Development of Photonic Multi-Sensing Systems Based on Molecular Gates Biorecognition and Plasmonic Sensors: The PHOTONGATE Project

This paper presents the concept of a novel adaptable sensing solution currently being developed under the EU Commission-founded PHOTONGATE project. This concept will allow for the quantification of multiple analytes of the same or different nature (chemicals, metals, bacteria, etc.) in a single test with levels of sensitivity and selectivity at/or over those offered by current solutions. PHOTONGATE relies on two core technologies: a biochemical technology (molecular gates), which will confer the specificity and, therefore, the capability to be adaptable to the analyte of interest, and which, combined with porous substrates, will increase the sensitivity, and a photonic technology based on localized surface plasmonic resonance (LSPR) structures that serve as transducers for light interaction. Both technologies are in the micron range, facilitating the integration of multiple sensors within a small area (mm2). The concept will be developed for its application in health diagnosis and food safety sectors. It is thought of as an easy-to-use modular concept, which will consist of the sensing module, mainly of a microfluidics cartridge that will house the photonic sensor, and a platform for fluidic handling, optical interrogation, and signal processing. The platform will include a new optical concept, which is fully European Union Made, avoiding optical fibers and expensive optical components.

Mesoporous Silica Nanoparticles in Chemical Detection: From Small Species to Large Bio-Molecules

A recompilation of applications of mesoporous silica nanoparticles in sensing from the last five years is presented. Its high potential, especially as hybrid materials combined with organic or bio-molecules, is shown. Adding to the multiplying effect of loading high amounts of the transducer into the pores, the selectivity attained by the interaction of the analyte with the layer decorating the material is described. Examples of the different methodologies are presented.

A CTP-dependent gating mechanism enables ParB spreading on DNA

Proper chromosome segregation is essential in all living organisms. The ParA-ParB-parS system is widely employed for chromosome segregation in bacteria. Previously, we showed that Caulobacter crescentus ParB requires cytidine triphosphate to escape the nucleation site parS and spread by sliding to the neighboring DNA (Jalal et al., 2020). Here, we provide the structural basis for this transition from nucleation to spreading by solving co-crystal structures of a C-terminal domain truncated C. crescentus ParB with parS and with a CTP analog. Nucleating ParB is an open clamp, in which parS is captured at the DNA-binding domain (the DNA-gate). Upon binding CTP, the N-terminal domain (NTD) self-dimerizes to close the NTD-gate of the clamp. The DNA-gate also closes, thus driving parS into a compartment between the DNA-gate and the C-terminal domain. CTP hydrolysis and/or the release of hydrolytic products are likely associated with reopening of the gates to release DNA and recycle ParB. Overall, we suggest a CTP-operated gating mechanism that regulates ParB nucleation, spreading, and recycling.

A CTP-dependent gating mechanism enables ParB spreading on DNA

Proper chromosome segregation is essential in all living organisms. The ParA-ParB-parS system is widely employed for chromosome segregation in bacteria. Previously, we showed that Caulobacter crescentus ParB requires cytidine triphosphate to escape the nucleation site parS and spread by sliding to the neighboring DNA (Jalal et al., 2020). Here, we provide the structural basis for this transition from nucleation to spreading by solving co-crystal structures of a C-terminal domain truncated C. crescentus ParB with parS and with a CTP analog. Nucleating ParB is an open clamp, in which parS is captured at the DNA-binding domain (the DNA-gate). Upon binding CTP, the N-terminal domain (NTD) self-dimerizes to close the NTD-gate of the clamp. The DNA-gate also closes, thus driving parS into a compartment between the DNA-gate and the C-terminal domain. CTP hydrolysis and/or the release of hydrolytic products are likely associated with reopening of the gates to release DNA and recycle ParB. Overall, we suggest a CTP-operated gating mechanism that regulates ParB nucleation, spreading, and recycling.

