In Situ Monitoring of Aptamer-Protein Binding on a ZnO Surface Using Spectroscopic Ellipsometry.

The dissolution of zinc oxide is investigated using spectroscopic ellipsometry to investigate its suitability as a platform for biosensing applications. The results indicate that once the ZnO surface has been functionalised, it is suitably protected, and no significant dissolving of the ZnO occurs. The binding kinetics of the SARS-CoV-2 spike protein on aptamer-functionalised zinc oxide surfaces are subsequently investigated. Values are extracted for the refractive index and associated optical constants for both the aptamer layer used and the protein itself. It is shown that upon an initial exposure to the protein, a rapid fluctuation in the surface density is observed. After around 20 min, this effect stabilises, and a fixed increase in the surface density is observed, which itself increases as the concentration of the protein is increased. This technique and setup are demonstrated to have a limit-of-detection down to 1 nanomole (nM) and display a linear response to concentrations up to 100 nM.

Selection and Functionalization of Germanium Nanowires for Bio-Sensing.

In this paper, we investigate the use of dielectrophoresis to align germanium nanowire arrays to realize nanowire-based diodes and their subsequent use for bio-sensing. After establishing that dielectrophoresis is a controllable and repeatable fabrication method to create devices from germanium nanowires, we use the optimum process conditions to form a series of diodes. These are subsequently functionalized with an aptamer, which is able to bind specifically to the spike protein of SARS-Cov2 and investigated as a potential sensor. We observe a linear increase in the source to drain current as the concentration of spike protein is increased from 100 fM/L to 1 nM/L.

An Aptamer-Functionalised Schottky-Field Effect Transistor for the Detection of Proteins.

The outbreak of the coronavirus disease 2019 (COVID-19) in December 2019 has highlighted the need for a flexible sensing system that can quickly and accurately determine the presence of biomarkers associated with the disease. This sensing system also needs to be easily adaptable to incorporate both novel diseases as well as changes in the existing ones. Here we report the feasibility of using a simple, low-cost silicon field-effect transistor functionalised with aptamers and designed to attach to the spike protein of SARS-CoV2. It is shown that a linear response can be obtained in a concentration range of 100 fM to 10 pM. Furthermore, by using a larger range of source-drain potentials compared with other FET based sensors, it is possible to look at a wider range of device parameters to optimise the response.

Calcium Microdomain Formation at the Perisynaptic Cradle Due to NCX Reversal: A Computational Study.

It has recently been proposed using a multi-compartmental mathematical model that negatively fixed charged membrane-associated sites constrain the flow of cations in perisynaptic astroglial processes. This restricted movement of ions between the perisynaptic cradle (PsC), principal astroglial processes and the astrocyte soma gives rise to potassium (K+) and sodium (Na+) microdomains at the PsC. The present paper extends the above model to demonstrate that the formation of an Na+ microdomain can reverse the Na+/Ca2+ exchanger (NCX) thus providing an additional source of calcium (Ca2+) at the PsC. Results presented clearly show that reversal of the Na+/Ca2+ exchanger is instigated by a glutamate transporter coupled increase in concentration of cytoplasmic [Na+]i at the PsC, which and instigates Ca2+ influx through the NCX. As the flow of Ca2+ along the astrocyte process and away from the PsC is also constrained by Ca2+ binding proteins, then a Ca2+ microdomain forms at the PsC. The paper also serves to demonstrate that the EAAT, NKA, and NCX represent the minimal requirement necessary and sufficient for the development of a Ca2+ microdomain and that these mechanisms directly link neuronal activity and glutamate release to the formation of localized Na+ and Ca2+ microdomains signals at the PsC. This local source of Ca2+ can provide a previously underexplored form of astroglial Ca2+ signaling.

Efficiency of the flagellar propulsion of Escherichia coli in confined microfluidic geometries.

Bacterial movement in confined spaces is routinely encountered either in a natural environment or in artificial structures. Consequently, the ability to understand and predict the behavior of motile bacterial cells in confined geometries is essential to many applications, spanning from the more classical, such as the management complex microbial networks involved in diseases, biomanufacturing, mining, and environment, to the more recent, such as single cell DNA sequencing and computation with biological agents. Fortunately, the development of this understanding can be helped by the decades-long advances in semiconductor microfabrication, which allow the design and the construction of complex confining structures used as test beds for the study of bacterial motility. To this end, here we use microfabricated channels with varying sizes to study the interaction of Escherichia coli with solid confining spaces. It is shown that an optimal channel size exists for which the hydrostatic potential allows the most efficient movement of the cells. The improved understanding of how bacteria move will result in the ability to design better microfluidic structures based on their interaction with bacterial movement.

Potassium and sodium microdomains in thin astroglial processes: A computational model study.

