Comparison of surface plasmon resonance spectroscopy and quartz crystal microbalance techniques for studying DNA assembly and hybridization

In this study we evaluate the strengths and weaknesses of surface plasmon resonance (SPR) spectroscopy and quartz crystal microbalance (QCM) technique for studying DNA assembly and hybridization reactions. Specifically, we apply in parallel an SPR instrument and a 5 MHz QCM device with dissipation monitoring (QCM-D) to monitor the assembly of biotinylated DNA (biotin-DNA) on a streptavidin-modified surface and the subsequent target DNA hybridization. Through the parallel measurements, we demonstrate that SPR is more suitable for quantitative analysis of DNA binding amount, which is essential for interfacial DNA probe density control and for the analysis of its effect on hybridization efficiency and kinetics. Although the QCM is not quantitative to the same extent as SPR (QCM measures the total mass of the bound DNA molecules together with the associated water), the dissipation factor of the QCM provides a qualitative measure of the viscoelastic properties of DNA films and the conformation of the bound DNA molecules. The complexity in mass measurement does not impair QCM's potential for a kinetic evaluation of the hybridization processes. For quantification of target DNA, the biotin-DNA modified SPR and QCM sensors are exposed to target DNA with increasing concentration. The plots of SPR/QCM signals versus target DNA concentration show that water entrapment between DNA strands make the QCM sensitivity for the hybridization assay well comparable with that of the SPR, although the intrinsic mass sensitivity of the 5 MHz QCM is approximately 20 times lower.     

Improved protein detection on an AC electrokinetic quartz crystal microbalance (EKQCM)

Microscale electrodes supplied with an AC field can generate rotational fluid patterns known as AC electroosmosis. In the present study, this effect was used to improve antibody binding on a biosensor surface. Antibodies, like many other large, slow moving biomolecules, tend to suffer from transport limitations during a reaction with a surface-bound receptor. Stirring such reactions with AC electroosmosis can alleviate this transport limitation by bringing fresh reagent to the surface. For the first time, the use of this phenomenon was used to improve the capture of protein on a sensor. Directly adsorbed antibodies were bound to the surface of specially modified quartz crystal microbalances, known as electrokinetic QCMs (EKQCMs) and the signal was enhanced by about 5.6 times. Modification of the QCM resulted in little reduction of quality factor (from ～ 5.3 k to ～ 4.6k) and an increased sensitivity to viscosity changes (151%). Full immunoassays performed on electrodes fabricated on glass surfaces were used to ensure antibody function was not significantly degraded by the enhancement technique.     

A novel ultrahigh-resolution surface plasmon resonance biosensor with an Au nanocluster-embedded dielectric film

The detection performance of conventional surface plasmon resonance (SPR) biosensors is limited to a 1 pg/mm(2) surface coverage of biomolecules, and consequently, such sensors struggle to detect the interaction of small molecules in low concentrations. The present study is attempted to propose the use of a novel SPR biosensor with Au nanoclusters embedded in a dielectric film to achieve a 10-fold improvement in the resolution performance. A co-sputtering method utilizing a multi-target sputtering system is used to fabricate the present dielectric films (SiO(2)) with embedded Au nanoclusters. It is shown that the sensitivity of the developed SPR biosensor can be improved by adjusting the size and volume fraction of the embedded Au nanoclusters in order to control the surface plasmon effect. The present gas detection and DNA hybridization experimental results confirm that the proposed Au nanocluster-enhanced SPR biosensor provides the potential to achieve an ultrahigh-resolution detection performance of approximately 0.1 pg/mm(2) surface coverage of biomolecules.     

Construction of viscoelastic biocompatible films via the layer-by-layer assembly of hyaluronan and phosphorylcholine-modified chitosan

Films of hyaluronan (HA) and a phosphorylcholine-modified chitosan (PC-CH) were constructed by the polyelectrolyte multilayer (PEM) deposition technique and their buildup in 0.15 M NaCl was followed by atomic force microscopy, surface plasmon resonance spectroscopy (SPR), and dissipative quartz crystal microbalance (QCM). The HA/PC-CH films were stable over a wide pH range (3.0-12.0), exhibiting a stronger resistance against alkaline conditions as compared to HA/CH films. The loss and storage moduli, G' and G", of the films throughout the growth of eight bilayer assemblies were derived from an impedance analysis of the QCM data recorded in situ. Both G' and G" values were one order of magnitude lower than the moduli of HA/CH films. The fluid gel-like characteristics of HA/PC-CH multilayers were attributed to their high water content (50 wt %), which was estimated by comparing the surface coverage values derived from SPR and QCM measurements. Given the versatility of the PEM methodology, HA/PC-CH films are attractive tools for developing biocompatible surface coatings of controlled mechanical properties.     

