Probing biomolecular interaction forces using an anharmonic acoustic technique for selective detection of bacterial spores

Receptor-based detection of pathogens often suffers from non-specific interactions, and as most detection techniques cannot distinguish between affinities of interactions, false positive responses remain a plaguing reality. Here, we report an anharmonic acoustic based method of detection that addresses the inherent weakness of current ligand dependant assays. Spores of Bacillus subtilis (Bacillus anthracis simulant) were immobilized on a thickness-shear mode AT-cut quartz crystal functionalized with anti-spore antibody and the sensor was driven by a pure sinusoidal oscillation at increasing amplitude. Biomolecular interaction forces between the coupled spores and the accelerating surface caused a nonlinear modulation of the acoustic response of the crystal. In particular, the deviation in the third harmonic of the transduced electrical response versus oscillation amplitude of the sensor (signal) was found to be significant. Signals from the specifically-bound spores were clearly distinguishable in shape from those of the physisorbed streptavidin-coated polystyrene microbeads. The analytical model presented here enables estimation of the biomolecular interaction forces from the measured response. Thus, probing biomolecular interaction forces using the described technique can quantitatively detect pathogens and distinguish specific from non-specific interactions, with potential applicability to rapid point-of-care detection. This also serves as a potential tool for rapid force-spectroscopy, affinity-based biomolecular screening and mapping of molecular interaction networks. © 2011 Elsevier B.V.

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages.

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation.

Direct comparison of the gravimetric responsivities of ZnO-based FBARs and SMRs

Film bulk acoustic resonators (FBARs) and solidly mounted resonators (SMRs) have the potential to significantly improve upon the sensitivity and minimum detection limit of traditional gravimetric sensors based on quartz crystal microbalances (QCMs) and surface acoustic wave resonators (SAWs). To date, neither FBAR nor SMR devices have been demonstrated to be superior to the other; hence the choice between them depends primarily on the users' ability to design/fabricate membranes and/or Bragg reflectors. In this work, it is shown that identically designed FBAR and SMR devices resonating at the same frequency exhibit different responsivities to mass loadings, Rm, and that the SMRs are less responsive than the FBARs. For the specific device design and resonant frequency (~2 GHz) of the resonators presented here, the FBARs' mass responsivity is ~20% greater than that of the SMRs', and although this value is not universal for all possible device designs, it clearly shows that FBAR devices should be favoured over SMRs in gravimetric sensing applications where the FBARs' fragility is not an issue. Numerical calculations based on Mason's model offer an insight into the physical mechanisms behind the greater FBARs responsivity, and it was shown that the Bragg reflector has an effect on the acoustic load at one of the facets of the piezoelectric films which is in turn responsible for the SMRs' lower responsivity to mass loadings. © 2013 Elsevier B.V.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation. © 2013 Elsevier Ltd.

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.

Effect of the interplay between protein and surface on the properties of adsorbed protein layers.

Although protein adsorption to surface is a common phenomenon, investigation of the process is challenging due to the complexity of the interplay between external factors, protein and surface properties. Therefore experimental approaches have to measure the properties of adsorbed protein layers with high accuracy in order to achieve a comprehensive description of the process. To this end, we used a combination of two biosensing techniques, dual polarization interferometry and quartz crystal microbalance with dissipation. From this, we are able to extract surface coverage values, layer structural parameters, water content and viscoelastic properties to examine the properties of protein layers formed at the liquid/solid interface. Layer parameters were examined upon adsorption of proteins of varying size and structural properties, on surfaces with opposite polarity. We show that "soft" proteins such as unfolded α-synuclein and high molecular weight albumin are highly influenced by the surface polarity, as they form a highly diffuse and hydrated layer on the hydrophilic silica surface as opposed to the denser, less hydrated layer formed on a hydrophobic methylated surface. These layer properties are a result of different orientations and packing of the proteins. By contrast, lysozyme is barely influenced by the surface polarity due to its intrinsic structural stability. Interestingly, we show that for a similar molecular weight, the unfolded α-synuclein forms a layer with the highest percentage of solvation not related to surface coverage but resulting from the highest water content trapped within the protein. Together, these data reveal a trend in layer properties highlighting the importance of the interplay between protein and surface for the design of biomaterials.

Effect of the interplay between protein and surface on the properties of adsorbed protein layers

Although protein adsorption to surface is a common phenomenon, investigation of the process is challenging due to the complexity of the interplay between external factors, protein and surface properties. Therefore experimental approaches have to measure the properties of adsorbed protein layers with high accuracy in order to achieve a comprehensive description of the process. To this end, we used a combination of two biosensing techniques, dual polarization interferometry and quartz crystal microbalance with dissipation. From this, we are able to extract surface coverage values, layer structural parameters, water content and viscoelastic properties to examine the properties of protein layers formed at the liquid/solid interface. Layer parameters were examined upon adsorption of proteins of varying size and structural properties, on surfaces with opposite polarity. We show that "soft" proteins such as unfolded α-synuclein and high molecular weight albumin are highly influenced by the surface polarity, as they form a highly diffuse and hydrated layer on the hydrophilic silica surface as opposed to the denser, less hydrated layer formed on a hydrophobic methylated surface. These layer properties are a result of different orientations and packing of the proteins. By contrast, lysozyme is barely influenced by the surface polarity due to its intrinsic structural stability. Interestingly, we show that for a similar molecular weight, the unfolded α-synuclein forms a layer with the highest percentage of solvation not related to surface coverage but resulting from the highest water content trapped within the protein. Together, these data reveal a trend in layer properties highlighting the importance of the interplay between protein and surface for the design of biomaterials. © 2014 The Authors.

