Optoelectric patterning: Effect of electrode material and thickness on laser‐induced AC electrothermal flow

Rapid electrokinetic patterning (REP) is an emerging optoelectric technique that takes advantage of laser‐induced AC electrothermal flow and particle‐electrode interactions to trap and translate particles. The electrothermal flow in REP is driven by the temperature rise induced by the laser absorption in the thin electrode layer. In previous REP applications 350–700 nm indium tin oxide (ITO) layers have been used as electrodes. In this study, we show that ITO is an inefficient electrode choice as more than 92% of the irradiated laser on the ITO electrodes is transmitted without absorption. Using theoretical, computational, and experimental approaches, we demonstrate that for a given laser power the temperature rise is controlled by both the electrode material and its thickness. A 25‐nm thick Ti electrode creates an electrothermal flow of the same speed as a 700‐nm thick ITO electrode while requiring only 14% of the laser power used by ITO. These results represent an important step in the design of low‐cost portable REP systems by lowering the material cost and power consumption of the system.     

Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking

BACKGROUND: Using fixed receptor sites derived from high-resolution crystal structures in structure-based drug design does not properly account for ligand-induced enzyme conformational change and imparts a bias into the discovery and design of novel ligands. We sought to facilitate the design of improved drug leads by defining residues most likely to change conformation, and then defining a minimal manifold of possible conformations of a target site for drug design based on a small number of identified flexible residues. RESULTS: The crystal structure of thymidylate synthase from an important pathogenic target Pneumocystis carinii (PcTS) bound to its substrate and the inhibitor, BW1843U89, is reported here and reveals a new conformation with respect to the structure of PcTS bound to substrate and the more conventional antifolate inhibitor, CB3717. We developed an algorithm for determining which residues provide 'soft spots' in the protein, regions where conformational adaptation suggests possible modifications for a drug lead that may yield higher affinity. Remodeling the active site of thymidylate synthase with new conformations for only three residues that were identified with this algorithm yields scores for ligands that are compatible with experimental kinetic data. CONCLUSIONS: Based on the examination of many protein/ligand complexes, we develop an algorithm (SOFTSPOTS) for identifying regions of a protein target that are more likely to accommodate plastically to regions of a drug molecule. Using these indicators we develop a second algorithm (PLASTIC) that provides a minimal manifold of possible conformations of a protein target for drug design, reducing the bias in structure-based drug design imparted by structures of enzymes co-crystallized with inhibitors.     

Observation of electrostatically released DNA from gold electrodes with controlled threshold voltages

DNA oligo-nucleotides, localized at Au metal electrodes in aqueous solution, are found to be released when applying a negative bias voltage to the electrode. The release was confirmed by monitoring the intensity of the fluorescence of cyanine dyes (Cy3) linked to the 5' end of the DNA. The threshold voltage of the release changes depending on the kind of linker added to the DNA 3'-terminal. The amount of released DNA depends on the duration of the voltage pulse. Using this technique, we can retain DNA at Au electrodes or Au needles, and release the desired amount of DNA at a precise location in a target. The results suggest that DNA injection into living cells is possible with this method.     

Electrochemically promoted photocatalytic oxidation of nitrite ion by using rutile form of TiO2/Ti electrode

The photocatalytic oxidation of nitrite ion in a NaCl aqueous solution using the rutile form of TiO₂/Ti as the working electrode was studied. Experimental results indicate that the rutile form of TiO₂/Ti film electrode has excellent photoactivity by applying a bias potential and irradiation simultaneously. The incident photo-to-current conversion efficiency (IPCE) of this working electrode is a function of the applying bias potential. The photocurrent efficiency of nitrite ion oxidation was 33–40% at a pH of about 7. The oxidation rate of the nitrite ion in brine wastewater using the rutile form of TiO₂/Ti electrode can be estimated by photocurrent measurements. The applying bias potential, light power and pH value were the major factors affecting the oxidation rate and the photocurrent efficiency of nitrite ion oxidation, while the concentrations of nitrite ion was minor.     

Electron flow in multicenter enzymes: theory, applications, and consequences on the natural design of redox chains

In protein film voltammetry, a redox enzyme is directly connected to an electrode; in the presence of substrate and when the driving force provided by the electrode is appropriate, a current flow reveals the steady-state turnover. We show that, in the case of a multicenter enzyme, this signal reports on the energetics and kinetics of electron transfer (ET) along the redox chain that wires the active site to the electrode, and this provides a new strategy for studying intramolecular ET. We propose a model which takes into account all the enzyme's redox microstates, and we prove it useful to interpret data for various enzymes. Several general ideas emerge from this analysis. Considering the reversibility of ET is a requirement: the usual picture, where ET is depicted as a series of irreversible steps, is oversimplified and lacks the important features that we emphasize. We give justification to the concept of apparent reduction potential on the time scale of turnover and we explain how the value of this potential relates to the thermodynamic and kinetic properties of the system. When intramolecular ET does not limit turnover, the redox chain merely mediates the driving force provided by the electrode or the soluble redox partner, whereas when intramolecular ET is slow, the enzyme behaves as if its active active site had apparent redox properties which depend on the reduction potentials of the relays. This suggests an alternative to the idea that redox chains are optimized in terms of speed: evolutionary pressure may have resulted in slowing down intramolecular ET in order to tune the enzyme's "operating potential".     

