Easy Surface Functionalization and Bioconjugation of Peptides as Capture Agents of a Microfluidic Biosensing Platform for Multiplex Assay in Serum.

The development of assays for protein biomarkers in complex matrices is a demanding task that still needs implementation of new approaches. Antibodies as capture agents have been largely used in bioassays but their low stability, low-efficiency production, and cross-reactivity in multiplex approaches impairs their larger applications. Instead, synthetic peptides, even with higher stability and easily adapted amino acid sequences, still remain largely unexplored in this field. Here, we provide a proof-of-concept of a microfluidic device for direct detection of biomarker overexpression. The multichannel microfluidic polydimethylsiloxane (PDMS) device was first derivatized with PAA (poly(acrylic acid)) solution. CRP-1, VEGF-114, and ΦG6 peptides were preliminarily tested to respectively bind the biomarkers, C-reactive protein (CRP), vascular endothelial growth factor (VEGF), and tumor necrosis factor-alpha (TNF-α). Each PDMS microchannel was then respectively bioconjugated with a specific peptide (CRP-1, VEGF-114, or ΦG6) to specifically capture CRP, VEGF, and TNF-α. With such microdevices, a fluorescence bioassay has been set up with sensitivity in the nanomolar range, both in buffered solution and in human serum. The proposed multiplex assay worked with a low amount of sample (25 µL) and detected biomarker overexpression (above nM concentration), representing a noninvasive and inexpensive screening platform.

Hydrogel Microparticles for Fluorescence Detection of miRNA in Mix-Read Bioassay.

Herein we describe the development of a mix-read bioassay based on a three-dimensional (3D) poly ethylene glycol-(PEG)-hydrogel microparticles for the detection of oligonucleotides in complex media. The key steps of hydrogels synthesis and molecular recognition in a 3D polymer network are elucidated. The design of the DNA probes and their density in polymer network were opportunely optimized. Furthermore, the diffusion into the polymer was tuned adjusting the polymer concentration and consequently the characteristic mesh size. Upon parameters optimization, 3D-PEG-hydrogels were synthetized in a microfluidic system and provided with fluorescent probe. Target detection occurred by double strand displacement assay associated to fluorescence depletion within the hydrogel microparticle. Proposed 3D-PEG-hydrogel microparticles were designed for miR-143-3p detection. Results showed 3D-hydrogel microparticles with working range comprise between 10-6-10-12 M, had limit of detection of 30 pM and good specificity. Moreover, due to the anti-fouling properties of PEG-hydrogel, the target detection occurred in human serum with performance comparable to that in buffer. Due to the approach versatility, such design could be easily adapted to other short oligonucleotides detection.

One-step scalable fluorescent microgel bioassay for the ultrasensitive detection of endogenous viral miR-US4-5p.

Human cytomegalovirus (hCMV) infection is the leading cause of birth defects in newborns and death in immunosuppressed people. Traditional techniques require time-consuming and costly analyses, and sometimes result in false positive results; thus, a rapid and accurate detection for hCMV infection is necessary. Recently, hcmv-miR-US4-5p was selected as the biomarker for cytomegalovirus diagnosis and follow-up. Herein, we propose a bioassay based on microgels endowed with optical fluorescent oligonucleotide probes for the detection of circulating endogenous hcmv-microRNAs. In particular, a double strand probe, based on the fluorescence recovery after target capture, was conjugated on microgels and the probe density was opportunely optimised. Then, the microgels were directly mixed with the sample. The fluorescence read-out was measured as a function of target concentration at a fixed number of microgels per tube. As a bead-based assay, the performances of optical detection in terms of dynamic working range and limit of detection could be finely tuned by tuning the number of microgels per tube. The limit of detection of the assay could be tuned in the range from 39.1 fM to 156 aM by changing the microgel concentration from 50 µg mL-1 to 0.5 µg mL-1, respectively. The assay results specific for the selected target were stable over a one-year time span and they were not affected by the presence of human serum. Therefore, this bioassay based on microgels might represent a flexible platform that should be able to predict, identify and follow-up several diseases by monitoring freely circulating oligonucleotides in body fluids.

Supramolecular spectrally encoded microgels with double strand probes for absolute and direct miRNA fluorescence detection at high sensitivity.