Electro-mass olfactory multi-sensor (EMMS)

For an olfactory sensor or electronic nose, the task is not only to detect the object concentration, but also to recognize it. It is well known that all the elements can be identified by their charge to mass ratio e(+)/m. We tried to imitate this principle for molecular recognition. Two kinds of sensors are used simultaneously in testing. One is quartz crystal microbalance (QCM) for detecting the change in mass, the other is interdigital electrode (IE) for detecting the change in conduction, as an electro-mass multi-sensor (EMMS). in this paper, the principle and the feasibility of this method are discussed. The preliminary results on the recognition of alcohol by EMMS coated with lipids are presented. Meanwhile, the multi-sensor can also be used as an instrument for research on some physico-chemistry problems. The change in conduction of coated membrane caused by one absorbed molecule is reported. It is found that when a QCM is coated with membrane, it still obeys the relationship Delta F (frequency change of QCM) = K Delta m (mass change of absorbed substance) and the proportional coefficient, K, depends not only on quartz properties but also on membrane characteristics as well. (C) 2000 Elsevier Science S.A. All rights reserved.

Electro-mass multi odor sensor

For an olfactory sensor or electronic nose the task is not only to detect the object concentration, but also to recognize it. It is well known that all the elements can be identified by their charge to mass ratio e+/m. We tried to use this principle for molecular recognition. Two kinds of sensors are used simultaneously in testing. One is Quartz Crystal Microbalance (QCM) for detecting the change in mass, the other is Interdigital Electrode (IE) for detecting the change in conduction. In this paper the principle and the feasibility of this method are reported. The preliminary results on the recognition of alcohols are presented. The multisensor can be used as an instrument for research on material properties and kinetic process as well.

Electro-mass olfactory multi-sensor (EMMS)

For an olfactory sensor or electronic nose, the task is not only to detect the object concentration, but also to recognize it. It is well known that all the elements can be identified by their charge to mass ratio e(+)/m. We tried to imitate this principle for molecular recognition. Two kinds of sensors are used simultaneously in testing. One is quartz crystal microbalance (QCM) for detecting the change in mass, the other is interdigital electrode (IE) for detecting the change in conduction, as an electro-mass multi-sensor (EMMS). in this paper, the principle and the feasibility of this method are discussed. The preliminary results on the recognition of alcohol by EMMS coated with lipids are presented. Meanwhile, the multi-sensor can also be used as an instrument for research on some physico-chemistry problems. The change in conduction of coated membrane caused by one absorbed molecule is reported. It is found that when a QCM is coated with membrane, it still obeys the relationship Delta F (frequency change of QCM) = K Delta m (mass change of absorbed substance) and the proportional coefficient, K, depends not only on quartz properties but also on membrane characteristics as well. (C) 2000 Elsevier Science S.A. All rights reserved.

Surface Initiated Polymerization from Substrates of Low Initiator Density and Its Applications in Biosensors

Surface initiated polymerization (SIP) has become an attractive method for tailoring physical and chemical properties of surfaces for a broad range of applications. Most of those application relied on the merit of a high density coating. In this study we explored a long overlooked field of SIP. SIP from substrates of low initiator density. We combined ellipsometry with AFM to investigate the effect of initiatior density and polymerization time on the morphology of polymer coatings. In addition, we carefully adjusted the nanoscale separation of polymer chains to achieve a balance between nonfouling and immobilization capacities. We further tested the performance of those coating on various biosensors, such as quartz crystal microbalance, surface plasmon resonance, and protein microarrays. The optimized matrices enhanced the performance of those biosensors. This report shall encourage researches to explore new frontiers in SIP that go beyond polymer brushes.

Layer-by-layer assembly of viral capsid for cell adhesion

Cowpea mosaic virus (CPMV)-based thin films are biologically active for cell culture. Using layer-by-layer assembly of CPMV and poly(diallyldimethylammonium chloride), quantitatively scalable biomolecular surfaces were constructed, which were well characterized using quartz crystal microbalance, UV-vis and atomic force microscopy. The surface coverage of CPMV nanoparticles depended on the adsorption time and pH of the virus solution, with a greater amount of CPMV adsorption occurring near its isoelectric point. It was found that the adhesion and proliferation of NIH-3T3 fibroblasts can be controlled by the coverage of viral particles using this multilayer technique.

Application of Ru(bpy)(3)(2+) in control and formation of gold surface nanostructure through oxidation-reduction cycling

It was studied that the nanostructure formed on a gold surface via a simple oxidation-reduction cycles (ORC) in 0.1 M KCl containing Ru(bpy)(3)(2+) with different concentrations. Atomic force microscopy (AFM) and energy-dispersed spectroscopy (EDS) were used to characterize the nanostructure formed on the gold surface. Sweep-step voltammetry and corresponding electroluminescence (ECL) response, in situ electrochemical quartz crystal microbalance (EQCM) measurement were used to monitor the ORC. procedure. It was found that the surface structure became more uniform in the presence of Ru(bpy)(3)(2+), and the surface roughness was decreasing with the increasing of Ru(bpY)(3)(2+) concentration, suggesting a simple and effective method to control the formation of nanostructure on the gold surface.

Electro-assisted precipitation of electrolytes in poly(3,4-ethylenedioxythiophene) film

The electrolyte, NaBF4, can be enriched into the matrix of poly(3,4-ethylenedioxythiophene) (PEDOT) film during the p-doping potential cycling between 0.6 and -0.9 V. It has been demonstrated that this enrichment is originated from the mixed ion transfer between doping and dedoping, i.e. BF4- anion migrate into the PEDOT film during the oxidation process, the Ne cation insert into the film during the reduction process, and then, the electrolyte is accumulated into the film matrix after the multiple CV cycling. The quantitative analysis of energy-dispersive X-ray spectroscopy (EDX) confirmed the enrichment of NaBF4 in the PEDOT film.