Electrical bias dependent photochemical functionalization of diamond surfaces

Diamond is an excellent substrate for many sensing and electronic applications because of its outstanding stability in biological and aqueous environments. When the diamond surface is H-terminated, it can be covalently modified with organic alkenes using wet photochemical methods that are surface-mediated and initiated by the ejection of electrons from the diamond. To develop a better understanding of the photochemical reaction mechanism, we examine the effect of applying an electrical bias to the diamond samples during the photochemical reaction. Applying a 1 V potential between two diamond electrodes significantly increases the rate of functionalization of the negative electrode. Cyclic voltammetry and electrochemical impedance measurements show that the 1 V potential induces strong downward band-bending within the diamond film of the negative electrode. At higher voltages a Faradaic current is observed, with no further acceleration of the functionalization rate. We attribute the bias-dependent changes in rate to a field effect, in which the applied potential induces a strong downward band-bending on the negative electrode and facilitates the ejection of electrons into the adjacent fluid of reactant organic alkenes. We also demonstrate the ability to directly photopattern the surface with reactant molecules on length scales of <25 microm, the smallest we have measured, using simple photomasking techniques.     

Photoelectrochemistry as a novel strategy for DNA hybridization detection

The special properties of ssDNA and dsDNA molecules in structure and electric behavior, may offer us some new ideas for the fabrication of genosensors and DNA-chips. In this work, the photoelectrochemical method was firstly employed to characterize the photoelectric behavior of a ssDNA probe electrode, which was prepared with the self-assembly technique, and its resulting dsDNA electrode. The obvious decrease in the photocurrent of the dsDNA modified electrode at open potential or a bias voltage indicated that photoelectrochemistry was another useful method for DNA hybridization detection. Using the special design of ssDNA probes, we attempt to discuss further the relationship between the properties of DNA molecules and their photoelectric behaviors. In addition, the electrochemical impedance method was employed to verify the occurrence of some modifications over the electrode interface before and after the hybridization event.     

On the application of accelerated molecular dynamics to liquid water simulations

Our group recently proposed a robust bias potential function that can be used in an efficient all-atom accelerated molecular dynamics (MD) approach to simulate the transition of high energy barriers without any advance knowledge of the potential-energy landscape. The main idea is to modify the potential-energy surface by adding a bias, or boost, potential in regions close to the local minima, such that all transitions rates are increased. By applying the accelerated MD simulation method to liquid water, we observed that this new simulation technique accelerates the molecular motion without losing its microscopic structure and equilibrium properties. Our results showed that the application of a small boost energy on the potential-energy surface significantly reduces the statistical inefficiency of the simulation while keeping all the other calculated properties unchanged. On the other hand, although aggressive acceleration of the dynamics simulation increases the self-diffusion coefficient of water molecules greatly and dramatically reduces the correlation time of the simulation, configurations representative of the true structure of liquid water are poorly sampled. Our results also showed the strength and robustness of this simulation technique, which confirm this approach as a very useful and promising tool to extend the time scale of the all-atom simulations of biological system with explicit solvent models. However, we should keep in mind that there is a compromise between the strength of the boost applied in the simulation and the reproduction of the ensemble average properties.     

Tuning surface charge property by floating gate field effect transistor

Tuning surface charge property by a floating gate field effect transistor (FGFET) is proposed and analyzed for the first time. The FGFET has an additional floating gate electrode embedded inside the dielectric channel wall and is superior to the conventional FET to tune the surface charge property of a dielectric material in contact with an aqueous solution.     

氢键介质的芳酰胺折叠体:从构象控制到功能演化

根据芳环上酰胺和氢键受体位置的不同,氢键介质的芳酰胺和酰肼折叠体可以产生折叠、螺旋、"之"字型、直线型及其他扩展型的构象.由于氢键具有较高的稳定性及芳酰胺固有的平面性特征,这一系列的芳酰胺寡聚体拥有较高的可预测的构象.芳酰胺骨架本身可以通过简单的酰胺键偶合反应构筑,而不同的官能团也可以选择性地引入到特定的骨架内部或其侧...     