A biophysical model that captures molecular homeostatic control of ions at the perisynaptic cradle (PsC) is of fundamental importance for understanding the interplay between astroglial and neuronal compartments. In this paper, we develop a multi-compartmental mathematical model which proposes a novel mechanism whereby the flow of cations in thin processes is restricted due to negatively charged membrane lipids which result in the formation of deep potential wells near the dipole heads. These wells restrict the flow of cations to "hopping" between adjacent wells as they transverse the process, and this surface retention of cations will be shown to give rise to the formation of potassium (K+) and sodium (Na+) microdomains at the PsC. We further propose that a K+ microdomain formed at the PsC, provides the driving force for the return of K+ to the extracellular space for uptake by the neurone, thereby preventing K+ undershoot. A slow decay of Na+ was also observed in our simulation after a period of glutamate stimulation which is in strong agreement with experimental observations. The pathological implications of microdomain formation during neuronal excitation are also discussed.

Surface-Controlled Properties of Myosin Studied by Electric Field Modulation.

The efficiency of dynamic nanodevices using surface-immobilized protein molecular motors, which have been proposed for diagnostics, drug discovery, and biocomputation, critically depends on the ability to precisely control the motion of motor-propelled, individual cytoskeletal filaments transporting cargo to designated locations. The efficiency of these devices also critically depends on the proper function of the propelling motors, which is controlled by their interaction with the surfaces they are immobilized on. Here we use a microfluidic device to study how the motion of the motile elements, i.e., actin filaments propelled by heavy mero-myosin (HMM) motor fragments immobilized on various surfaces, is altered by the application of electrical loads generated by an external electric field with strengths ranging from 0 to 8 kVm(-1). Because the motility is intimately linked to the function of surface-immobilized motors, the study also showed how the adsorption properties of HMM on various surfaces, such as nitrocellulose (NC), trimethylclorosilane (TMCS), poly(methyl methacrylate) (PMMA), poly(tert-butyl methacrylate) (PtBMA), and poly(butyl methacrylate) (PBMA), can be characterized using an external field. It was found that at an electric field of 5 kVm(-1) the force exerted on the filaments is sufficient to overcome the frictionlike resistive force of the inactive motors. It was also found that the effect of assisting electric fields on the relative increase in the sliding velocity was markedly higher for the TMCS-derivatized surface than for all other polymer-based surfaces. An explanation of this behavior, based on the molecular rigidity of the TMCS-on-glass surfaces as opposed to the flexibility of the polymer-based ones, is considered. To this end, the proposed microfluidic device could be used to select appropriate surfaces for future lab-on-a-chip applications as illustrated here for the almost ideal TMCS surface. Furthermore, the proposed methodology can be used to gain fundamental insights into the functioning of protein molecular motors, such as the force exerted by the motors under different operational conditions.

Control and gating of kinesin-microtubule motility on electrically heated thermo-chips.

First lab-on-chip devices based on active transport by biomolecular motors have been demonstrated for basic detection and sorting applications. However, to fully employ the advantages of such hybrid nanotechnology, versatile spatial and temporal control mechanisms are required. Using a thermo-responsive polymer, we demonstrated a temperature controlled gate that either allows or disallows the passing of microtubules through a topographically defined channel. The gate is addressed by a narrow gold wire, which acts as a local heating element. It is shown that the electrical current flowing through a narrow gold channel can control the local temperature and as a result the conformation of the polymer. This is the first demonstration of a spatially addressable gate for microtubule motility which is a key element of nanodevices based on biomolecular motors.

Actin filament motility induced variation of resonance frequency and rigidity of polymer surfaces studied by quartz crystal microbalance.

This contribution reports on the quantification of the parameters of the motility assays for actomyosin system using a quartz crystal microbalance (QCM). In particular, we report on the difference in the observed resonance frequency and dissipation of a quartz crystal when actin filaments are stationary as opposed to when they are motile. The changes in QCM measurements were studied for various polymer-coated surfaces functionalized with heavy meromyosin (HMM). The results of the QCM experiments show that the HMM-induced sliding velocity of actin filaments is modulated by a combination of the viscoelastic properties of the polymer layer including the HMM motors.

A molecular wire incorporating a robust hexanuclear platinum cluster.

Reaction of [Pt(6)(CO)(4)(P(t)Bu(2))(4)Cl(2)] with excess HS(CH(2))(4)SH in Et(2)NH gave highly stable [Pt(6)(CO)(4)(P(t)Bu(2))(4){S(CH(2))(4)SH}(2)], which adsorbs unchanged onto gold surfaces. This permitted the fabrication and electrical characterisation of gold|molecule|gold junctions involving a well-defined metal carbonyl cluster compound.

Structure-property relationships in redox-gated single molecule junctions--a comparison of pyrrolo-tetrathiafulvalene and viologen redox groups.

