A Single and a Dual-Fractal Analysis of Analyte-Receptor Binding Kinetics for Surface Plasmon Resonance Biosensor Applications

The diffusion-limited binding kinetics of analyte in solution to either a receptor immobilized on a surface or to a receptorless surface is analyzed within a fractal framework for a surface plasmon resonance biosensor. The data is adequately described by a single- or a dual-fractal analysis. Initially, the data was modeled by a single-fractal analysis. If an inadequate fit was obtained then a dual-fractal analysis was utilized. The regression analysis provided by Sigmaplot (32) was used to determine if a single fractal analysis is sufficient or if a dual-fractal analysis is required. In general, it is of interest to note that the binding rate coefficient and the fractal dimension exhibit changes in the same direction (except for a single example) for the analyte-receptor systems analyzed. Binding rate coefficient expressions as a function of the fractal dimension developed for the analyte-receptor binding systems indicate, in general, the high sensitivity of the binding rate coefficient on the fractal dimension when both a single- and a dual-fractal analysis is used. For example, for a single-fractal analysis and for the binding of human endothelin-1 (ET-1) antibody in solution to ET-115-21.BSA immobilized on a surface plasmon resonance (SPR) surface (33), the order of dependence of the binding rate coefficient, k, on the fractal dimension, Df, is 6.4405. Similarly, for a dual-fractal analysis and for the binding of 10(-6) to 10(-4) M bSA in solution to a receptorless surface (direct binding to SPR surface) (41) the order of dependence of k1 and k2 on Df1 and Df2 were -2.356 and 6.241, respectively. Binding rate coefficient expressions are also developed as a function of the analyte concentration in solution. The binding rate coefficient expressions developed as a function of the fractal dimension(s) are of particular value since they provide a means to better control SPR biosensor performance by linking it to the degree of heterogeneity that exists on the SPR biosensor surface. Copyright 1999 Academic Press.     

Antigen-antibody binding kinetics for biosensor applications

The diffusion-limited binding kinetics of antigen (or antibody) in solution to antibody (or antigen) immobilized on a biosensor surface is analyzed within a fractal framework. The fit obtained by a dual-fractal analysis is compared with that obtained from a single-fractal analysis. In some cases, the dual-fractal analysis provides an improved fit when compared with a single-fractal analysis. This was indicated by the regression analysis provided by Sigmaplot (San Rafael, CA). These examples are presented. It is of interest to note that the state of disorder (or the fractal dimension) and the binding rate coefficient both increase (or decrease, a single example is presented for this case) as the reaction progresses on the biosensor surface. For example, for the binding of monoclonal antibody MAb 49 in solution to surface-immobilized antigen, a 90.4% increase in the fractal dimension (D_f1 toD _f2 ) from 1.327 to 2.527 leads to an increase in the binding rate coefficient (k₁ to k₂) by a factor of 9.4 from 11.74 to 110.3. The different examples analyzed and presented together provide a means by which the antigen-antibody reactions may be better controlled by noting the magnitude of the changes in the fractal dimension and in the binding rate coefficient as the reaction progresses on the biosensor surface.     

Analyte-receptor binding kinetics for biosensor applications

The diffusion-limited binding kinetics of antigen (analyte), in solution with antibody (receptor) immobilized on a biosensor surface, is analyzed within a fractal framework. Most of the data presented is adequately described by a single-fractal analysis. This was indicated by the regression analysis provided by Sigmaplot. A single example of a dual-fractal analysis is also presented. It is of interest to note that the binding-rate coefficient (k) and the fractal dimension (D_f) both exhibit changes in the same and in the reverse direction for the antigen-antibody systems analyzed. Binding-rate coefficient expressions, as a function of the D_f developed for the antigen-antibody binding systems, indicate the high sensitivity of thek on the D_f when both a single- and a dual-fractal analysis are used. For example, for a single-fractal analysis, and for the binding of antibody Mab 0.5β in solution to gpl20 peptide immobilized on a BIAcore biosensor, the order of dependence on the D_f was 4.0926. For a dual-fractal analysis, and for the binding of 25-100 ng/mL TRITC-LPS (lipopolysaccharide) in solution with polymyxin B immobilized on a fiberoptic biosensor, the order of dependence of the binding-rate coefficients, k₁ and k₂ on the fractal dimensions, D_f1 and D_f2, were 7.6335 and-11.55, respectively. The fractional order of dependence of thek(s) on the D_f(s) further reinforces the fractal nature of the system. Thek(s) expressions developed as a function of the D_f(s) are of particular value, since they provide a means to better control biosensor performance, by linking it to the heterogeneity on the surface, and further emphasize, in a quantitative sense, the importance of the nature of the surface in biosensor performance.     

