Dual and tetraelectrode QCMs using imprinted polymers as receptors for ions and neutral analytes

Polymers as coating materials were combined with quartz crystal microbalances (QCMs) to design sensor devices for the detection of both ionic and neutral analytes in liquid phase. The design and geometry of dual and tetraelectrode QCMs have been optimized to reduce electric field interferences. An unusual Sauerbrey effect was observed while exposing potassium salt solution to 10- and 20-MHz QCMs, i.e. increase in the frequency shifts by a factor of seven, which is attributed to electro-acoustic phenomena. Non-functionalized sol-gel materials were synthesized by templating with hydrophobic salt such as tetraethyl ammonium picrate. Imprinting with these ions of low charge density leads to sensitive layers, and UV–Vis spectroscopy was used to check re-inclusion of this analyte. In the next strategy, functionalized polyurethane for potassium ions and sol-gel materials with aminopropyl group as ligand were generated to tune selectivity and sensitivity towards Ni²⁺ and Cu²⁺. Methacrylic acid polymers were optimized for the detection of atrazine by hydrogen bonding; double molecular imprinted polyurethane approach was followed for pyrene recognition. Finally, these imprinted polymers were combined with tetraelectrode QCM to develop sensor platform.     

SLICK--scoring and energy functions for protein-carbohydrate interactions

Protein-carbohydrate interactions are increasingly being recognized as essential for many important biomolecular recognition processes. From these, numerous biomedical applications arise in areas as diverse as drug design, immunology, or drug transport. We introduce SLICK, a package containing a scoring and an energy function, which were specifically designed to predict binding modes and free energies of sugars and sugarlike compounds to proteins. SLICK accounts for van der Waals interactions, solvation effects, electrostatics, hydrogen bonds, and CH...pi interactions, the latter being a particular feature of most protein-carbohydrate interactions. Parameters for the empirical energy function were calibrated on a set of high-resolution crystal structures of protein-sugar complexes with known experimental binding free energies. We show that SLICK predicts the binding free energies of predicted complexes (through molecular docking) with high accuracy. SLICK is available as part of our molecular modeling package BALL (www.ball-project.org).     

Volatile Organic Compound Sensing by Quartz Crystal Microbalances Coated with Nanostructured Macromolecular Metal Complexes

We report the construction of a molecular recognition layer composed of polyelectrolyte brushes and metal complexes on the surface of a quartz crystal microbalance (QCM) and the sensing abilities for various volatile organic compounds (VOCs). Atom‐transfer radical polymerization of 2‐(dimethylamino)ethyl acrylate from an initiator‐terminated self‐assembled monolayer yielded polyelectrolyte brushes on the surface of a weight‐detectable quartz crystal microbalance. One end of a poly[(2‐dimethylamino)ethyl methacrylate] brush was covalently attached onto the surface of a sensor. We found that metallophthalocyanines with four bulky pentaphenylbenzene substituents could adsorb volatile organic compounds selectively into their cavities. Macromolecular metal complexes were prepared by immersing polymer‐brush‐modified QCMs into an aqueous solution of sterically protected cobalt phthalocyanine. Anionic cobalt phthalocyanine was trapped in the polymer brushes and acted as a molecular receptor for the sensing of VOC molecules.     

Detecting cells on the surface of a silver electrode quartz crystal microbalance using plasma treatment and graft polymerization

This paper utilizes a silver electrode quartz crystal microbalance (QCM) mass sensor to detect the physiology of cells. This study also investigates the plasma surface modification of silver electrode QCMs through deposition of hexamethyldisilazane (HMDSZ) films as a protection film. To improve the cell growth, this paper also performs post-treatments by surface-grafting acrylic acid (AAc), acrylamide (AAm), and oxygen plasma treatment onto the QCM electrodes. Experimental results indicate that plasma deposition is a useful technique to protect the surface of silver electrodes. This technique extends the unpeeling time of silver electrodes from 1 to 7 days. The hydrophilic silver electrode QCM surface modified by AAm exhibited a better storage time effect than other post-treatments.     

Potential use of Plasma-Deposition Techniques in the Preparation of Recognition Coatings for Mass Sensors 1

Abstract

The potential use of plasma-deposition techniques for the preparation of recognition coatings for mass sensors was investigated. Ethylenediamine and 4-vinylpyridine plasma-produced coatings and solution-deposited coatings from commercially available polyethyleneimine and poly(4-vinylpyridine) on quartz crystal microbalances (QCMs) were examined for the detection of acetic acid and other vapors. Freshly prepared QCM plasma-deposited recognition coatings from both ethylenediamine and 4-vinylpyridine were found to be very sensitive to acetic acid vapors. However the sensitivity decreased rapidly with time. Aging effects with solution deposited polymers films were noted as well. It was concluded that plasma-deposition of recognition coatings has great potential in the preparation of recognition coatings. In addition to well known advantages of the use of plasmas for surface film preparation or modification, the technique offers a one-step process of synthesizing and depositing high molecular weight films from volatile compounds not polymerizable by conventional means. A major disadvantage is that the chemical nature of the resulting coating is not easily predictable. However, careful choice of carrier gas and recognition film precursor can do much to simplify the design of effective recognition coatings.

