Nanomolar fluorescent detection of c-di-GMP using a modular aptamer strategy

C-di-GMP regulates important processes involved in biofilm formation and virulence factors production in several bacteria. Herein we report a simple fluorescent strategy that allows for the detection of c-di-GMP (as low as 320 nM) using a Vc2 class I riboswitch domain as the sensing region and spinach as the fluorescent reporting module.     

A general strategy to convert the MerR family proteins into highly sensitive and selective fluorescent biosensors for metal ions

The MerR family metal-regulatory proteins are converted into fluorescent biosensors that can detect different metal ions with high sensitivity and selectivity.     

A theoretical approach for designing fluorescent reagentless biosensors: The optical model

In this paper a mathematical model describing the analytical signal obtained in fluorescence sensors is presented and compared with other commonly used models. The model starts from the Kubelka-Munk theory for solid surfaces but incorporates new theoretical improvements, being principally: (a) the increase in the effective optical pathlength due to the Scattering Induced Path Variation (SIPV), the incorporation of this parameter allows us to deduce that the fluorescence intensity from solid surfaces does not linearly change with the fluorophore concentrations; (b) the influence of the inner filter effect and how the error can be rectified and (c) the calculation of the scattering coefficients in sensor films for this kind of sensor. From this model it is possible to predict the effect of the fluorophore concentration, the sensor film scattering coefficient and the sample inner filter effect on the fluorescence signal. The conclusions obtained can be extended to other types of fluorescence measurements from solid surfaces.     

On-line monitoring of polymer deposition for tailoring the waveguide characteristics of love-wave biosensors

The Love-wave sensor is an acoustic sensing device which is particularly suitable for sensing in a liquid environment. The superior characteristics of the device are achieved by the use of an acoustic waveguide, consisting of a thin layer deposited on the surface of the substrate material. The exact thickness and material properties of the layer will not only determine sensitivity and sensing performance of the resulting device but can also be adjusted to generate higher-order Love modes. Thus, to obtain a sensing device with the desired specifications, precise control over the process of waveguide deposition is required. This has been realized by implementation of a vapor deposition polymerization system where the transmission curve (amplitude vs frequency) of one of the sensing devices is continuously monitored during deposition. As soon as the desired device specifications are reached, the deposition can be interrupted immediately. From the recorded transmission curves, information about the sensitivity of the device can be deduced, and the formation of higher-order Love modes can be visualized. The system has been used to produce biosensors based on various Love modes. It is shown that sensors operated on higher-order Love modes have a high mass sensitivity which, together with their excellent shielding properties, makes them advantageous for biosensing in conducting buffer solutions.     

An organophosphonate strategy for functionalizing silicon photonic biosensors

Silicon photonic microring resonators have established their potential for label-free and low-cost biosensing applications. However, the long-term performance of this optical sensing platform requires robust surface modification and biofunctionalization. Herein, we demonstrate a conjugation strategy based on an organophosphonate surface coating and vinyl sulfone linker to biofunctionalize silicon resonators for biomolecular sensing. To validate this method, a series of glycans, including carbohydrates and glycoconjugates, were immobilized on divinyl sulfone (DVS)/organophosphonate-modified microrings and used to characterize carbohydrate-protein and norovirus particle interactions. This biofunctional platform was able to orthogonally detect multiple specific carbohydrate-protein interactions simultaneously. Additionally, the platform was capable of reproducible binding after multiple regenerations by high-salt, high-pH, or low-pH solutions and after 1 month storage in ambient conditions. This remarkable stability and durability of the organophosphonate immobilization strategy will facilitate the application of silicon microring resonators in various sensing conditions, prolong their lifetime, and minimize the cost for storage and delivery; these characteristics are requisite for developing biosensors for point-of-care and distributed diagnostics and other biomedical applications. In addition, the platform demonstrated its ability to characterize carbohydrate-mediated host-virus interactions, providing a facile method for discovering new antiviral agents to prevent infectious disease.     

Reagentless fluorescent biosensors based on proteins for continuous monitoring systems

There is a lack of commercially available efficient and autonomous systems capable of continuous monitoring of (bio)chemical data for clinical, environmental, food, or industrial samples. The weakest link in the design of these systems is the (bio)chemical receptor (bCR). The bCR should have transducer ability, the recognition event should be a single reaction, and the bCR should be easily regenerated. Transport proteins and enzymes are well placed as bCR for optical continuous monitoring systems (OCMS). In this paper we review quantitative aspects and the main transducer strategies which have been developed for transport proteins, using periplasmic binding proteins (linking an environmentally sensitive fluorophore or FRET between two fluorophores) and concanavalin A (competitive reversible assays) as representative examples. Efficient immobilization systems and implementation in OCMS are also reviewed. Some kinds of enzymes can fulfil the necessary requirements to be appropriate bCR. Strategies using flavoenzymes chemically modified with fluorophores can be successfully implemented in OCMS and they are, in our opinion, the most appropriate option.     