Analyte-receptor binding kinetics for different types of biosensors

A fractal analysis is presented for analyte-receptor binding kinetics for different types of biosensor applications. Data taken from the literature may be modeled using a single-fractal analysis, a single- and a dual-fractal analysis, or a dual-fractal analysis. The latter two methods represent a change in the binding mechanism as the reaction progresses on the surface. Predictive relationships developed for the binding rate coefficient as a function of the analyte concentration are of particular value since they provide a means by which the binding rate coefficients may be manipulated. Relationships are presented for the binding rate coefficients as a function of the fractal dimension D _f or the degree of heterogeneity that exists on the surface. When analyte-receptor binding is involved, an increase in the heterogeneity on the surface (increase in D _f ) leads to an increase in the binding rate coefficient. It is suggested that an increase in the degree of heterogeneity on the surface leads to an increase in the turbulence on the surface owing to the irregularities on the surface. This turbulence promotes mixing, minimizes diffusional limitations, and leads subsequently to an increase in the binding rate coefficient. The binding rate coefficient is rather sensitive to the degree of heterogeneity, D _f , that exists on the biosensor surface. For example, the order of dependence on D _f1 is 7.25 for the binding rate coefficient k ₁ for the binding of a Fab fragment of an antiparaquat monoclonal antibody in solution to an antigen in the form of a paraquat analog immobilized on a sensor surface. The predictive relationships presented for the binding rate coefficient and the fractal dimension as a function of the analyte concentration in solution provide further physical insights into the binding reactions on the surface, and should assist in enhancing biosensor performance. In general, the technique is applicable to other reactions occurring on different types of surfaces, such as cell-surface reactions.     

An Evaluation of Cellular Analyte-Receptor Binding Kinetics Utilizing Biosensors: A Fractal Analysis

A fractal analysis is presented for cellular analyte-receptor binding kinetics utilizing biosensors. Data taken from the literature can be modeled by using (a) a single-fractal analysis and (b) a single- and a dual-fractal analysis. Case (b) represents a change in the binding mechanism as the reaction progresses on the biosensor surface. Relationships are presented for the binding rate coefficient(s) as a function of the fractal dimension for the single-fractal analysis examples. In general, the binding rate coefficient is rather sensitive to the degree of heterogeneity that exists on the biosensor surface. For example, for the binding of mutagenized and back-mutagenized forms of peptide E1037 in solution to salivary agglutinin immobilized on a sensor chip, the order of dependence of the binding rate coefficient, k, on the fractal dimension, D(f), is 13.2. It is of interest to note that examples are presented where the binding coefficient (k) exhibits an increase as the fractal dimension (D(f)) or the degree of heterogeneity increases on the surface. The predictive relationships presented provide further physical insights into the binding reactions occurring on the surface. These should assist us in understanding the cellular binding reaction occurring on surfaces, even though the analysis presented is for the cases where the cellular "receptor" is actually immobilized on a biosensor or other surface. The analysis suggests possible modulations of cell surfaces in desired directions to help manipulate the binding rate coefficients (or affinities). In general, the technique presented is applicable for the most part to other reactions occurring on different types of biosensors or other surfaces. Copyright 2000 Academic Press.     

A Predictive Approach Using Fractal Analysis for Analyte-Receptor Binding and Dissociation Kinetics for Surface Plasmon Resonance Biosensor Applications