Lactose-Gated Mesoporous Silica Particles for Intestinal Controlled Delivery of Essential Oil Components: An In Vitro and In Vivo Study

Mesoporous silica microparticles functionalized with lactose for the specific release of essential oil components (EOCs) in the small intestine are presented. In vitro and in vivo intestinal models were applied to validate the microparticles (M41-EOC-L), in which the presence of lactase acts as the triggering stimulus for the controlled release of EOCs. Among the different microdevices prepared (containing thymol, eugenol and cinnamaldehyde), the one loaded with cinnamaldehyde showed the most significant Caco-2 cell viability reduction. On the other hand, interaction of the particles with enterocyte-like monolayers showed a reduction of EOCs permeability when protected into the designed microdevices. Then, a microdevice loaded with cinnamaldehyde was applied in the in vivo model of Wistar rat. The results showed a reduction in cinnamaldehyde plasma levels and an increase in its concentration in the lumen of the gastrointestinal tract (GIT). The absence of payload release in the stomach, the progressive release throughout the intestine and the prolonged stay of the payload in the GIT-lumen increased the bioavailability of the encapsulated compound at the site of the desired action. These innovative results, based on the specific intestinal controlled delivery, suggest that the M41-payload-L could be a potential hybrid microdevice for the protection and administration of bioactive molecules in the small intestine and colon.

Oligonucleotide-capped nanoporous anodic alumina biosensor as diagnostic tool for rapid and accurate detection of Candida auris in clinical samples

Candida auris has arisen as an important multidrug-resistant fungus because of several nosocomial outbreaks and elevated rates of mortality. Accurate and rapid diagnosis of C. auris is highly desired; nevertheless, current methods often present severe limitations and produce misidentification. Herein a sensitive, selective, and time-competitive biosensor based on oligonucleotide-gated nanomaterials for effective detection of C. auris is presented. In the proposed design, a nanoporous anodic alumina scaffold is filled with the fluorescent indicator rhodamine B and the pores blocked with different oligonucleotides capable of specifically recognize C. auris genomic DNA. Gate opening modulation and cargo delivery is controlled by successful DNA recognition. C. auris is detected at a concentration as low as 6 CFU/mL allowing obtaining a diagnostic result in clinical samples in one hour with no prior DNA extraction or amplification steps.

Triplex Hybridization-Based Nanosystem for the Rapid Screening of Pneumocystis Pneumonia in Clinical Samples

Pneumocystis pneumonia (PcP) is a disease produced by the opportunistic infection of the fungus Pneumocystis jirovecii. As delayed or unsuitable treatments increase the risk of mortality, the development of rapid and accurate diagnostic tools for PcP are of great importance. Unfortunately, current standard methods present severe limitations and are far from adequate. In this work, a time-competitive, sensitive and selective biosensor based on DNA-gated nanomaterials for the identification of P. jirovecii is presented. The biosensor consists of a nanoporous anodic alumina (NAA) scaffold which pores are filled with a dye reporter and capped with specific DNA oligonucleotides. In the presence of P. jirovecii genomic DNA, the gated biosensor is open, and the cargo is delivered to the solution where it is monitored through fluorescence spectroscopy. The use of capping oligonucleotides able to form duplex or triplex with P. jirovecii DNA is studied. The final diagnostic tool shows a limit of detection (LOD) of 1 nM of target complementary DNA and does not require previous amplification steps. The method was applied to identify DNA from P. jirovecii in unmodified bronchoalveolar lavage, nasopharyngeal aspirates, and sputum samples in 60 min. This is a promising alternative method for the routinely diagnosis of Pneumocystis pneumonia.

Visible Light Photocleavable Ruthenium-Based Molecular Gates to Reversibly Control Release from Mesoporous Silica Nanoparticles

Herein we present hybrid mesoporous silica nanomaterials (MSN) with visible light-sensitive ruthenium complexes acting as gates. Two different [Ru(bpy)₂L1L2]²⁺ complexes were investigated by grafting [Ru(bpy)₂(4AMP)₂](PF₆)₂ (RC1) and [Ru(bpy)₂(PPh₃)Cl]Cl (RC2) via two or one ligands onto the surface of mesoporous silica nanoparticles (MSNs), to give MSN1-RC1 and MSN2-RC2, respectively. The pores were previously loaded with a common dye, safranin O, and release studies were conducted. The number and position of the ligands were shown to influence the photocages behavior and thus the release of the cargo. Release studies from MSN1-RC1 in acetonitrile showed that in the dark the amount of dye released was minimal after 300 min, whereas a significant increase was measured upon visible light irradiation (ca. 90%). While successful as a photochemically-controlled gated system, RC1 was restricted to organic solvents since it required cleavage of two ligands in order to be cleaved from the surface, and in water only one is cleaved. Release studies from the second nanomaterial MSN2-RC2, where the complex RC2 was bound to the MSN via only one ligand, showed stability under darkness and in aqueous solution up to 180 min and, rapid release of the dye when irradiated with visible light. Furthermore, this system was demonstrated to be reversible, since, upon heating to 80 °C, the system could effectively re-close the pores and re-open it again upon visible light irradiation. This work, thus, demonstrates the potential reversible gate mechanism of the ruthenium-gated nanomaterials upon visible light irradiation, and could be envisioned as a future design of photochemically-driven drug delivery nanosystems or on/off switches for nanorelease systems.