Molecular interactions in the insulin-like growth factor (IGF) axis: a surface plasmon resonance (SPR) based biosensor study

This review describes a comprehensive analysis of a surface plasmon resonance (SPR)-based biosensor study of molecular interactions in the insulin-like growth factor (IGF) molecular axis. In this study, we focus on the interaction between the polypeptide growth factors IGF-I and IGF-II with six soluble IGF binding proteins (IGFBP 1-6), which occur naturally in various biological fluids. We have describe the conditions required for the accurate determination of kinetic rate constants for these interactions and highlight the experimental and theoretical pitfalls, which may be encountered in the early stages of such a study. We focus on IGFBP-5 and describe a site-directed mutagenesis study, which examines the contribution of various residues in the protein to high affinity interaction with IGF-I and -II. We analyse the interaction of IGFBP-5 (and IGFBP-3) with heparin and other biomolecules and describe experiments, which were designed to monitor multi-protein complex formation in this molecular axis.     

Analysis of native proteins from biological fluids by biomolecular interaction analysis mass spectrometry (BIA/MS): exploring the limit of detection, identification of non-specific binding and detection of multi-protein complexes

Biomolecular interaction analysis mass spectrometry (BIA/MS) is a two-dimensional analytical technique that quantitatively and qualitatively detects analytes of interests. In the first dimension, surface plasmon resonance (SPR) is utilized for detection of biomolecules in their native environment. Because SPR detection is non-destructive, analyte(s) retained on the SPR-active sensor surface can be analyzed in a second dimension using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The qualitative nature of the MALDI-TOF MS analysis complements the quantitative character of SPR sensing and overcomes the shortcomings of the SPR detection stemming from the inability to differentiate and characterize multi-protein complexes and non-specific binding. In this work, the benefit of performing MS analysis following SPR sensing is established. Retrieval and detection of four markers present in biological fluids (cystatin C, beta-2-microglobulin, urinary protein 1 and retinol binding protein) was explored to demonstrate the effectiveness of BIA/MS in simultaneous detection of clinically related biomarkers and delineation of non-specific binding. Furthermore, the BIA/MS limit of detection at very low SPR responses was investigated. Finally, detection of in-vivo assembled protein complexes was achieved for the first time using BIA/MS.     

Real Time Measurements of Membrane Protein:Receptor Interactions Using Surface Plasmon Resonance (SPR)

Protein-protein interactions are pivotal to most, if not all, physiological processes, and understanding the nature of such interactions is a central step in biological research. Surface Plasmon Resonance (SPR) is a sensitive detection technique for label-free study of bio-molecular interactions in real time. In a typical SPR experiment, one component (usually a protein, termed ''ligand'') is immobilized onto a sensor chip surface, while the other (the ''analyte'') is free in solution and is injected over the surface. Association and dissociation of the analyte from the ligand are measured and plotted in real time on a graph called a sensogram, from which pre-equilibrium and equilibrium data is derived. Being label-free, consuming low amounts of material, and providing pre-equilibrium kinetic data, often makes SPR the method of choice when studying dynamics of protein interactions. However, one has to keep in mind that due to the method''s high sensitivity, the data obtained needs to be carefully analyzed, and supported by other biochemical methods. SPR is particularly suitable for studying membrane proteins since it consumes small amounts of purified material, and is compatible with lipids and detergents. This protocol describes an SPR experiment characterizing the kinetic properties of the interaction between a membrane protein (an ABC transporter) and a soluble protein (the transporter''s cognate substrate binding protein).     

Surface plasmon resonance measurement of pH-induced responses of immobilized biomolecules: conformational change or electrostatic interaction effects?

Recently, the observation of pH-induced conformational changes of biomolecules supported on carboxymethyldextran (CMD)-coated surfaces measured using surface plasmon resonance (SPR) has been reported. However, it is apparent that the evidence reported in the literature is ambiguous. The research presented in this paper describes investigations to study the changing SPR signal of immobilized biomolecules as a function of varying pH, to provide a detailed understanding of the origin of the pH-induced changes in the SPR profile. SPR measurements were performed with cytochrome c, concanavalin A, and poly-L-lysine, biomolecules that exhibit diverse conformational responses to changing pH, covalently immobilized onto CMD-coated supports. These SPR measurements were supported by circular dichroism (CD) solution studies. The SPR profiles recorded were not consistent with the conformational transitions of the biomolecules as observed using CD. An alternative explanation for the observed shifts in SPR is proposed, which explains the SPR profiles in terms of electrostatic interaction effects between the immobilized biomolecules and the carboxymethyldextran matrix.     