A modular assembly strategy for improving the substrate specificity of small catalytic peptides

In contrast to large proteins, small peptide catalysts typically display limited specificity for small molecule substrates. This is presumably a result of the limited opportunities small peptides have to fold in a manner that provides for the formation of an isolated reaction vessel that effectively binds and sequesters substrates from bulk solvent while at the same time catalyzing their transformation. For the preparation of small peptide catalysts that possess improved substrate specificity, we have developed a modular assembly strategy that involves appending phage display-derived substrate binding-domain modules to catalytically active peptide domains. We demonstrate the potential of this strategy with the construction of a small 35-amino acid residue aldolase peptide with improved substrate specificity. The advantages of this approach are that it reduces the demand on the functionalization of the catalytic site and it is modular, therefore making its adaptation to a variety of specificities rapid. The modular assembly strategy studied here may present advantages over exhaustive searches of large random-sequence peptide libraries for peptides with singular function.     

Patterning pallet arrays for cell selection based on high-resolution measurements of fluorescent biosensors

Pallet arrays enable cells to be separated while they remain adherent to a surface and provide a much greater range of cell selection criteria relative to that of current technologies. However there remains a need to further broaden cell selection criteria to include dynamic intracellular signaling events. To demonstrate the feasibility of measuring cellular protein behavior on the arrays using high resolution microscopy, the surfaces of individual pallets were modified to minimize the impact of scattered light at the pallet edges. The surfaces of the three-dimensional pallets on an array were patterned with a coating such as fibronectin using a customized stamping tool. Micropatterns of varying shape and size were printed in designated regions on the pallets in single or multiple steps to demonstrate the reliability and precision of patterning molecules on the pallet surface. Use of a fibronectin matrix stamped at the center of each pallet permitted the localization of H1299 and mouse embryonic fibroblast (MEF) cells to the pallet centers and away from the edges. Compared to pallet arrays with fibronectin coating the entire top surface, arrays with a central fibronectin pattern increased the percentage of cells localized to the pallet center by 3-4-fold. Localization of cells to the pallet center also enabled the physical separation of cells from optical artifacts created by the rough pallet side walls. To demonstrate the measurement of dynamic intracellular signaling on the arrays, fluorescence measurements of high spatial resolution were performed using a RhoA GTPase biosensor. This biosensor utilized fluorescence resonance energy transfer (FRET) between cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) to measure localized RhoA activity in cellular ruffles at the cell periphery. These results demonstrated the ability to perform spatially resolved measurements of fluorescence-based sensors on the pallet arrays. Thus, the patterned pallet arrays should enable novel cell separations in which cell selection is based on complex cellular signaling properties.     

Novel tailoring reaction for two adjacent coordinated nitriles giving platinum 1,3,5-triazapentadiene complexes

The tailoring reaction of the two adjacent nitrile ligands in cis-[PtCl(2)(RCN)(2)] (R = Me, Et, CH(2)Ph, Ph) and [Pt(tmeda)(EtCN)(2)][SO(3)CF(3)](2) (8.(OTf)(2); tmeda = N,N,N',N'-tetramethylethylenediamine) upon their interplay with N,N'-diphenylguanidine (DPG; NH=C(NHPh)(2)), in a 1:2 molar ratio gives the 1,3,5-triazapentadiene complexes [PtCl(2){NHC(R)NHC(R)=NH}] (1-4) and [Pt(tmeda){NHC(Et)NHC(Et)NH}][SO(3)CF(3)](2) (10.(OTf)(2)), respectively. In contrast to the reaction of 8.(OTf)(2) with NH=C(NHPh)(2), interaction of 8.(OTf)(2) with excess gaseous NH(3) leads to formation of the platinum(II) bis(amidine) complex cis-[Pt(tmeda){NH=C(NH(2))Et}(2)][SO(3)CF(3)](2) (9.(OTf)(2)). Treatment of trans-[PtCl(2)(RCN)(2)] (R = Et, CH(2)Ph, Ph) with 2 equiv of NH=C(NHPh)(2) in EtCN (R = Et) and CH(2)Cl(2) (R = CH(2)Ph, Ph) solutions at 20-25 degrees C leads to [PtCl{NH=C(R)NC(NHPh)=NPh}(RCN)] (11-13). When any of the trans-[PtCl(2)(RCN)(2)] (R = Et, CH(2)Ph, Ph) complexes reacts in the corresponding nitrile RCN with 4 equiv of DPG at prolonged reaction time (75 degrees C, 1-2 days), complexes containing two bidentate 1,3,5-triazapentadiene ligands, i.e. [Pt{NH=C(R)NC(NHPh)=NPh}(2)] (14-16), are formed. Complexes 14-16 exhibit strong phosphorescence in the solid state, with quantum yields (peak wavelengths) of 0.39 (530 nm), 0.61 (460 nm), and 0.74 (530 nm), respectively. The formulation of the obtained complexes was supported by satisfactory C, H, and N elemental analyses, in agreement with FAB-MS, ESI-MS, IR, and (1)H and (13)C{(1)H} NMR spectra. The structures of 1, 2, 4, 11, 13, 14, 9.(picrate)(2), and 10.(picrate)(2) were determined by single-crystal X-ray diffraction.     