     

石英晶体微天平用于预测非对映体盐结晶分离手性扁桃酸的分离效率

研究了以石英晶体微天平(QCM)手性识别结果预测手性选择剂对外消旋物的手性识别能力的新方法。经过两步组装方式将手性选择剂L-苯丙氨酸(L-Phe)组装到QCM电极表面。通过检测电极共振频率、接触角和X射线光电子能谱的变化对组装结果进行了表征。应用蒸气扩散分子组装(VDMA)方式检测L-Phe修饰QCM电极对L-扁桃酸(MA)的手性识别能力,其手性识别选择性系数约为8。随后用L-Phe作为拆分剂试验了非对映体盐结晶法拆分手性扁桃酸,并优化了手性拆分条件。结果显示,以L-Phe作为拆分剂进行非对映体盐结晶法拆分手性扁桃酸的结果与QCM手性识别结果高度吻合,表明QCM手性识别可用作辅助筛选和预测非对映体盐结晶手性拆分法的手性拆分剂。     

耗散型石英晶体微天平在生物医用高分子材料中的应用

石英晶体微天平(QCM)是一种基于石英晶体压电效应的分析检测技术,可实时在线提供石英晶体表面吸附层质量、厚度、粘弹性等信息,由此获得表面分子相互作用关系。 耗散型石英晶体微天平(QCM-D)因其独特的对粘弹性的解析,使其在高分子材料中的应用迅速发展,尤其是生物医用高分子材料领域,已用来评价生物医用高分子材料的表界面相互作用,力学和生物相容性等。 本文简单介绍了耗散型石英晶体微天平的基本原理及理论模型,重点综述了近几年QCM-D在高分子链构象、蛋白质吸附、生物大分子相互作用、药物释放以及水凝胶中的应用,并且展望了QCM-D的未来发展趋势。     

Present and future of surface plasmon resonance biosensors

Surface plasmon resonance (SPR) biosensors are optical sensors exploiting special electromagnetic waves—surface plasmon-polaritons—to probe interactions between an analyte in solution and a biomolecular recognition element immobilized on the SPR sensor surface. Major application areas include detection of biological analytes and analysis of biomolecular interactions where SPR biosensors provide benefits of label-free real-time analytical technology. This paper reviews fundamentals of SPR affinity biosensors and discusses recent advances in development and applications of SPR biosensors.     

Measurement of the unwinding force of a DNA double helix

The review is devoted to measurement methods of bond rupture forces in complex biological molecules, namely, the unwinding forces of a DNA double helix. Mechanical methods not affecting electromagnetically a system under study, which is especially significant for biological systems, are considered. We describe two main methods: atomic force microscopy and rupture event scanning. The latter is a new method also based on the mechanical action but it has a much simpler instrumental implementation. The capabilities of both methods are compared and they are shown to be promising to investigate chemical bond rupture forces in biological systems. The application of these methods to study the strength of chemical bonds is associated with overcoming numerous technical difficulties in both performance of measurements themselves and chemical modification of conjugated surfaces. We demonstrate the applicability of these methods not only for fundamental studies of the strength of chemical bonds determining the stability and the related possibility of functioning of three-dimensional biomolecular complexes, but also for the design of biosensors based on the mechanical effect (quartz crystal microbalance, QCM), e.g., with an opportunity of rapid analysis of DNA.     

Synthesis of magnetic nanoparticles and their application to bioassays

Magnetic nanoparticles have been attracting much interest as a labeling material in the fields of advanced biological and medical applications such as drug delivery, magnetic resonance imaging, and array-based assaying. In this review, synthesis of iron oxide magnetic nanoparticles via a reverse micelle system and modification of their surface by an organosilane agent are discussed. Furthermore, as a practical biological assay system, the magnetic detection of biomolecular interactions is demonstrated by using the combination of a patterned substrate modified with a self-assembled monolayer and the magnetic nanoparticles.     