Camptothecin binds to a synthetic peptide identified by a T7 phage display screen

An analysis of non-biotinylated camptothecin (CPT) binding to the C-20-biotinylated CPT binding peptide NSSQSARR was carried out using two methods, quartz-crystal microbalance (QCM) and surface plasmon resonance (SPR). The peptide was immobilized peptide on a sensor chip and showed a dissociation constant (KD) of approximately 0.1 microM against CPT in QCM and SPR experiments.     

Analysis of the composite response of shear wave resonators to the attachment of mammalian cells

The suitability of the quartz crystal microbalance (QCM) technique for monitoring the attachment and spreading of mammalian cells has recently been established. Different cell species were shown to generate an individual response of the QCM when they make contact with the resonator surface. Little is known, however, about the underlying mechanisms that determine the QCM signal for a particular cell type. Here we describe our results for different experimental approaches designed to probe the particular contributions of various subcellular compartments to the overall QCM signal. Using AC impedance analysis in a frequency range that closely embraces the resonators' fundamental frequency, we have explored the signal contribution of the extracellular matrix, the actin cytoskeleton, the medium that overlays the cell layer, as well as the liquid compartment that is known to exist between the basal plasma membrane and the culture substrate. Results indicate that the QCM technique is only sensitive to those parts of the cellular body that are involved in cell substrate adhesion and are therefore close to the resonator surface. Because of its noninvasive nature, sensitivity, and time resolution, the QCM is a powerful means of quantitatively studying various aspects of cell-substrate interactions.     

Molecularly imprinted polymers (MIP) in electroanalysis of proteins

The review summarizes current knowledge on the main approaches used for creation of high affinity polymer analogs of antibodies (known as molecularly imprinted polymers, MIP) applicable for electroanalysis of functionally important proteins such as myoglobin, troponin T, albumin, ferritin, lysozyme, calmodulin. The main types of monomers for MIP preparation as well as methods convenient for analysis of MIP/protein interactions, such as surface plasmon resonance (SPR), nanogravimetry with the use of a quartz crystal resonator (QCM), spectral and electrochemical methods have been considered. Special attention is paid to experimental data on electrochemical registration of myoglobin by means of o-phenylenediaminebased MIP electrodes. It was shown that the imprinting factor calculated as a ratio of the myoglobin signal obtained after myoglobin insertion in MIP to the myoglobin signal obtained after myoglobin insertion in the polymer lacking the molecular template (NIP) is 2–4.     

Development of surface plasmon resonance imaging for detection of Acidovorax avenae subsp. citrulli (Aac) using specific monoclonal antibody

An immunosensor based on surface plasmon resonance imaging (SPR imaging) using a specific monoclonal antibody 11E5 (MAb 11E5) was developed for the detection of the seed-borne bacterium Acidovorax avenae subsp. citrulli (Aac), which causes fruit blotch in watermelons and cantaloupes, and compared to the conventional ELISA technique. The 1:40 mixed self-assembled monolayer (mixed SAM) surface was used for the immobilized MAb 11E5 on sensor surface for the detection of Aac. Both whole cells and broken cells of Aac were tested by using direct and sandwich detection assay. The limit of detection (LOD) of Aac using the SPR imaging technique and a direct detection assay was 10(6)cfu/ml and a subsequent amplification of the SPR signal using a polyclonal antibody (PAb) lowered the LOD to 5×10(5) cfu/ml. The LOD for the ELISA technique was 5×10(4) cfu/ml for the detection of Aac, which was slightly better than that for the SPR technique. However, the sensor surface based on SPR imaging offered a major advantage in terms of surface regeneration, allowing at least five cycles with a shorter time assay, multi-channel analysis with an application on multiplex detection, and an ease of the surface usage for the detection of Aac in the naturally infected plant. The surface was tested against the naturally infected sample and showed good selectivity toward the Aac bacteria.     