We present novel microgels as a particle-based suspension array for direct and absolute microRNA (miRNA) detection. The microgels feature a flexible molecular architecture, antifouling properties, and enhanced sensitivity with a large dynamic range of detection. Specifically, they possess a core-shell molecular architecture with two different fluorescent dyes for multiplex spectral analyses and are endowed with a fluorescent probe for miRNA detection. Encoding and detection fluorescence signals are distinguishable by nonoverlapping emission spectra. Tunable fluorescence probe conjugation and emission confinement on single microgels allow for ultrasensitive miRNA detection. Indeed, the suspension array has high selectivity and sensitivity with absolute quantification, a detection limit of 10(-15) M, a dynamic range from 10(-9) to 10(-15) M, and higher accuracy than qRT-PCR. The antifouling properties of the microgels also permit the direct measurement of miRNAs in serum, without sample pretreatment or target amplification. A multiplexed assay has been tested for a set of miRNAs chosen as cancer biomarkers.

MicroLOCK: Highly stable microgel biosensor using locked nucleic acids as bioreceptors for sensitive and selective detection of let-7a.

Chemically modified oligonucleotides can solve biosensing issues for the development of capture probes, antisense, CRISPR/Cas, and siRNA, by enhancing their duplex-forming ability, their stability against enzymatic degradation, and their specificity for targets with high sequence similarity as microRNA families. However, the use of modified oligonucleotides such as locked nucleic acids (LNA) for biosensors is still limited by hurdles in design and from performances on the material interface. Here we developed a fluorogenic biosensor for non-coding RNAs, represented by polymeric PEG microgels conjugated with molecular beacons (MB) modified with locked nucleic acids (MicroLOCK). By 3D modeling and computational analysis, we designed molecular beacons (MB) inserting spot-on LNAs for high specificity among targets with high sequence similarity (95%). MicroLOCK can reversibly detect microRNA targets in a tiny amount of biological sample (2 µL) at 25 °C with a higher sensitivity (LOD 1.3 fM) without any reverse transcription or amplification. MicroLOCK can hybridize the target with fast kinetic (about 30 min), high duplex stability without interferences from the polymer interface, showing high signal-to-noise ratio (up to S/N = 7.3). MicroLOCK also demonstrated excellent resistance to highly nuclease-rich environments, in real samples. These findings represent a great breakthrough for using the LNA in developing low-cost biosensing approaches and can be applied not only for nucleic acids and protein detection but also for real-time imaging and quantitative assessment of gene targeting both in vitro and in vivo.

Multistage Nanocarrier Based on an Oil Core-Graphene Oxide Shell.

Potent synthetic drugs, as well as biomolecules extracted from plants, have been investigated for their selectivity toward cancer cells. The main limitation in cancer treatment is the ability to bring such molecules within each single cancer cell, which requires accumulation in the peritumoral region followed by homogeneous spreading within the entire tissue. In the last decades, nanotechnology has emerged as a powerful tool due to its ability to protect the drug during blood circulation and allow enhanced accumulation around the leaky regions of the tumor vasculature. However, the ideal size for accumulation of around 100 nm is too large for effective penetration into the dense collagen matrix. Therefore, we propose a multistage system based on graphene oxide nanosheet-based quantum dots (GOQDs) with dimensions that are 12 nm, functionalized with hyaluronic acid (GOQDs-HA), and deposited using the layer-by-layer technique onto an oil-in-water nanoemulsion (O/W NE) template that is around 100 nm in size, previously stabilized by a biodegradable polymer, chitosan. The choice of a biodegradable core for the nanocarrier is to degrade once inside the tumor, thus promoting the release of smaller compounds, GOQDs-HA, carrying the adsorbed anticancer compound, which in this work is represented by curcumin as a model bioactive anticancer molecule. Additionally, modification with HA aims to promote active targeting of stromal and cancer cells. Cell uptake experiments and preliminary penetration experiments in three-dimensional microtissues were performed to assess the proposed multistage nanocarrier.

The role of elasticity on adhesion and clustering of neurons on soft surfaces.