Biocompatible Phenylboronic-Acid-Capped ZnS Nanocrystals Designed As Caps in Mesoporous Silica Hybrid Materials for on-Demand pH-Triggered Release In Cancer Cells

Biocompatible ZnS-based nanocrystals capped with 4-mercaptophenylboronic acid (ZnS@B) have been size-designed as excellent pH-responsive gatekeepers on mesoporous silica nanoparticles (MSNs), which encapsulate fluorophore safranin O (S2-Saf) or anticancer drug epirubicin hydrochloride (S2-Epi) for delivery applications in cancer cells. In this novel hybrid system, the gate mechanism consists of reversible pH-sensitive boronate ester moieties linking the nanocrystals directly to the alcohol groups from silica surface scaffold, avoiding tedious intermediate functionalization steps. The ∼3 nm size of the ZnS@B nanocrystals was tailored to allow efficient sealing of the pore voids and achieve a "zero premature cargo release" at neutral pH (7.4). The system selectively released the cargo in acidic conditions (pH 5.4 and 3.0) because of the hydrolysis of the boronate esters, which unblocked the pore voids. Delivery of the cargo by off-on cycles was demonstrated by changes in pH from 7.4 to 3.0, showing its potential pH-switching behavior. Cellular uptake of these nanocarriers within human cervix adenocarcinoma (HeLa) cells was achieved and the controlled release of the chemotherapeutic drug epirubicin was shown to occur within the endogenous endosomal/lysosomal acidified cancer cell microenvironment and further diffused into the cytosol. Cytotoxicity tests done on the mesoporous support without cargo and covalently linked with ZnS@B nanocrystals as caps were negative, suggesting that the proposed system is biocompatible and can be considered as a very promising drug nanocarrier.

Smart Adsorbents with Photoregulated Molecular Gates for Both Selective Adsorption and Efficient Regeneration

Selective adsorption and efficient regeneration are two crucial issues for adsorption processes; unfortunately, only one of them instead of both is favored by traditional adsorbents with fixed pore orifices. Herein, we fabricated a new generation of smart adsorbents through grafting photoresponsive molecules, namely, 4-(3-triethoxysilylpropyl-ureido)azobenzene (AB-TPI), onto pore orifices of the support mesoporous silica. The azobenzene (AB) derivatives serve as the molecular gates of mesopores and are reversibly opened and closed upon light irradiation. Irradiation with visible light (450 nm) causes AB molecules to isomerize from cis to trans configuration, and the molecular gates are closed. It is easy for smaller adsorbates to enter while difficult for the larger ones, and the selective adsorption is consequently facilitated. Upon irradiation with UV light (365 nm), the AB molecules are transformed from trans to cis isomers, promoting the desorption of adsorbates due to the opened molecular gates. The present smart adsorbents can consequently benefit not only selective adsorption but also efficient desorption, which are exceedingly desirable for adsorptive separation but impossible for traditional adsorbents with fixed pore orifices.