Immobilizing bifenthrin on wood for termite control

Termites are world-wide pests causing significant losses to annual and perennial crops, as well as damages to wooden components in buildings. Although various chemical, physical, and biological methods have been explored to prevent termite attack on wooden structures, new guiding principles are still needed for environmental protection. In this study, by combining the effective chemical control of bifenthrin and photo-immobilization technique of biomolecules, we developed chitosan as a carrier to embed bifenthrin, which was then immobilized by ultraviolet treatment on the surface of wood (Cunninghamia lanceolata). The immobilized bifenthrin embedded in the photoactive chitosan was characterized by Fourier transform infrared spectroscopy (FTIR), C.H.N analysis, ultraviolet, and fluorescence measurements. The surface structures and biological activity were examined by scanning electron microscopy (SEM), atomic force microscope (AFM), electron spectroscopy for chemical analysis (ESCA), and bioassays. The results indicated that the immobilized bifenthrin can be well protected from free and non-controlled releasing, and has a long-term stability allowing high efficiency against the termite at a dose of 2.5 ??g/cm². This study provides a novel and environmentally-benign technique for the termite control by photo-immobilizing the bifenthrin-embedded chitosan on the surface of C. lanceolata. This technique may be used in combination with the traditional methods for effective termite control.     

Nonspecific hydrophobic interactions of a repressor protein, PhaR, with poly[(R)-3-hydroxybutyrate] film studied with a quartz crystal microbalance

The gene expression for phasins (PhaP), which are predominantly polyhydroxyalkanoates (PHAs) granule-associated proteins, is regulated by a repressor protein of PhaR through the dual binding abilities of PhaR to the target DNAs and the granules. In this study, the binding functions of PhaR to poly[(R)-3-hydroxybutyrate] (P(3HB)) were investigated quantitatively by using a quartz crystal microbalance (QCM) technique. Adsorption of PhaR onto a melt-crystallized film of P(3HB) (cr-P(3HB)) was detected as a negative frequency shift of the QCM. The time course of the frequency changes observed for PhaR adsorption was composed of a quick frequency decrease at an initial stage and a subsequent slower frequency decrease for several hours, indicating multilayered adsorption of PhaR molecules onto cr-P(3HB). The initial rapid adsorption, which corresponds to direct adsorption of PhaR molecules onto a bare surface of cr-P(3HB), was a diffusion-controlled process. Strong interactions between PhaR and cr-P(3HB) were also observed as apparently irreversible adsorption. The comparative QCM measurement of PhaR adsorption onto various types of polymers with different aliphatic chemical structures revealed that PhaR was adsorbed onto the surfaces of polymers, including cr-P(3HB), mainly by nonspecific hydrophobic interactions. These results illustrate the high affinity and low specificity for adsorption of PhaR to P(3HB).     

Microfluidic systems integrated with two-dimensional surface plasmon resonance phase imaging systems for microarray immunoassay

This study reports a microfluidic chip integrated with an arrayed immunoassay for surface plasmon resonance (SPR) phase imaging of specific bio-samples. The SPR phase imaging system uses a surface-sensitive optical technique to detect two-dimensional (2D) spatial phase variation caused by rabbit immunoglobulin G (IgG) adsorbed on an anti-rabbit IgG film. The microfluidic chip was fabricated by using micro-electro-mechanical-systems (MEMS) technology on glass and polydimethylsiloxane (PDMS) substrates to facilitate well-controlled and reproducible sample delivery and detection. Since SPR detection is very sensitive to temperature variation, a micromachine-based temperature control module comprising micro-heaters and temperature sensors was used to maintain a uniform temperature distribution inside the arrayed detection area with a variation of less than 0.3 degrees C. A self-assembled monolayer (SAM) technique was used to pattern the surface chemistry on a gold layer to immobilize anti-rabbit IgG on the modified substrates. The microfluidic chip is capable of transporting a precise amount of IgG solution by using micropumps/valves to the arrayed detection area such that highly sensitive, highly specific bio-sensing can be achieved. The developed microfluidic chips, which employed SPR phase imaging for immunoassay analysis, could successfully detect the interaction of anti-rabbit IgG and IgG. The interactions between immobilized anti-rabbit IgG and IgG with various concentrations have been measured. The detection limit is experimentally found to be 1 x 10(-4)mg/ml (0.67 nM). The specificity of the arrayed immunoassay was also explored. Experimental data show that only the rabbit IgG can be detected and the porcine IgG cannot be adsorbed. The developed microfluidic system is promising for various applications including medical diagnostics, microarray detection and observing protein-protein interactions.     