Shape changes induced by N-terminal platination of ubiquitin by cisplatin

The three-dimensional conformation of a protein is an important property and plays a key role in its biological activity. We show here that ion mobility-mass spectrometry (IM-MS) can be used to detect conformational changes in the protein ubiquitin in the gas phase induced by reaction with the anticancer drug cisplatin. The primary adduct was ubiquitin-{Pt(NH₃)₂} under denaturing conditions. Up to three different conformations appear to be generated upon platination depending on the charge state. The collision cross-sections (Ω) for each conformation indicate that the conformations of the platinated protein are contracted in size compared with unmodified ubiquitin with generally smaller Ω values. Ion mobility-tandem MS allowed determination of the platinum binding site without a requirement for prior Chromatographic separation. A rapid 30-min digestion of cisplatin-modified ubiquitin with trypsin allowed the platination site to be identified as the N-terminal methionine following low-energy collision-induced dissociation (CID) studies of the modified peptide. The data were generated using a Traveling-Wave based ion mobility-MS approach. Such cisplatin-induced shape changes may have a significant effect on its function in vivo. This work highlights the usefulness of the ion-mobility mass spectrometry technique for shedding new light on such protein interactions.     

Enzyme-catalyzed signal amplification for electrochemical DNA detection with a PNA-modified electrode

The signal amplification technique of peptide nucleic acid (PNA)-based electrochemical DNA sensor was developed in a label-free and one-step method utilizing enzymatic catalysis. Electrochemical detection of DNA hybridization on a PNA-modified electrode is based on the change of surface charge caused by the hybridization of negatively charged DNA molecules. The negatively charged mediator, ferrocenedicarboxylic acid, cannot diffuse to the DNA hybridized electrode surface due to the charge repulsion with the hybridized DNA molecule while it can easily approach the neutral PNA-modified electrode surface without the hybridization. By employing glucose oxidase catalysis on this PNA-based electrochemical system, the oxidized mediator could be immediately reduced leading to greatly increased electrochemical signals. Using the enzymatic strategy, we successfully demonstrated its clinical utility by detecting one of the mutation sequences of the breast cancer susceptibility gene BRCA1 at a sample concentration lower than 10(-9) M. Furthermore, a single base-mismatched sample could be also discriminated from a perfectly matched sample.     

Superhydrophobic thermoplastic polyurethane films with transparent/fluorescent performance

In this paper, we report a simple and versatile route for the fabrication of superhydrophobic thermoplastic polyurethane (TPU) films. The approach is based on octadecanamide (ODAA)-directed assembly of nanosilica/TPU/ODAA hybrid with a well-defined sheetlike microstructure. The superhydrophobic hybrid film shows a transparent property, and its water contact angle reaches as high as 163.5° without any further low surface energy treatment. In addition, the superhydrophobic TPU hybrid film with fluorescent properties is achieved by smartly introducing CdTe quantum dots, which will extend potential application of the film to optoelectronic areas. The resulting fluorescent surface produced in this system is stable and has a water contact angle of 172.3°. This assembly method to control surface structures represents an intriguing and valuable route to tune the surface properties of organic-inorganic hybrid films.     

Spatial and temporal electrochemical control of singlet oxygen production and decay in photosensitized experiments

Active spatial and temporal modulation of domains of singlet oxygen activity is demonstrated using electrochemical tools. Using singlet oxygen microscopy in photosensitized experiments, it is shown that singlet oxygen concentrations around an ultramicroelectrode can be controlled by applying a bias voltage to the electrode. Two phenomena that can be exploited separately or collectively are examined: (1) the singlet oxygen concentration can be altered by local oxidation or reduction of the photosensitizer, which is the precursor to singlet oxygen, and (2) the reduction of oxygen to produce the superoxide anion which, among other things, is an effective singlet oxygen quencher, results in a local decrease in the concentration of singlet oxygen around the electrode. Both of these phenomena depend significantly on the diffusion of molecules along concentration gradients established by the biased electrode. The results reported herein demonstrate that one can indeed exert local electrochemical control and readily manipulate the population of singlet oxygen produced in a photosensitized process.     

On‐Chip Spyhole Mass Spectrometry for Droplet‐Based Microfluidics

For efficient coupling of droplet‐based microfluidics with mass spectrometry (MS), a spyhole drilled on the top of a microchip is used to sample the passing droplets by electrostatic‐spray ionization (ESTASI) MS. The technique involves placing an electrode below the chip under the spyhole and applying high‐voltage pulses. Electrospray occurs directly from the spyhole, and the droplet content is analyzed by MS without a dilution or oil removal step. To demonstrate the versatility of this technique, we have successfully monitored a droplet‐based tryptic digestion, as well as a biphasic reaction between β‐lactoglobulin in water and α‐tocopheryl acetate in 1,2‐dichloroethane, where the protein extracts the antioxidant from the oil phase and becomes reduced.     