The thinnest molecular separation sheet by graphene gates of single-walled carbon nanohorns

Graphene is possibly the thinnest membrane that could be used as a molecular separation gate. Several techniques including absorption, cryogenic distillation, adsorption, and membrane separation have been adopted for constructing separation systems. Molecular separation using graphene as the membrane has been studied because large area synthesis of graphene is possible by chemical vapor deposition. Control of the gate sizes is necessary to achieve high separation performances in graphene membranes. The separation of molecules and ions using graphene and graphene oxide layers could be achieved by the intrinsic defects and defect donation of graphene. However, the controllability of the graphene gates is still under debate because gate size control at the picometer level is inevitable for the fabrication of the thinnest graphene membranes. In this paper, the controlled gate size in the graphene sheets in single-walled carbon nanohorns (NHs) is studied and the molecular separation ability of the graphene sheets is assessed by molecular probing with CO2, O2, N2, CH4, and SF6. Graphene sheets in NHs with different sized gates of 310, 370, and >500 pm were prepared and assessed by molecular probing. The 310 pm-gates in the graphene sheets could separate the molecules tested, whereas weak separation properties were observed for 370 pm-gates. The amount of CO2 that penetrated the 310 pm-gates was more than 35 times larger than that of CH4. These results were supported by molecular dynamics simulations of the penetration of molecules through 300, 400, and 700 pm-gates in graphene sheets. Therefore, a gas separation membrane using a 340-pm-thick graphene sheet has high potential. These findings provide unambiguous evidence of the importance of graphene gates on the picometer level. Control of the gates is the primary challenge for high-performance separation membranes made of graphene.

Antibody-capped mesoporous nanoscopic materials: design of a probe for the selective chromo-fluorogenic detection of finasteride

The synthesis of capped mesoporous silica nanoparticles (MSN) conjugated with an antibody (AB) as a gatekeeper has been carried out in order to obtain a delivery system able to release an entrapped cargo (dye) in the presence of a target molecule (antigen) to which the conjugated antibody binds selectively. In particular, MSN loaded with rhodamine B and functionalized on the external surface with a suitable derivative of N-(t-butyl)-3-oxo-(5α,17β)-4-aza-androst-1-ene-17-carboxamide (finasteride) have been prepared (S1). The addition of polyclonal antibodies against finasteride induced capping of the pores due to the interaction with the anchored hapten-like finasteride derivative to give a MSN–hapten–AB nanoparticle S1-AB. It was found that the addition of capped material S1-AB to water solutions containing finasteride resulted in displacement of the antibody, pore uncapping and entrapped-dye release. The response of the gated material is highly selective, and only finasteride, among other steroids, was able to induce a significant uncapping process. Compared with finasteride, the finasteride metabolite was able to release 17 % of the dye, whereas the exogen steroids testosterone, metenolone and 16-β-hydroxystanozolol only induced very little release of rhodamine B (lower than 10 %) from aqueous suspensions containing sensing solid S1-AB. A detection limit as low as 20 ppb was found for the fluorimetric detection of finasteride. In order to evaluate a possible application of the material for label-free detection of finasteride, the capped material was isolated and stored to give final sensing solid S1-AB-i. It was found to display a similar behavior towards finasteride as to that shown by freshly prepared S1-AB; even after a period of two months, no significant loss of selectivity or sensitivity was noted. Moreover, to study the application for the detection of finasteride in biological samples, this “aged” material, S1-AB-i, was tested using commercially available blank urine as matrix. Samples containing 70 and 90 % blank urine were spiked with a defined amount of finasteride, and the concentration was determined using capped S1-AB-i. Recovery ranges from 94 % to 118 % were reached.

Quasi-classical modeling of molecular quantum-dot cellular automata multidriver gates

Molecular quantum-dot cellular automata (mQCA) has received considerable attention in nanoscience. Unlike the current-based molecular switches, where the digital data is represented by the on/off states of the switches, in mQCA devices, binary information is encoded in charge configuration within molecular redox centers. The mQCA paradigm allows high device density and ultra-low power consumption. Digital mQCA gates are the building blocks of circuits in this paradigm. Design and analysis of these gates require quantum chemical calculations, which are demanding in computer time and memory. Therefore, developing simple models to probe mQCA gates is of paramount importance. We derive a semi-classical model to study the steady-state output polarization of mQCA multidriver gates, directly from the two-state approximation in electron transfer theory. The accuracy and validity of this model are analyzed using full quantum chemistry calculations. A complete set of logic gates, including inverters and minority voters, are implemented to provide an appropriate test bench in the two-dot mQCA regime. We also briefly discuss how the QCADesigner tool could find its application in simulation of mQCA devices.