The question of whether material stiffness enhances cell adhesion and clustering is still open to debate. Results from the literature are seemingly contradictory, with some reports illustrating that adhesion increases with surface stiffness and others suggesting that the performance of a system of cells is curbed by high values of elasticity. To address the role of elasticity as a regulator in neuronal cell adhesion and clustering, we investigated the topological characteristics of networks of neurons on polydimethylsiloxane (PDMS) surfaces - with values of elasticity (E) varying in the 0.55-2.65 MPa range. Results illustrate that, as elasticity increases, the number of neurons adhering on the surface decreases. Notably, the small-world coefficient - a topological measure of networks - also decreases. Numerical simulations and functional multi-calcium imaging experiments further indicated that the activity of neuronal cells on soft surfaces improves for decreasing E. Experimental findings are supported by a mathematical model, that explains adhesion and clustering of cells on soft materials as a function of few parameters - including the Young's modulus and roughness of the material. Overall, results indicate that - in the considered elasticity interval - increasing the compliance of a material improves adhesion, improves clustering, and enhances communication of neurons.

Direct, precise, enzyme-free detection of miR-103-3p in real samples by microgels with highly specific molecular beacons.

Low abundance, small size, and sequence similarities render microRNA (miRNAs) detection challenging, particularly in real samples, where quantifying weakly expressed miRNAs can be arduous due to interference of more abundant molecules. The standard quantitative reverse transcription polymerase chain reaction (qRT-PCR) requires multiple steps, thermal cycles, and costly enzymatic reactions that can negatively affect results. Here we present a direct, precise, enzyme-free assay based on microgels particles conjugating molecular beacons (MB) capable of optically detecting low abundant miRNAs in real samples. We validate the applicability of microgels assay using qRT-PCR as a reference technology. As a relevant case, we chose miR-103-3p, a valuable diagnostic biomarker for breast cancer, both in serum samples and MCF7 cells. As a result, microgels assay quantifies miRNA molecules at room temperature in a single step, 1 h (vs. 4 hrs for qRT-PCR) without complementary DNA synthesis, amplification, or expensive reagents. Microgels assay exhibits femtomolar sensitivity, single nucleotide specificity, and a wide linear range (102-107 fM) (wider than qRT-PCR), with low sample consumption (2 µL) and excellent linearity (R2= 0.98). To test the selectivity of the microgel assay in real samples, MCF7 cells were considered where the pool of 8 other miRNAs were further upregulated with respect to miRNA 103-3p. In such complex environments, microgels assay selectively detects the miRNA target, mainly due to MB advanced stability and specificity as well as high microgel antifouling properties. These results show the reliability of microgels assay to detect miRNAs in real samples.

Hydrogel particles-on-chip (HyPoC): a fluorescence micro-sensor array for IgG immunoassay.

Novel microparticles have generated growing interest in diagnostics for potential sensitivity and specificity in biomolecule detection and for the possibility to be integrated in a micro-system array as a lab-on-chip. Indeed, bead-based technologies integrated in microfluidics could speed up incubation steps, reduce reagent consumption and improve accessibility of diagnostic devices to non-expert users. To limit non-specific interactions with interfering molecules and to exploit the whole particle volume for bioconjugation, hydrogel microparticles, particularly polyethylene glycol-based, have emerged as promising materials to develop high-performing biosensors since their network can be functionalized to concentrate the target and improve detection. However, the limitations in positioning, trapping and mainly fine manipulation of a precise number of particles in microfluidics have largely impaired point-of-care applications. Herein, we developed an on-chip sandwich immunoassay for the detection of human immunoglobulin G in biological fluids. The detection system is based on finely engineered cleavable PEG-based microparticles, functionalized with specific monoclonal antibodies. By changing the particle number, we demonstrated tuneable specificity and sensitivity (down to 3 pM) in serum and urine. Therefore, a controlled number of hydrogel particles have been integrated in a microfluidic device for on-chip detection (HyPoC) allowing for their precise positioning and fluid exchange for incubation, washing and target detection. HyPoC dramatically decreases incubation time from 180 minutes to one minute and reduces washing volumes from 3.5 ml to 90 µL, achieving a limit of detection of 0.07 nM (with a dynamic range of 0.07-1 nM). Thus, the developed approach represents a versatile, fast and easy point-of-care testing platform for immunoassays.

Fluorescence lifetimes and quantum yields of rhodamine derivatives: new insights from theory and experiment.