A predictive approach using fractal analysis is presented for analyte-receptor binding and dissociation kinetics for biosensor applications. Data taken from the literature may be modeled, in the case of binding using a single-fractal analysis or a dual-fractal analysis. The dual-fractal analysis represents a change in the binding mechanism as the reaction progresses on the surface. A single-fractal analysis is adequate to model the dissociation kinetics in the examples presented. Predictive relationships developed for the binding and the affinity (k(diss)/k(bind)) as a function of the analyte concentration are of particular value since they provide a means by which the binding and the affinity rate coefficients may be manipulated. Relationships are also presented for the binding and the dissociation rate coefficients and for the affinity as a function of their corresponding fractal dimension, D(f), or the degree of heterogeneity that exists on the surface. When analyte-receptor binding or dissociation is involved, an increase in the heterogeneity on the surface (increase in D(f)) leads to an increase in the binding and in the dissociation rate coefficient. It is suggested that an increase in the degree of heterogeneity on the surface leads to an increase in the turbulence on the surface owing to the irregularities on the surface. This turbulence promotes mixing, minimizes diffusional limitations, and leads subsequently to an increase in the binding and in the dissociation rate coefficient. The binding and the dissociation rate coefficients are rather sensitive to the degree of heterogeneity, D(f,bind) (or D(f1)) and D(f,diss), respectively, that exists on the biosensor surface. For example, the order of dependence on D(f,bind) (or D(f1)) and D(f2) is 6.69 and 6.96 for k(bind,1) (or k(1)) and k(2), respectively, for the binding of 0.085 to 0.339 μM Fab fragment 48G7(L)48G7(H) in solution to p-nitrophenyl phosphonate (PNP) transition state analogue immobilized on a surface plasmon resonance (SPR) biosensor. The order of dependence on D(f,diss) (or D(f,d)) is 3.26 for the dissociation rate coefficient, k(diss), for the dissociation of the 48G7(L)48G7(H)-PNP complex from the SPR surface to the solution. The predictive relationships presented for the binding and the affinity as a function of the analyte concentration in solution provide further physical insights into the reactions on the surface and should assist in enhancing SPR biosensor performance. In general, the technique is applicable to other reactions occurring on different types of biosensor surfaces and other surfaces such as cell-surface reactions. Copyright 2000 Academic Press.     

A fractal analysis of analyte-estrogen receptor binding and dissociation kinetics using biosensors: environmental effects

A fractal analysis is used to model the binding and dissociation kinetics between analytes in solution and estrogen receptors (ER) immobilized on a sensor chip of a surface plasmon resonance (SPR) biosensor. Both cases are analyzed: unliganded as well as liganded. The influence of different ligands is also analyzed. A better understanding of the kinetics provides physical insights into the interactions and suggests means by which appropriate interactions (to promote correct signaling) and inappropriate interactions such as with xenoestrogens (to minimize inappropriate signaling and signaling deleterious to health) may be better controlled. The fractal approach is applied to analyte-ER interaction data available in the literature. Numerical values obtained for the binding and the dissociation rate coefficients are linked to the degree of roughness or heterogeneity (fractal dimension, D(f)) present on the biosensor chip surface. In general, the binding and the dissociation rate coefficients are very sensitive to the degree of heterogeneity on the surface. For example, the binding rate coefficient, k, exhibits a 4.60 order of dependence on the fractal dimension, D(f), for the binding of unliganded and liganded VDR mixed with GST-RXR in solution to Spp-1 VDRE (1,25-dihydroxyvitamin D(3) receptor element) DNA immobilized on a sensor chip surface (Cheskis and Freedman, Biochemistry 35 (1996) 3300-3318). A single-fractal analysis is adequate in some cases. In others (that exhibit complexities in the binding or the dissociation curves) a dual-fractal analysis is required to obtain a better fit. A predictive relationship is also presented for the ratio K(A)(=k/k(d)) as a function of the ratio of the fractal dimensions (D(f)/D(fd)). This has biomedical and environmental implications in that the dissociation and binding rate coefficients may be used to alleviate deleterious effects or enhance beneficial effects by selective modulation of the surface. The K(A) exhibits a 112-order dependence on the ratio of the fractal dimensions for the ligand effects on VDR-RXR interaction with specific DNA.     

A beta-cyclodextrin based fiber-optic chemical sensor: a fractal analysis

A fractal analysis is presented for the binding of pyrene in solution to beta-cyclodextrin attached to a fiber-optic chemical sensor. The specific (k(l)) and non-specific binding rate coefficients and the fractal dimension (D(f)) (specific binding case only) both tend to increase as the pyrene concentration in solution increases from 12.4 to 124 ng ml(-1). Predictive relations for the binding rate coefficient (specific as well as non-specific binding) and for D(f) (specific binding case only) as a function of pyrene concentration are provided. These relations fit the calculated k(l) and D(f) values in the pyrene concentration range reasonably well. Fractal analysis data seem to indicate that an increase in the pyrene concentration in solution increases the "ruggedness" or inhomogeneity on the fiber-optic biosensor surface. The fractal analysis provides novel physical insights into the reactions occuring on the fiber-optic chemical surface and should assist in the design of fiber-optic chemical sensors.     