A versatile QCM matrix system for online and high-throughput bio-sensing

A 3 x 3 quartz crystal microbalance (QCM) sensor matrix, fabricated on an A-T cut quartz crystal, has the ability to detect online a variety of labeled DNA samples in a parallel and comparative fashion. The QCM matrix was equipped with a single oscillator circuit, which activated only one QCM at any given time, and was controlled by programmable time-shared electronic relays. The gold electrode had a diameter of 0.8 mm and operated at a fundamental resonating frequency of 40 MHz; the dimensions of the matrix were 1.2 cm x 1.2 cm. The sensitivity of an individual QCM was in the pictogram regime. Selected QCMs were coated with either streptavidin or the anti-DIG antibody; the specificity of their detections was monitored using various concentrations of samples of biotin- and DIG-labeled DNA. The basic design of the QCM matrix is readily expandable, without any conceivable difficulties, in both geometry and circuitry.     

Method study for the preparation of a wet sediment quality control material

Quality control materials (QCMs) to be used in daily quality control in environmental laboratories are required to be similar to real samples in terms both of composition and of physical state. The present paper describes in detail the procedure of preparation and the results of homogeneity and stability studies performed on wet sediments QCMs. For this purpose, two sediments with different matrix composition were selected and the main factors involved in the preparation of the material were carefully studied and established with the aim of guaranteeing long-term stability of the QCM: pre-treatment steps, homogenisation, bottling and storage. The results obtained from the homogeneity and from 12 months of stability studies for Cd, Cr, Cu, Ni, Pb and Zn following the aqua regia extraction procedure (ISO 11466), showed that the wet sediment QCMs we have developed are feasible, constituting a new and useful material among the aquatic sediments for quality control purposes in monitoring.     

Fluid dynamics modeling for synchronizing surface plasmon resonance and quartz crystal microbalance as tools for biomolecular and targeted drug delivery studies

We have used computational fluid dynamics modeling (CFD) to synchronize the flow conditions in the flow channels of two complementary surface-sensitive characterization techniques: surface plasmon resonance (SPR) and quartz crystal microbalance (QCM). Since the footprint of the flow channels of the two devices is specified by their function, the flow behavior can only be varied either by altering the height of the flow channel, or altering the volumetric rate of flow (flow rate) through the channel. The relevant quantity that must be calibrated is the shear strain on the measurement surface (center and bottom) of the flow channel. Our CFD modeling shows that the flow behavior is in the Stokes flow regime. We were thus able to generate a scaling expression with parameters for flow rate and flow channel height for each of the two devices: f(QCM)=2.64f(SPR)(h(QCM)/h(SPR)(2), where f(QCM) and f(SPR) are the flow rates in the SPR and QCM flow channels, respectively, and h(QCM)/h(SPR) is the ratio of the heights of the two channels. We demonstrate the success of our calibration procedure through the combined use of commercially available SPR and QCM flow channel devices on both a biomolecular interaction system of surface immobilized biotin and streptavidin and a targeted drug delivery model system of biotinylated liposomes interacting with a streptavidin functionalized surface.     

Acoustic Wave Mass Sensors

The application of acoustic wave microsensors for mass sensing will be reviewed with focus on the quartz crystal microbalance (QCM) and surface acoustic wave (SAW) devices. The use of QCM and SAW devices in chemical sensing as well as in the determination of solid and liquid properties will be described. In chemical sensing, it is unlikely that a single sensor with a single coating will display a selective and reversible response to a given analyte in a mixture. Alternative strategies such as the use of sensor arrays and the use of sampling devices can be used to improve performance. QCM sensors (QCMs) will oscillate under liquids; their use in under-liquid sensing will be discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Characterization of molecular interactions of an immobilized biotinylated monolayer and streptavidin-coated microspheres by bond-rupture scanning

Bond-rupture approach has been used in the understanding of biomolecular interactions of highly specific recognition, e.g., an antibody and its antigen, by a functionalized and self-assembled monolayer (SAM). One of the most challenging issues of diagnostics is to distinguish between true binding and the ever-present non-specific binding in which a species gives false results in conventional affinity methods. In this study, bond-rupture scanning was proposed to characterize bindings by introducing energy mechanically through displacement of a resonant quartz crystal. This system was able to measure the resonant frequency difference, due to mass changes and bond breakages between supramolecular interaction of biotinylated SAM and streptavidin-coated polystyrene microsphere (SCPM). Both 2-μm and 4-μm of SCPMs revealed two recognized desorption patterns at 4 V and 2 V amplitudes respectively. It rapidly provided confirmation of the presence of a target analyte. From this study, it can be shown that an established approach of dynamic bond-rupture scanning can be adopted as a promising diagnostic tool for investigating various interactions of bacteria or virus on an immobilized biomolecular surface by measuring the characteristic level of mechanical energy required to break bonds.     