Although lifetimes and quantum yields of widely used fluorophores are often largely characterized, a systematic approach providing a rationale of their photophysical behavior on a quantitative basis is still a challenging goal. Here we combine methods rooted in the time-dependent density functional theory and fluorescence lifetime imaging microscopy to accurately determine and analyze fluorescence signatures (lifetime, quantum yield, and band peaks) of several commonly used rhodamine and pyronin dyes. We show that the radiative lifetime of rhodamines can be correlated to the charge transfer from the phenyl toward the xanthene moiety occurring upon the S(0) ← S(1) de-excitation, and to the xanthene/phenyl relative orientation assumed in the S(1) minimum structure, which in turn is variable upon the amino and the phenyl substituents. These findings encourage the synergy of experiment and theory as unique tool to design finely tuned fluorescent probes, such those conceived for modern optical sensors.

PEG-based cleavable hydrogel microparticles with controlled porosity for permiselective trafficking of biomolecular complexes in biosensing applications.

In the last decade, PEG-based hydrogels have been extensively used for the production of microparticles for biosensing applications. The biomolecule accessibility and mass transport rate represent key parameters for the realization of sensitive microparticles, therefore porous materials have been developed, mainly resorting to the use of inert porogens and copolymers with different chain lengths. However, very limited information is reported regarding the addition of cleavable crosslinkers to modulate the network porosity. In this scenario, the aim of this work is to design, synthesize and characterize hydrogel microparticles, based on the copolymerization between PEG-diacrylate and N,N'-(1,2-dihydroxyethylene)-bisacrylamide, a cleavable crosslinker that simultaneously produces pores and reactive groups for bioprobe 3D bioconjugation. The results show great accessibility of these microparticles to antibodies and their complexes, without affecting their diffusion rate. Furthermore, the presence of a well-defined number of reactive aldehydes, produced by the cleavage reaction, allows modulating biosensor sensitivity through a fine control of the conjugation degree. The antibody-conjugated microparticles can efficiently capture the analyte down to a few picograms. These novel microparticles could be used as a highly sensitive platform for biomacromolecule detection in complex fluids, exploiting the combined effects of PEG's anti-fouling properties, large network porosity and interconnections, and three-dimensional bioconjugation.

Small Oligonucleotides Detection in Three-Dimensional Polymer Network of DNA-PEG Hydrogels.

The control of the three-dimensional (3D) polymer network structure is important for permselective materials when specific biomolecule detection is needed. Here we investigate conditions to obtain a tailored hydrogel network that combines both molecular filtering and molecular capture capabilities for biosensing applications. Along this line, short oligonucleotide detection in a displacement assay is set within PEGDA hydrogels synthetized by UV radical photopolymerization. To provide insights on the molecular filter capability, diffusion studies of several probes (sulforhodamine G and dextrans) with different hydrodynamic radii were carried out using NMR technique. Moreover, fluorometric analyses of hybridization of DNA oligonucleotides inside PEGDA hydrogels shed light on the mechanisms of recognition in 3D, highlighting that mesh size and crowding effect greatly impact the hybridization mechanism on a polymer network. Finally, we found the best probe density and diffusion transport conditions to allow the specific oligonucleotide capture and detection inside PEGDA hydrogels for oligonucleotide detection and the filtering out of higher molecular weight molecules.

A theoretical and experimental study on l-tyrosine and citrate mediated sustainable production of near infrared absorbing twisted gold nanorods.

Anisotropic gold nanoparticles displaying plasmon band in the near infrared region can play a crucial role in cancer therapy particularly with techniques such as photothermal therapy (PTT) and photodynamic therapy (PDT). Herein, we report an efficient, sustainable, one pot protocol for the fabrication of an unusual gold anisotropic shape, which we have named as twisted gold nanorods. These particles, though having dimensions in the nanoscale regime comparable to those of gold nanorods, display a continuous flat plasmon band like that of 2-D gold nanowire networks, extended up to the NIR-III (SWIR) range. The proposed strategy is simple and does not require any seed mediation, heating or potential toxic templates or organic solvents. Our process is based on the slow reduction of gold salt in presence of two mild reducing agents viz. l-tyrosine (an amino acid) and trisodium citrate. We observed that when both molecules are present together in particular concentrations, they direct the growth in form of twisted gold nanorods. The mechanism of growth has been described by a Diffusion Limited Aggregation numerical scheme, where it was assumed that both l-tyrosine and the gold ions in solution undergo a stochastic Brownian motion. The predictions of the model matched with the experiments with a good accuracy, indicating that the initial hypothesis is correct. The final structure has been thoroughly characterized in terms of morphology, while SERS and cytotoxic activity have also been demonstrated.