We demonstrate that the electrical "switching" behavior of single molecules connected between two electrode contacts can be controlled by altering their structure and electrochemical characteristics. The electrical properties of gold|molecule|gold single molecule junctions incorporating HS(CH2)6-X-(CH2)6SH, where X = viologen (4,4'-bipyridinium) or pyrrolotetrathiafulvalene, are determined using a scanning tunneling microscopy based technique. The switching behavior, controlled through a tuneable electrochemical gate, changes from an on-off response (viologen) to an off-on-off response (pyrrolotetrathiafulvalene) on changing the central redox group. In contrast, the electrical properties of junctions incorporating redox-inactive HS(CH2)6-1,4-C6H4-(CH2)6SH do not alter significantly as a function of applied potential.

Chemical control of double barrier tunnelling in alpha,omega-dithiaalkane molecular wires.

Single molecule conductance measurements on 1,4-bis-(6-thia-hexyl)-benzene derivatives reveal (i) that benzene rings serve as an effective indentation in the tunnelling barrier, and (ii) that more electron-rich benzene rings give higher conductances, consistent with hole conduction (i.e.via the benzene HOMO).

Thermal gating of the single molecule conductance of alkanedithiols.

The temperature dependence of the single molecule conductance (SMC) of alpha,omega-alkanedithiols has been investigated using a scanning tunnelling microscopy (STM) method. This is based on trapping molecules between a gold STM tip and a gold substrate and measuring directly the current across the molecule under different applied potentials. A pronounced temperature dependence of the conductance, which scales logarithmically with T(1), is observed in the temperature range between 293 and 353 K. It is proposed the origin of this dependence is the change in distribution between molecular conformers rather than changes in either the conduction mechanism or the electronic structure of molecule. For alkanedithiols the time averaged conformer distribution shifts to less elongated conformers at higher temperatures thus giving rise to higher conductance across the molecular bridges. This is analysed by first calculating energy differences between different conformers and then calculating their partition distribution. A simple tunnelling model is then used to calculate the temperature dependent conductance based on the conformer distribution. These findings demonstrate that charge transport through single organic molecules at ambient temperatures is a subtle and highly dynamic process that cannot be described by analysing only one molecular conformation corresponding to the lowest energy geometry of the molecule.

A combined top-down bottom-up approach for introducing nanoparticle networks into nanoelectrode gaps.

We report here on the fabrication of a three-dimensional array of nanoparticles which bridges the gap between lithographically defined gold electrode contacts separated by 20 nm. The nanoparticle assemblies are formed from about 5 nm gold nanoparticles and benzenedimethanethiol (BDMT) bridging ligands. These assemblies are introduced between the contacts using a layer-by-layer protocol with successive BDMT self-assembly being followed by nanoparticle adsorption until the gap is bridged. The temperature dependent electrical properties of these devices are analysed to establish whether they are consistent with the notion that the networks are built up from molecularly interlinked discrete gold nanoparticles. To aid this analysis the molecular conductance of single bridging molecules is also characterized at room temperature using a recently introduced method based on the scanning tunnelling microscope (STM). From these measurements it is concluded that the room temperature electrical properties of the nanostructured networks are limited by the small interparticle connectivity and the inherent resistance of the linker molecules.

Molecular wire formation from viologen assemblies.

The adsorption behavior of viologen alpha,omega-dithiols (viologen dithiols) on gold has been investigated. At short exposures, a low-coverage phase consisting of flat-lying molecules has been determined by STM and IR spectroscopy. In contrast, multilayer films are formed after long adsorption times. Single molecular wires could be formed between a gold STM tip and a surface with a low coverage of the adsorbed dithiols, and their electrical behavior was investigated. Molecular conductivity was determined either by the repeated measurement of I(s) curves or by recording I-V curves for different tip-sample separations. These methods concurred in producing a value of (0.5 +/- 0.1) nS for the single-molecule conductivity of the alpha,omega-viologen dithiol molecule HS-6V6-SH. The high conductivity of HS-6V6-SH, as compared to that of HS-C12-SH, may be related to the low-lying LUMO, which provides a barrier indentation for electron transport in a two-step electron-transfer mechanism.

Redox state dependence of single molecule conductivity.

Spontaneous formation of stable molecular wires between a gold scanning tunneling microscopy (STM) tip and substrate is observed when the sample has a low coverage of alpha,omega-dithiol molecules and the tunneling resistance is made sufficiently small. Current-distance curves taken under these conditions exhibit characteristic current plateaux at large tip-substrate separations from which the conductivity of a single molecule can be obtained. The versatility of this technique is demonstrated using redox-active molecules under potential control, where substantial reversible conductivity changes from 0.5 to 2.8 nS were observed when the molecule was electrochemically switched from the oxidized to the reduced state.