Selective electrochemical biosensors from state-switching of bilayer and monolayer lipid membranes by lectin-polysaccharide complexes

Interaction of the lectin concanavalin A with the polysaccharide glycogen can provide rapid spontaneous transients of the surface potential at bilayer and monolayer lipid membranes. The selective binding process can cause large, rapid potassium ion current fluctuations across bilayer membranes in a manner that is periodic and reproducible. The frequency of these transient ion current signals was shown to be related to sub-nanomolar concentrations of the reactive agents in aqueous solution. The physical mechanism responsible for ion current modulation was investigated by fluorescence methods using lipid vesicles, by the thermal dependence of the potassium ion current across planar bilayers and by pressure-area and dipolar potential measurements of lipid monolayers at an air-water interface. The mechanism is primarily associated with physical perturbations of lipid membranes by lectin-polysaccharide aggregates, resulting in the formation of localised domains of variable electrostatic potential and conductivity.     

Interpolyelectrolyte complexes of conjugated copolymers and DNA: platforms for multicolor biosensors

Interchain interactions modulate the frequency of emission from a cationic water-soluble conjugated polymer. The polymer, PFPB, is obtained by a Suzuki copolymerization of p-phenylenebisboronic acid with a 95:5 mixture of 2,7-dibromo-9,9-bis(6'-bromohexyl)fluorene and 4,7-dibromo-2,1,3-benzothiadiazole, followed by quarternization of the pendant groups by addition of NMe3. The structure of PFPB contains 5% of the 2,1,3-benzothiadiazole (BT) chromophore within a cationic poly(fluorene-co-phenylene) polymer chain. The emission of PFPB is blue under dilute conditions (<1 x 10-6 M in repeat units) and green at higher concentrations. Energy transfer to dye-labeled ss-DNA is more efficient, relative to the parent polymer poly(9,9-bis(6'-N,N,N,-trimethylammonium)hexyl)fluorene-co-alt-1,4-phenylene) dibromide (PFP), as a result of improved spectral overlap. By using a peptide nucleic acid (PNA-C*) labeled with a red-emitting chromophore one can obtain three different emission colors, depending on the nature of the substrate under interrogation. If no ss-DNA is present, the solution emits blue. With a ss-DNA that is noncomplementary to PNA-C*, green emission is observed. Red emission occurs upon addition of ss-DNA complementary to the PNA sequence.     

A strategy of tailoring stable electrolyte material for high performance proton-conducting solid oxide fuel cells (SOFCs)

A facile strategy was proposed to synthesize Nb-containing BaCeO₃-based material, which is a potential electrolyte for proton-conducting solid oxide fuel cells (SOFCs), via a wet chemical route while the conventional synthesis of Nb-containing oxides relied on the solid state reaction method due to the unavailability of suitable Nb-precursors such as Nb-nitrates resulting in a less desirable fuel cell performance when used as an electrolyte. The BaCe_0.7Nb_0.1Y_0.2O_3 − δ (BCNY) electrolyte material in this study persisted a good chemical stability against CO₂ and exhibited good performance in the fuel cell application. The fuel cell with BCNY electrolyte film showed a high performance of 533 mW cm^− 2 at 700 °C. This cell performance based on BCNY electrolyte was superior to that of many stable modified BaCeO₃-based proton-conducting SOFCs where the electrolytes were tailored by other strategies. This result indicated that the strategy presented in this study could be an effective way to prepare a stable electrolyte for high performance proton-conducting SOFCs, which could advance the development of proton-conducting SOFCs.     

A simple and general strategy for the design of fluorescent cation sensor beads

[Structure: see text] Chenodeoxycholic acid based PET sensors for alkali metal ions have been immobilized on Merrifield resin and on Tentagel. The fluorescence of the sensor beads is enhanced upon binding the cations. The modular nature of the sensor allows designing different sensors based on this concept.     