Antigen-antibody binding kinetics for biosensors

The diffusion-limited binding kinetics of antigen in solution to antibody immobilized on a biosensor surface is analyzed within a fractal framework. Changes in the fractal dimension, D_f observed are in the same and in the reverse directions as the forward binding rate coefficientk. For example, an increase in the concentration of the isoenzyme human creatine kinase isoenzyme MB form (CK-MB) (antigen) solution from 0.1 to 50 ng/mL and bound to anti-CK-MB antibody immobilized on fused silica fiber rods leads to increases in the fractal dimension D_f from 0.294 to 0.5080, and in the forward binding rate coefficientk from 0.1194 to 9.716, respectively. The error in the fractal dimension D_f decreases with an increase in the CK-MB isoenzyme concentration in solution. An increase in the concentration of human chorionic gonadotrophin (hCG) in solution from 4000 to 6000 mIU/mL hCG and bound to anti-hCG antibody immobilized on a fluorescence capillary fill device leads to a decrease in the fractal dimension D_f from 2.6806 to 2.6164, and to an increase in the forward binding rate coefficientk from 3.571 to 4.033, respectively. The different examples analyzed and presented together indicate one means by which the forward binding rate coefficientk may be controlled, that is by changing the fractal dimension or the ‘disorder’ on the surface. The analysis should assist in helping to improve the stability, the sensitivity, and the response time of biosensors.     

Antigen-antibody diffusion-limited binding kinetics for biosensors

A fractal analysis is made for antigen-antibody binding kinetics for different biosensor applications available in the literature. Both types of examples are considered wherein: (1) the antigen is in solution and the antibody is immobilized on the fiberoptic surface, and (2) the antibody is in solution and the antigen is immobilized on the fiberoptic surface. For example, when the antibody is immobilized on the surface, an increase in the antigenClostridium botulinum toxin A concentration in solution leads to (1) a decrease in the fractal dimension value or state of disorder, and (2) a higher rate constant for binding on the fiberoptic surface. An analysis of the effect of the influence of different parameters on the fractal dimension values for a particular example, such as varying treatments or incubation procedures, helps provide insights into the conformational states and reactions occurring on the fiberoptic surface. The analysis of the different examples taken together provides novel physical insights into the state of “disorder” and reactions occurring on the surface. Such types of analysis should help contribute toward manipulating the reactions occurring on the fiberoptic surfaces in desired directions.     

Label free capacitive immunosensor for detecting calpastatin — A meat tenderness biomarker

An immunological capacitive biosensor for calpastatin was developed, optimized and applied for the analysis of meat extract samples. Anti-calpastatin antibody was immobilized on a gold electrode modified with a self-assembled monolayer of mercaptoundecanoic acid and Protein A from Staphylococcus aureus, and the obtained immunosensor was inserted as the working electrode in an electrochemical cell of a flow injection system. The dynamic range of the sensor was 20 to 160 ng/mL calpastatin. The electrode could be regenerated and re-used for more than 7 days with minimal reduction in sensitivity. For the analysis of real samples, the target analyte was extracted from the Longissimus dorsi muscle from beef carcasses directly after slaughtering. The extract was analyzed both with the developed immunosensor and microtiter plate ELISA, and a good correlation was obtained. However the immunosensor offers advantages of speed, simplicity, sensitivity and possibility for miniaturization over conventional assays for calpastatin quantification.     

An ITO Based Disposable Biosensor for Ultrasensitive Analysis of Retinol Binding Protein

A highly sensitive electrochemical biosensor based on anti‐RBP biorecognition capable to analyze concentrations of retinol binding protein (RBP) was developed. The construction of the biosensor interfaces was carefully characterized by techniques such as electrochemistry, EIS, and scanning electron microscopy. In order to characterize impedance data, Kramers‐Kronig Transform was performed on the experimental impedance data. Besides, for an immunosensor system the Single Frequency Impedance technique was firstly used for the characterization of the interaction between RBP and anti‐RBP. Finally, artificial serum samples spiked with RBP were analyzed by the proposed ITO based immunosensor to investigate the usefulness of the biosensor for early biomarker diagnosis.     