Solidified liquid layer model makes quartz crystal microbalance a convenient molecular ruler

The applications of quartz crystal microbalance (QCM) in biointerfaces are limited by its quantitative ambiguities caused by viscoelasticity and solution effects. Although many studies clearly indicated that the quantitative interpretation of QCM data needed caution, none of those studies provided a practical solution that enabled general and quantitative interpretation of QCM data. Recently we proposed a "solidified liquid layer" model that enabled QCM to be used as a biomolecular ruler. Here we applied five kinds of proteins with significant differences in their sizes and shapes to further validate this model. The effective thickness (T(eff)) of surface immobilized, hydrated proteins were 10.2, 4.7, 1.8 and 4.8 nm for rabbit IgG, streptavidin, lysozyme, and bovine serum albumin, respectively. The critical number of stakes needed for the formation of a solidified liquid layer was found to be protein dependent. We believed this "solidified liquid layer" model will facilitate the popularization of QCM as a valuable tool in biointerface studies, such as protein adsorption process or the conformational change on surface.     

Advances in high-throughput screening: biomolecular interaction monitoring in real-time with colloidal metal nanoparticles

The post-genomic era is revolutionizing the drug discovery process. The new challenges in the identification of therapeutic targets require efficient technological tools in order to be properly addressed. Label-free detection systems use proteins or ligands coupled to materials of which the physical properties are measurably modified upon specific interactions. Among the label-free systems currently available, the use of metal nanocolloids offers enhanced throughput and flexibility for real-time biomolecular recognition monitoring at a reasonable cost.     

The Nature of Activated Non‐classical Hydrogen Bonds: A Case Study on Acetylcholinesterase–Ligand Complexes

Molecular recognition events in biological systems are driven by non‐covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CH???Y type involving electron‐deficient CH donors using dispersion‐corrected density functional theory (DFT) calculations applied to acetylcholinesterase–ligand complexes. The strengths of CH???Y interactions activated by a proximal cation were considerably strong; comparable to or greater than those of classical hydrogen bonds. Significant differences in the energetic components compared to classical hydrogen bonds and non‐activated CH???Y interactions were observed. Comparison between DFT and molecular mechanics calculations showed that common force fields could not reproduce the interaction energy values of the studied hydrogen bonds. The presented results highlight the importance of considering CH???Y interactions when analysing protein–ligand complexes, call for a review of current force fields, and opens up possibilities for the development of improved design tools for drug discovery.     

Protein p53 Binding to Cisplatin‐modified DNA Targets Evaluated by Modification‐specific Electrochemical Immunoprecipitation Assay

Studies of protein interactions with chemically modified nucleic acids are of importance in various areas of biomolecular and biomedical research, including investigations of the binding of proteins important in medicine with DNA modified with drugs and diagnostic applications of modified DNAs in biosensing and bioanalysis. Chemical modification of DNA substrates with various species inside or outside specific protein binding sites can affect the protein‐DNA recognition. In this paper we present a simple electrochemical immunoprecipitation technique designed for evaluation of the effects of antitumor drug cisplatin on the p53‐DNA binding. The cisplatin‐DNA adducts are utilized as electroactive labels allowing a facile determination of the p53‐bound modified DNA. Effects observed using this technique accord with results of previous biochemical assays. This approach is potentially applicable in studies that deal with the influence of any electroactive DNA modifications on the protein‐DNA binding.     

Macrocyclic β-Sheets Stabilized by Hydrogen Bond Surrogates

Mimics of protein secondary and tertiary structure offer rationally-designed inhibitors of biomolecular interactions. β-Sheet mimics have a storied history in bioorganic chemistry and are typically designed with synthetic or natural turn segments. We hypothesized that replacement of terminal inter-β-strand hydrogen bonds with hydrogen bond surrogates (HBS) may lead to conformationally-defined macrocyclic β-sheets without the requirement for natural or synthetic β-turns, thereby providing a minimal mimic of a protein β-sheet. To access turn-less antiparallel β-sheet mimics, we developed a facile solid phase synthesis protocol. We surveyed a dataset of protein β-sheets for naturally observed interstrand side chain interactions. This bioinformatics survey highlighted an over-abundance of aromatic–aromatic, cation-π and ionic interactions in β-sheets. In correspondence with natural β-sheets, we find that minimal HBS mimics show robust β-sheet formation when specific amino acid residue pairings are incorporated. In isolated β-sheets, aromatic interactions endow superior conformational stability over ionic or cation-π interactions. Circular dichroism and NMR spectroscopies, along with high-resolution X-ray crystallography, support our design principles.