Multistate organization of transmembrane helical protein dimers governed by the host membrane

Association of transmembrane (TM) helices taking place in the cell membrane has an important contribution to the biological function of bitopic proteins, among which receptor tyrosine kinases represent a typical example and a potent target for medical applications. Since this process depends on a complex interplay of different factors (primary structures of TM domains and juxtamembrane regions, composition and phase of the local membrane environment, etc.), it is still far from being fully understood. Here, we present a computational modeling framework, which we have applied to systematically analyze dimerization of 18 TM helical homo- and heterodimers of different bitopic proteins, including the family of epidermal growth factor receptors (ErbBs). For this purpose, we have developed a novel surface-based modeling approach, which not only is able to predict particular conformations of TM dimers in good agreement with experiment but also provides screening of their conformational heterogeneity. Using all-atom molecular dynamics simulations of several of the predicted dimers in different model membranes, we have elucidated a putative role of the environment in selection of particular conformations. Simulation results clearly show that each particular bilayer preferentially stabilizes one of possible dimer conformations, and that the energy gain depends on the interplay between structural properties of the protein and the membrane. Moreover, the character of protein-driven perturbations of the bilayer is reflected in the contribution of a particular membrane to the free energy gain. We have found that the approximated dimerization strength for ErbBs family can be related to their oncogenic ability.     

Electrochemically controlled self-assembly of an organometallic block copolymer

A new means of controlling the order-disorder transition of block copolymers is presented. By applying small electrical potentials (2 V/cm) to disordered solutions of an organometallic block copolymer, oriented ordered grains were obtained near the positive electrode. After reversing the electrical bias on the system, the ordered grains disappeared, and new, oriented, ordered regions were formed at the opposite electrode. Our work establishes the concept of electrochemical self-assembly for controlling order formation in block copolymers.     

Zinc-bacteriochlorophyllide dimers in de novo designed four-helix bundle proteins. A model system for natural light energy harvesting and dissipation

Photosynthetic organisms utilize interacting pairs of chlorophylls and bacteriochlorophylls as excitation energy donors and acceptors in light harvesting complexes, as photosensitizers of charge separation in reaction centers, and maybe as photoprotective quenching centers that dissipate excess excitation energy under high light intensities. To better understand how the pigment's local environment and spatial organization within the protein tune its ground- and excited-state properties to perform different functions, we prepared and characterized the simplest possible system of interacting bacteriochlorophylls within a protein scaffold. Using HP7, a high-affinity heme-binding protein of the HP class of de novo designed four-helix bundles, we incorporated 13(2)-OH-zinc-bacteriochlorophyllide-a (ZnBChlide), a water-soluble bacteriochlorophyll derivative, into specific binding sites within the four-helix bundle protein core. We capitalized on the rich and informative optical spectrum of ZnBChlide to rigorously characterize its complexes with HP7 and two variants, in which a single heme-binding site is eliminated by replacing histidine residues at positions 7 or 42 by phenylalanine. Surprisingly, we found the ZnBChlide binding capacity of HP7 and its variants to be higher than for heme: up to three ZnBChlide pigments bind per HP7, or two per each single histidine variant. The formation of dimers within HP7 results in dramatic quenching of ZnBChlide fluorescence, reducing its quantum yield by about 80%, and the singlet excited-state lifetime by 2 orders of magnitudes compared to the monomer. Thus, HP7 and its variants are the first examples of a simple protein environment that can isolate a self-quenching pair of photosynthetic pigments in pure form. Unlike its complicated natural analogues, this system can be constructed from the ground up, starting with the simplest functional element, increasing the complexity as needed.     

Enhanced Wang Landau sampling of adsorbed protein conformations

Using computer simulations to model the folding of proteins into their native states is computationally expensive due to the extraordinarily low degeneracy of the ground state. In this paper, we develop an efficient way to sample these folded conformations using Wang Landau sampling coupled with the configurational bias method (which uses an unphysical "temperature" that lies between the collapse and folding transition temperatures of the protein). This method speeds up the folding process by roughly an order of magnitude over existing algorithms for the sequences studied. We apply this method to study the adsorption of intrinsically disordered hydrophobic polar protein fragments on a hydrophobic surface. We find that these fragments, which are unstructured in the bulk, acquire secondary structure upon adsorption onto a strong hydrophobic surface. Apparently, the presence of a hydrophobic surface allows these random coil fragments to fold by providing hydrophobic contacts that were lost in protein fragmentation.