.4 and 45 ± 8 nm out of the PCL13.6 reproducibly. By encapsulation of paclitaxel the diameter of that nanoparticles did not increase, and we were able to encapsulate 73 ± 7 fmol paclitaxel per 1000 particles in the PCL5.4-nanoparticles and 35 ± 8 fmol PTX per 1000 PCL13.6-nanoparticles. Furthermore, we coupled the aptamer S15 to preformed PCL5.4-nanoparticles resulting in particles with a hydrodynamic diameter of 153 nm. This offers the opportunity to use these nanoparticles for targeted drug delivery.

Aptamer-Modified Magnetic Beads in Biosensing.

Magnetic beads (MBs) are versatile tools for the purification, detection, and quantitative analysis of analytes from complex matrices. The superparamagnetic property of magnetic beads qualifies them for various analytical applications. To provide specificity, MBs can be decorated with ligands like aptamers, antibodies and peptides. In this context, aptamers are emerging as particular promising ligands due to a number of advantages. Most importantly, the chemical synthesis of aptamers enables straightforward and controlled chemical modification with linker molecules and dyes. Moreover, aptamers facilitate novel sensing strategies based on their oligonucleotide nature that cannot be realized with conventional peptide-based ligands. Due to these benefits, the combination of aptamers and MBs was already used in various analytical applications which are summarized in this article.

Aptamer-based detection of adenosine triphosphate via qPCR.

Sensitive and specific detection and quantification of small molecules often remain challenging. We developed a novel magnetic bead-based aptamer-assisted real-time PCR (Apta-qPCR) assay to provide a versatile platform for quantification of small molecules. The assay has been realized for the detection of ATP as a model system. The assay relies on a combination of qPCR with the target-induced dissociation (TID) of ATP aptamer from an oligonucleotide, complementary to the ATP binding site of the aptamer. The complementary oligonucleotide was immobilized on deoxythymidine (dT)-modified magnetic beads (dT-beads) and hybridized with the aptamer. The presence of ATP resulted in dissociation of the aptamer from the dT-beads and the dissociated aptamer was quantified using qPCR. The Apta-qPCR assay was able to detect 17nM ATP with a broad dynamic range from 50nM to 5mM. The assay is label-free, and real-time PCR-based detection of aptamer facilitates high sensitivity. The presented method is highly versatile and can be applied to various aptamer-target pairs to allow detection of a broad range of target analytes.

Rapid and label-free detection of protein a by aptamer-tethered porous silicon nanostructures.

Protein A, which is secreted by and displayed on the cell membrane of Staphylococcus aureus is an important biomarker for S. aureus. Thus, its rapid and specific detection may facilitate the pathogen identification and initiation of proper treatment. Herein, we present a simple, label-free and rapid optical biosensor enabling specific detection of protein A. Protein A-binding aptamer serves as the capture probe and is immobilized onto a nanostructured porous silicon thin film, which serves as the optical transducer element. We demonstrate high sensitivity of the biosensor with a linear detection range between 8 and 23µM. The apparent dissociation constant was determined as 13.98µM and the LoD is 3.17µM. Harnessing the affinity between protein A and antibodies, a sandwich assay format was developed to amplify the optical signal associated with protein A capture by the aptamer. Using this approach, we increase the sensitivity of the biosensor, resulting in a three times lower LoD.

Detection of ochratoxin A by aptamer-assisted real-time PCR-based assay (Apta-qPCR).

Detection of food toxins with high sensitivity is very important and challenging. Ochratoxin A (OTA) is frequently present as food contaminant in contaminated grains and grain derivatives such as bread and beer. In this work, a target-induced dissociation (TID) based aptamer-assisted real-time PCR-based assay (apta-qPCR) is developed that features effective detection of OTA. Apta-qPCR effectively combines the capabilities of aptamer to be amplified, being a nucleotide sequence, with its specific interaction with the corresponding target molecule. Compared to commonly used fluorescence-based and colorimetric methods, the sensitivity of qPCR to detect a nucleotide sequence (aptamer) has ameliorated the sensitivity of the aptamer-based detection of OTA. Here, the OTA aptamer was immobilized on the magnetic beads coated with d(T)25 (dT beads). A sequence complementary to the OTA-binding portion of the aptamer was used as a linker between dT beads and the aptamer sequence. When OTA was added, the aptamer was released from the dT beads due to TID. The resulting assay was able to detect 0.009 ng/mL OTA with a wide dynamic range of 0.039-1000 ng/mL. Apta-qPCR can be easily transferred to other small molecules for highly sensitive detection using corresponding aptamers.

Comparing two conventional methods of emulsion PCR and optimizing of Tegosoft-based emulsion PCR.