A modular strategy for generating starting conformations and data structures of polynucleotide helices for potential energy calculations

We describe a simple and rapid algorithm for generating data structures and starting coordinates of polynucleotides for potential energy calculations. The algorithm is tailored to investigations in cartesian coordinate, rather than dihedral angle, space. First, instead of a tree structure for molecular design, we set up a helix from a simple list of bonds for the basic DNA subunits (sugar, phosphate, and bases). Second, instead of using successive transformations to obtain a set of coordinates in one reference frame, we apply a simple “matching” routine to patch DNA subunits. Third, we avoid ring closure and geometry optimization by allowing deviations from equilibrium values only for P? O3′ bond lengths and O5′? P? O3′ bond angles at the residue connection sites. A double-stranded helix is constructed from duplex building blocks (2 hydrogen-bonded nucleotides) which are in turn built from the basic structural units. Every building block is constructed from two sets of geometric variables: {α, β, γ, χ, P, τ_max}, one for each strand. The building blocks are then assembled into a helix by using the 6 rigid body transformations {Δx, Δy, Δz, Θ_ROLL , Θ_TILT , Θ_TWIST }. For cartesian space programs, generating starting coordinates by this procedure is particularly useful as an alternative to using actual crystal structure coordinates. After describing the algorithm in detail, we illustrate how it was used to generate model A, B, and Z DNA helices. We conclude by suggesting how the algorithm can be used to pursue a build-up technique and to set up a wide range of starting conformations in the goal of locating novel helical structures.     

A highly modular and convergent approach for the synthesis of stimulant-responsive heteroligated cofacial porphyrin tweezer complexes

The synthesis of new hemilabile phosphine ligands and their reaction with [Rh(COE)2Cl]2 to form dissymmetric heteroligated tweezer complexes using a halide-induced ligand rearrangement reaction are reported. These complexes can undergo reactions with small-molecule ligands and elemental anions quantitatively in situ, which serve to regulate the porphyrin-porphyrin distances and interactions within the assembly.     

A modular strategy toward the synthesis of heparin-like oligosaccharides using monomeric building blocks in a sequential glycosylation strategy

A novel flexible assembly strategy is described for the modular synthesis of heparin and heparan sulfates. The reported strategy uses monomeric building blocks to construct the oligosaccharide chain to attain a maximum degree of flexibility. In the assembly, 1-hydroxyl glucosazido- and 1-thio uronic acid donors are combined in a sequential glycosylation protocol using sulfonium triflate activator systems. The key 1-thio uronic acids were obtained in an efficient manner from diacetone glucose employing a chemo- and regioselective oxidation of partially protected glucose and idose thioglycosides.     

Construction of artificial signal transducers on a lectin surface by post-photoaffinity-labeling modification for fluorescent saccharide biosensors

A new general method, post-photoaffinity-labeling modification (PPALM), for constructing fluorescent saccharide biosensors based on naturally occurring saccharide-binding proteins, lectins, is described in detail. An active-site-directed incorporation of a masked reactive site into a lectin was conducted by using a photoaffinity labeling technique followed by demasking and then chemical modification to yield a fluorescent lectin. Two photoaffinity labeling reagents were designed and synthesized in this study. The labeling reagent with a photoreactive site appended through a disulfide link to a mannoside unit was bound to the saccharide-binding pocket of the lectin concanavalin A (Con A). After light irradiation, the mannoside unit was cleaved by reduction. The unique thiol group thus produced was site-specifically modified with various fluorescent groups (dansyl, coumarin, or dimethylaminobenzoate derivatives) to afford fluorescent Con As. The labeling site was characterized by protease-catalyzed digestion followed by HPLC, MALDI-TOF MS, and tandem mass-mass spectrometry; these methods indicated that the photolabeling step is remarkably site specific. Strong fluorescence was observed in the engineered Con A with a fluorophore, and the emission changed sensitively upon saccharide complexation. The binding constants for various saccharides were determined by fluorescence titration and demonstrated that the binding selectivity and affinity of the engineered Con As are comparable to those of native Con A. The red shift of the emission maximum, the decrease in the fluorescence anisotropy of the dansyl unit, and the increase in the twisted intramolecular charge transfer emission caused by sugar binding to the engineered Con A explicitly indicate that the microenvironment of the appended fluorophores changes from a restricted and relatively hydrophobic environment into a rather freely mobile and hydrophilic environment.     

Tetraphenylethene based zinc complexes as fluorescent chemosensors for pyrophosphate sensing

We described a serious of zinc complexes that exhibit characteristic fluorescence responses toward pyrophosphate(PPi) and adenosine triphosphate(ATP) in aqueous media. These novel probes exploited tetraphenylethene(TPE) as fluorophore and macrocycle-polyamine(including 1,4,7,10-tetraazacyclododecane and 1,4,7-triazacyclononane) Zn(II) complexes as binding group. These ‘‘OFF–ON' type probes exhibited promising selectivity and sensitivity to PPi and ATP via a restriction of intramolecular rotation(RIR) mechanism. The detection limit for PPi was found within nmol/L range.