Surface investigation on biomimetic materials to control cell adhesion: the case of RGD conjugation on PCL.

The cell recognition of bioactive ligands immobilized on polymeric surfaces is strongly dependent on ligand presentation at the cell/material interface. While small peptide sequences such as Arg-Gly-Asp (RGD) are being widely used to obtain biomimetic interfaces, surface characteristics after immobilization as well as presentation of such ligands to cell receptors deserve more detailed investigation. Here, we immobilized an RGD-based sequence on poly(epsilon-caprolactone) (PCL), a largely widespread polymeric material used in biomedical applications, after polymer aminolysis. The surface characteristics along with the efficacy of the functionalization was monitored by surface analysis (FTIR-ATR, contact angle measurements, surface free energy determination) and spectrophotometric assays specially adapted for the analytical quantification of functional groups and/or peptides at the interface. Particular attention was paid to the evaluation of a number, morphology, and penetration depth of immobilized functional groups and/or peptides engrafted on polymeric substrates. In particular, a typical morphology in peptide distribution was evidenced on the surface raised from polymer crystallites, while a significant penetration depth of the engrafted molecules was revealed. NIH3T3 fibroblast adhesion studies verified the correct presentation of the ligand with enhanced cell attachment after peptide conjugation. Such work proposes a morphological and analytical approach in surface characterization to study the surface treatment and the distribution of ligands immobilized on polymeric substrates.

Supramolecular Microgels with Molecular Beacons at the Interface for Ultrasensitive, Amplification-Free, and SNP-Selective miRNA Fluorescence Detection.

In this study, a supramolecular structure with femtomolar biorecognition properties is proposed for use in analytical devices. It is obtained by an innovative interface between synthetic hydrogel polymers and molecular beacon (mb) probes. Supramolecularly structured microgels are synthetized with a core-shell architecture with specific dyes polymerized in a desired compartment. Mb probes are opportunely conjugated at the microgel interface so that their recognition mechanism is preserved and their spatial distribution is optimized to avoid crowding effects. The miR-21, a microRNA involved in various biological processes and usually used as a biomarker in early cancer diagnosis, has been selected as the target. The results demonstrate that by tuning the spatial distribution of molecular probes immobilized on the microgel and/or the amount of microgels, the assay shows scalable sensitivity reaching a limit of detection down to about 10 fM, without amplification steps and with detection time as short as 1 h. The assay results specific toward single mutated targets, and it is stable in the presence of high-interfering oligonucleotides concentrations. The miRNA target is also detected in human serum with performances similar to those observed in PBS buffer because of microgel antifouling properties without the need of any surface treatment. All tests were performed in a low sample volume (20 µL). As a result, mb-microgel represents an innovative biosensor to precisely quantify microRNAs in a direct (mix&read), scalable, and selective way. Such an approach paves the way for creating innovative biosensing interfaces with other probes, such as hairpins, aptamers, and PNA.

Biosensor for Point-of-Care Analysis of Immunoglobulins in Urine by Metal Enhanced Fluorescence from Gold Nanoparticles.

Biosensors are easy-to-use and cost-effective devices that are emerging as an attractive tool, not only in settling diagnosis or in disease monitoring, but also in mass screening tests, a timely topic that impacts on daily life of the whole society. Nanotechnologies lend themselves to the development of highly sensitive devices whose realization has become a very interdisciplinary topic. Relying on the enhancement of the fluorescence signal detected at the surface of patterned gold nanoparticles, we report the behavior of an analytical device in detecting immunoglobulins in real urine samples that shows a limit of detection of approximately 8 µg/L and a linear range of 10-100 µg/L well below the detection limit of nephelometric method, which is the reference method for this analysis. These performances have been reached thanks to an effective surface functionalization technique and can be improved even more if superydrophobic features of the substrate we produce will be exploited. Since the analyte recognition is realized by antibodies the specificity is very high and, in fact, no interference has been detected by other compounds also present in the real urine samples. The device has been assessed on serum samples by comparing IgG concentrations values obtained by the biosensor with those provided by a nephelometer. In this step we found that our approach allows the analysis of the whole blood without any pretreatment; moreover, it is inherently extendable to the analysis of most biochemical markers in biological fluids.