The selection of aptamers represents a promising route in the development of high affinity ligands. In these processes the formation of by-products is a common problem during the PCR-based amplification of complex oligonucleotide libraries. One approach to overcome this drawback is to separate each template oligonucleotide into an individual reaction compartment provided by a droplet. This method, termed emulsion PCR (ePCR), has already emerged to a standard method in sample preparation for 2nd generation sequencing. In this work, we compare different literature protocols that have been developed to generate stable emulsions for ePCR. We investigate different emulsification methods and evaluate the importance of the initial template concentration. We demonstrate that emulsion stability is of utmost importance for the successful inhibition of by-product formation and give an optimized protocol for generation of an emulsified PCR.

Living Cell Microarrays: An Overview of Concepts.

Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays.

Aqueous Synthesis of PEGylated Quantum Dots with Increased Colloidal Stability and Reduced Cytotoxicity.

Ligands used on the surface of colloidal nanoparticles (NPs) have a significant impact on physiochemical properties of NPs and their interaction in biological environments. In this study, we report a one-pot aqueous synthesis of 3-mercaptopropionic acid (MPA)-functionalized CdTe/CdS/ZnS quantum dots (Qdots) in the presence of thiol-terminated methoxy polyethylene glycol (mPEG) molecules as a surface coordinating ligand. The resulting mPEG-Qdots were characterized by using ζ potential, FTIR, thermogravimetric (TG) analysis, and microscale thermophoresis (MST) studies. We investigated the effect of mPEG molecules and their grafting density on the Qdots photophysical properties, colloidal stability, protein binding affinity, and in vitro cellular toxicity. Moreover, cellular binding features of the resulting Qdots were examined by using three-dimensional (3D) tumor-like spheroids, and the results were discussed in detail. Promisingly, mPEG ligands were found to increase colloidal stability of Qdots, reduce adsorption of proteins to the Qdot surface, and mitigate Qdot-induced side effects to a great extent. Flow cytometry and confocal microscopy studies revealed that PEGylated Qdots exhibited distinctive cellular interactions with respect to their mPEG grafting density. As a result, mPEG molecules demonstrated a minimal effect on the ZnS shell deposition and the Qdot fluorescence efficiency at a low mPEG density, whereas they showed pronounced effect on Qdot colloidal stability, protein binding affinity, cytotoxicity, and nonspecific binding at a higher mPEG grafting amount.

Evaluation of CdTe/CdS/ZnS core/shell/shell quantum dot toxicity on three-dimensional spheroid cultures.

In this work, three-dimensional (3D) spheroid cultures of human adipose-derived mesenchymal stem cells (hAD-MSCs), with tissue-mimetic morphology through well developed cell-cell and cell-matrix interactions and distinct diffusion/transport characteristics, were assessed for dose-dependent toxic effects of red-emitting CdTe/CdS/ZnS quantum dots (Qdots). Morphological investigations and time-resolved microscopy analysis in addition to cell metabolic activity studies revealed that 3D spheroid cultures are more resistant to Qdot-induced cytotoxicity in comparison to conventional 2D cultures. The obtained results suggest the presence of two distinct cell populations in 2D cultures with different sensitivity to Qdots, however that effect wasn't observed in 3D spheroids. Our investigations were aimed to improve the prediction of nanotoxicity of Qdot on tissue-level and provide the essential screening steps prior to any in vivo application. Moreover, penetration ability of highly fluorescent Qdots to densely-packed spheroids will fortify the biological application of developed Qdots in tissue-like structures.

Aptamer-modified magnetic beads in affinity separation of proteins.

Aptamers are valuable alternative ligands for affinity separations. Here, we describe the aptamer-based affinity separation of His-tagged proteins using an aptamer directed against the His-tag. The immobilization of the aptamer to magnetic beads is described as well as the aptamer-based purification and proper methods for the characterization of the process. Moreover, indications for the transfer of the process to other aptamers are given.

Label-free optical biosensors based on aptamer-functionalized porous silicon scaffolds.

A proof-of-concept for a label-free and reagentless optical biosensing platform based on nanostructured porous silicon (PSi) and aptamers is presented in this work. Aptamers are oligonucleotides (single-stranded DNA or RNA) that can bind their targets with high affinity and specificity, making them excellent recognition elements for biosensor design. Here we describe the fabrication and characterization of aptamer-conjugated PSi biosensors, where a previously characterized his-tag binding aptamer (6H7) is used as model system. Exposure of the aptamer-functionalized PSi to the target proteins as well as to complex fluids (i.e., bacteria lysates containing target proteins) results in robust and well-defined changes in the PSi optical interference spectrum, ascribed to specific aptamer-protein binding events occurring within the nanoscale pores, monitored in real time. The biosensors show exceptional stability and can be easily regenerated by a short rinsing step for multiple biosensing analyses. This proof-of-concept study demonstrates the possibility of designing highly stable and specific label-free optical PSi biosensors, employing aptamers as capture probes, holding immense potential for application in detection of a broad range of targets, in a simple yet reliable manner.