Convection, diffusion and reaction in a surface-based biosensor: modeling of cooperativity and binding site competition on the surface and in the hydrogel

We study theoretically the transport and kinetic processes underlying the operation of a biosensor (particularly the surface plasmon sensor "Biacore") used to study the surface binding kinetics of biomolecules in solution to immobilized receptors. Unlike previous studies, we concentrate mainly on the modeling of system-specific phenomena rather than on the influence of mass transport limitations on the intrinsic kinetic rate constants determined from binding data. In the first problem, the case of two-site binding where each receptor unit on the surface can accommodate two analyte molecules on two different sites is considered. One analyte molecule always binds first to a specific site. Subsequently, the second analyte molecule can bind to the adjacent unoccupied site. In the second problem, two different analytes compete for one binding site on the same surface receptor. Finally, the third problem considers the case of positive cooperativity among bound molecules in the hydrogel using a simple mean-field approach. The transport in both the flow channel and the hydrogel phases of the biosensor is taken into account in this case (with few exceptions, most previous studies assume a simpler model in which the hydrogel is treated as a planar surface with the receptors). We consider simultaneously diffusion and convection through the flow channel together with diffusion and cooperativity binding on the surface and in the hydrogel. In each case, typical results for the concentration contours of the free and bound molecules in the flow channel and hydrogel regions are presented together with the time-dependent association/dissociation curves and reaction rates. For binding site competition, the analysis predicts overshoot phenomena.     

Evaluation of electrodeposited gold nanostructures for applications in QCM sensing

The electrodeposition of gold nanostructures increases the surface area of a biosensor, which brings an enhancement of the sensitivity by increasing the amount of analyte binding to the surface. To evaluate the relationship among the surface structure, the area and the analyte binding, we quantitatively analyzed them for quartz crystal microbalance (QCM) sensing by scanning electron microscopy and cyclic voltammetry measurements. The results indicate a several-times increase of analyte bindings, and also the limitation of the sensing performance.     

On-line determination of 3,5,6-trichloro-2-pyridinol in human urine samples by surface plasmon resonance immunosensing

An immunochemical method for the analysis of 3,5,6-trichloro-2-pyridinol (TCP), a major urinary metabolite of chlorpyrifos, is developed using a surface plasmon resonance (SPR)-based biosensor. The stability of the assay was assessed by covalently linking the analyte derivative to a thin, gold-modified sensor surface. For optimization of analyte derivative immobilization, sensor chips were activated via alkanethiol monolayers with terminal amine or carboxyl groups. Binding inhibition tests were performed in untreated urine samples and compared to those obtained in distilled water and PBS was used as control. In all cases, similar detection limits, at the micrograms per litre level (0.1–0.24 μg L⁻¹), were attained for TCP assays independently of the dilution buffer. Reproducibility of measurements was studied throughout more than 130 regeneration cycles, which allowed the repeated use of the same immunosensor surface without significant variation of the SPR signal. All measurements were developed in real-time in only 10 min, using a SPR portable system. The device could be applied as a valuable analytical method to both environmental screening and clinic diagnostics.     

Application and analysis of structure-switching aptamers for small molecule quantification

Modern tools for the analysis of cellular function aim for the quantitative measurement of all members of a given class of biological molecules. Of the analyte classes, nucleic acid measurements are typically the most tractable, both on an individual analyte basis and in parallel. Thus, tools are being sought to enable measurement of other cellular molecules using nucleic acid biosensors. Of the variety of potential nucleic acid biosensor strategies, structure-switching aptamers (SSAs) present a unique opportunity to couple sensing and readout of the target molecule. However, little has been characterized about the parameters that determine the fidelity of the signal from SSA biosensors. In this study, a small molecule biosensor based on a SSA was engineered to detect the model small molecule, theophylline, in solution. Quantitative theophylline detection over nearly three orders-of-magnitude was achieved by scintillation counting and quantitative PCR. Further analysis showed that the biosensor fidelity is primarily controlled by the relative stability of the two conformations of the SSA.     