Molecularly endowed hydrogel with an in silico-assisted screened peptide for highly sensitive small molecule harvesting.

We present a novel method for the detection of small molecules in complex fluids based on the selection of a specific peptide for target capture and its integration into an antifouling polymeric network. Such an approach can represent a universal platform for the direct and ultra-sensitive detection of small molecules in complex media.

Turn-on fluorescence detection of protein by molecularly imprinted hydrogels based on supramolecular assembly of peptide multi-functional blocks.

Synthetic receptors for biomacromolecules lack the supramolecular self-assembly behavior typical of biological systems. Here we propose a new method for the preparation of protein imprinted polymers based on the specific interaction of a peptide multi-functional block with a protein target. This peptide block contains a protein-binding peptide domain, a polymerizable moiety at the C-terminus and an environment-sensitive fluorescent molecule at the N-terminus. The method relies on a preliminary step consisting of peptide/protein supramolecular assembly, followed by copolymerization with the most common acrylate monomers (acrylamide, acrylic acid and bis-acrylamide) to produce a protein imprinted hydrogel polymer. Such a peptide block can function as an active assistant recognition element to improve affinity, and guarantees its effective polymerization at the protein/cavity interface, allowing for proper placement of a dye. As a proof of concept, we chose Bovine Serum Albumin (BSA) as the protein target and built the peptide block around a BSA binding dodecapeptide, with an allyl group as the polymerizable moiety and a dansyl molecule as the responsive dye. Compared to conventional approaches these hydrogels showed higher affinity (more than 45%) and imprinted sensitivity (about twenty fold) to the target, with a great BSA selectivity with respect to ovalbumin (α = 1.25) and lysozyme (α = 6.02). Upon protein binding, computational and experimental observations showed a blue shift of the emission peak (down to 440 nm) and an increase of fluorescence emission (twofold) and average lifetime (Δτ = 4.3 ns). Such an approach generates recognition cavities with controlled chemical information and represents an a priori method for self-responsive materials. Provided a specific peptide and minimal optimization conditions are used, such a method could be easily implemented for any protein target.

Bioengineering Microgels and Hydrogel Microparticles for Sensing Biomolecular Targets.

Hydrogels, and in particular microgels, are playing an increasingly important role in a diverse range of applications due to their hydrophilic, biocompatible, and highly flexible chemical characteristics. On this basis, solution-like environment, non-fouling nature, easy probe accessibility and target diffusion, effective inclusion of reporting moieties can be achieved, making them ideal substrates for bio-sensing applications. In fact, hydrogels are already successfully used in immunoassays as well as sensitive nucleic acid assays, also enabling hydrogel-based suspension arrays. In this review, we discuss key parameters of hydrogels in the form of micron-sized particles to be used in sensing applications, paying attention to the protein and oligonucleotides (i.e., miRNAs) targets as most representative kind of biomarkers.

Preparation and Characterization of Magnetic and Porous Metal-Ceramic Nanocomposites from a Zeolite Precursor and Their Application for DNA Separation.

In this work, metal-ceramic nanocomposites were obtained through short (up to 2 h) thermal treatments at relatively moderate temperatures (750­800 °C) under a reducing atmosphere, using Fe-exchanged zeolite A as the precursor. The as-obtained materials were characterized by X-ray powder diffraction analysis, N2 adsorption at ­196 °C, and highresolution transmission electron microscopy. The results of these analyses showed that the nanocomposites consisted of a dispersion of metallic Fe nanoparticles within a porous ceramic matrix, mainly based on amorphous silica and alumina. These nanocomposites were magnetically characterized, and their magnetic response was studied. Finally, the obtained metal-ceramic nanocomposite materials were used in the separation of Escherichia coli DNA from a crude cell lysate. The results of the DNA separation experiments showed that the obtained materials could perform this type of separation.