Rapidly-Deposited Polydopamine Coating via High Temperature and Vigorous Stirring: Formation,Characterization and Biofunctional Evaluation

Polydopamine (PDA) coating provides a promising approach for immobilization of biomolecules onto almost all kinds of solid substrates. However, the deposition kinetics of PDA coating as a function of temperature and reaction method is not well elucidated. Since dopamine self-polymerization usually takes a long time, therefore, rapid-formation of PDA film becomes imperative for surface modification of biomaterials and medical devices. In the present study, a practical method for preparation of rapidly-deposited PDA coating was developed using a uniquely designed device, and the kinetics of dopamine self-polymerization was investigated by QCM sensor system. It was found that high temperature and vigorous stirring could dramatically speed up the formation of PDA film on QCM chip surface. Surface characterization, BSA binding study, cell viability assay and antibacterial test demonstrates that the polydopamine coating after polymerization for 30 min by our approach exhibits similar properties to those of 24 h counterpart. The method has a great potential for rapid-deposition of polydopamine films to modify biomaterial surfaces.     

Label-enhanced surface plasmon resonance applied to label-free interaction analysis of small molecules and fragments

Surface plasmon resonance (SPR) is a well-established method for studying interactions between small molecules and biomolecules. In particular, SPR is being increasingly applied within fragment-based drug discovery; however, within this application area, the limited sensitivity of SPR may constitute a problem. This problem can be circumvented by the use of label-enhanced SPR that shows a 100-fold higher sensitivity as compared with conventional SPR. Truly label-free interaction data for small molecules can be obtained by applying label-enhanced SPR in a surface competition assay format. The enhanced sensitivity is accompanied by an increased specificity and inertness toward disturbances (e.g., bulk refractive index disturbances). Label-enhanced SPR can be used for fragment screening in a competitive assay format; the competitive format has the added advantage of confirming the specificity of the molecular interaction. In addition, label-enhanced SPR extends the accessible kinetic regime of SPR to the analysis of very fast fragment binding kinetics. In this article, we demonstrate the working principles and benchmark the performance of label-enhanced SPR in a model system—the interaction between carbonic anhydrase II and a number of small-molecule sulfonamide-based inhibitors.     

Surface plasmon resonance (SPR) analysis of coagulation in whole blood with application in prothrombin time assay

It is previously shown that surface plasmon resonance (SPR) can be used to study blood plasma coagulation. This work explores the use of this technique for the analysis of tissue factor induced coagulation, i.e. prothrombin time (PT) analysis, of whole blood and plasma. The reference method was nephelometry. The prothrombin time analysis by SPR was performed by mixing two volumes of blood/plasma, one volume of thromboplastin, and one volume of CaCl2 solution directly on a sensor surface. The measurements show good agreement between nephelometry and SPR plasma analysis and also between SPR plasma and whole blood analysis. The effect of anticoagulant treatment on the clotting times was significant both quantitatively and qualitatively. The impact on the SPR signal of different physiological events in the coagulation process is discussed, and tentative interpretations of the sensorgram features are given. The major advantage of the SPR method compared to nephelometry is the possibility to perform analysis on whole blood instead of plasma. In conclusion, SPR is a promising method for whole blood coagulation analysis.     

Determination of monoenzyme- and bienzyme-stimulated precipitation by a cuvette-based surface plasmon resonance instrument.

This paper describes the use of a cuvette-based surface plasmon resonance (SPR) instrument to measure biocatalyzed precipitation reactions. Enzyme-modified SPR sensor disk forms the base of a cuvette, in which the substrate solution is added with stirring. The determination of the substrate concentration relies on the measurement of SPR angle shift (Deltatheta(SPR)) induced by the deposition of the insoluble products without involving in any electrochemical reactions. As examples, horseradish peroxidase (HRP)-modified monoenzyme SPR sensor and HRP-glucose oxidase bienzyme-layered sensor are created to determine hydrogen peroxide and glucose via the catalyzed oxidation of 4-chloro-1-naphthol (4-CN). The deposition of the oxidized 4-CN-insoluble products leads to SPR angle shifts, which are linear to H(2)O(2) and glucose in the concentration ranges of 0.067-7.24 x 10(-5) and 0.7-8.3 x 10(-4) mM, respectively. The SPR sensitivities are greater than those of nonelectrochemical quartz crystal microbalance (QCM) (the parallel results in this study) and compare favorable with those of electrochemical QCM and electrochemical SPR methods. This study opens the field for enhanced SPR measurements by using biocatalyzed precipitation as a signal amplification method.