Ultrasonic quantification using smart hydrogel sensors

Analyte quantification in samples with extensive matrix effects can be challenging using conventional analytical techniques. Ultrasound has been shown to easily penetrate samples that can be difficult to measure optically or electrochemically, though it provides little chemical information. Recent ultrasound contrast agents provide highly localized contrast within a sample based on concentration. We have developed a general approach for creating smart biosensors based on molecularly imprinted hydrogel polymers that recognize and bind a target analyte, changing ultrasonic properties with analyte concentration. Multilinear analyte calibration in hydrogel solutions provided quantification of the chosen analyte, theophylline, from 8.4 μM to 6.1 mM with a high degree of linearity (correlation coefficient exceeding 0.99). Simultaneous quantification of both theophylline and of an interfering species, caffeine, was also carried out, providing an avenue for simultaneous analyte analysis with one smart biosensor that can be dispersed and remotely detected.     

Reflective interferometric fourier transform spectroscopy: a self-compensating label-free immunosensor using double-layers of porous SiO2

An interferometric biosensor comprised of two layers of porous Si, stacked one on top of the other, is described. A fast Fourier transform (FFT) of the reflectivity spectrum reveals three peaks that correspond to the optical thickness of the top layer, the bottom layer, and both layers together. Binding of immunoglobulin G to a protein A capture probe adsorbed to the surface of the top layer induces changes in reflectivity at the top layer/solution interface. The FFT method allows discrimination of target analyte binding from matrix effects due to nonspecific changes in the analyte solution. The sensor response is shown to be insensitive to the addition of 4000-fold excess sucrose or 80-fold excess bovine serum albumin interferents.     

Investigation of SPR and electrochemical detection of antigen with polypyrrole functionalized by biotinylated single-chain antibody: A review

An electrochemical label-free immunosensor based on a biotinylated single-chain variable fragment (Sc-Fv) antibody immobilized on copolypyrrole film is described. An efficient immunosensor device formed by immobilization of a biotinylated single-chain antibody on an electropolymerized copolymer film of polypyrrole using biotin/streptavidin system has been demonstrated for the first time. The response of the biosensor toward antigen detection was monitored by surface plasmon resonance (SPR) and electrochemical analysis of the polypyrrole response by differential pulse voltammetry (DPV). The composition of the copolymer formed from a mixture of pyrrole (py) as spacer and a pyrrole bearing a N-hydroxyphthalimidyl ester group on its 3-position (pyNHP), acting as agent linker for biomolecule immobilization, was optimized for an efficient immunosensor device. The ratio of py:pyNHP for copolymer formation was studied with respect to the antibody immobilization and antigen detection. SPR was employed to monitor in real time the electropolymerization process as well as the step-by-step construction of the biosensor. FT-IR demonstrates the chemical copolymer composition and the efficiency of the covalent attachment of biomolecules. The film morphology was analyzed by electron scanning microscopy (SEM).Results show that a well organized layer is obtained after Sc-Fv antibody immobilization thanks to the copolymer composition defined with optimized pyrrole and functionalized pyrrole leading to high and intense redox signal of the polypyrrole layer obtained by the DPV method. Detection of specific antigen was demonstrated by both SPR and DPV, and a low concentration of 1 pg mL⁻¹ was detected by measuring the variation of the redox signal of polypyrrole.     

纳米结构聚吡咯构建的生物传感器

本文总结了纳米结构聚吡咯对生物分子的固定方法如吸附法、电化学聚合包埋法、共价键偶联法以及分子印迹法,重点评述了基于纳米结构聚吡咯的电流型生物传感器,如酶、核酸、免疫传感器等的工作原理和探测性能.指出聚吡咯纳米敏感材料优良的选择透过性和高比表面积有利于生物分子的固定,提高了生物传感器的敏感度;聚吡咯良好的生物相容性和抗干扰性,可以很好地保持生物分子的活性,提高生物传感器的选择性和环境稳定性;聚吡咯与其它敏感材料如碳纳米管或金属纳米粒子复合,两者的协同效应使电极的电化学信号放大、电催化活性可提高2～4个数量级.检出限最高可提升5万倍;聚吡咯纳米生物传感器在生物医学工程、临床诊断、环境监测、食品卫生和科学等领域展现出广阔的应用前景.