Single- and Dual-Fractal Analysis of Hybridization Binding Kinetics: Biosensor Applications

Abstract

The diffusion-limited hybridization kinetics of analyte in solution to a receptor immobilized on a biosensor or immunosensor surface is analyzed within a fractal framework. The data may be analyzed by a single- or a dual-fractal analysis. This was indicated by the regression analysis provided by Sigmaplot. It is of interest to note that the binding rate coefficient and the fractal dimension both exhibit changes in the same direction for both the single-fractal and the dual-fractal analysis examples presented. For example, for a single-fractal analysis and for the hybridization of 10 nM 16CFl (oligonucleotide) to 16B immobilized via sulfosuccinimidyl-6-(biotinamido)hexanoate and streptavidin using chemical and thermal regeneration (Abel, A. P.; Weller, M. G.; Duveneck, G. L.; Ehrat, M. Widmer, H. M. Anal. Chem. 1996, 68, 2905-2912), an increase in the fractal dimension, Df from 1.211 (chemical regeneration) to 1.394 (thermal regeneration), leads to an increase in the binding rate coefficient, k, from 86.53 (chemical regeneration) to 100.0 (thermal regeneration). An increase in the degree of heterogeneity on the biosensor surface leads to an increase in the binding rate coefficient. When a dual-fractal analysis was utilized, an increase in the fractal dimension value from Df1 to Df2 leads to an increase in the binding rate coefficient value from k1 to k2. The fractional order of dependence of the binding rate coefficient, k1, on (a) the analyte (rRNA) concentration in solution and (b) on the fractal dimension, Df1, for the hybridization kinetics to detect Listeria species (Fliss, R.; St-Laurent, M.; Emond, E.; Simard, R. E.; Lemieux, R.; Ettriki, A.; Pandian, S. Appl. Microbiol. Biotechnol. 1995, 43, 717-724.) further reinforces the fractal nature of the system. The binding rate coefficient(s) expressions developed as a function of the analyte concentration in solution and the fractal dimension are of particular value since they provide a means to better control of biosensor or immunosensor performance.

A Fractal Analysis Approach for the Evaluation of Hybridization Kinetics in Biosensors

“…More data need to be analyzed to see if this holds for other hybridization reactions when they are utilized for diagnostic purposes. This has been observed previously for antibody-antigen and analyte-receptor binding reactions observed in biosensor reactions (42) and also in hybridization reactions occurring on biosensor surfaces (24). The present results further confirm the importance of the nature of the surface and its quantitative characterization to help understand and hopefully modulate the hybridization reactions occurring on biosensor and other surfaces.…”

“…The present analysis along with a previous analysis (24) are initial studies where the binding rate coefficient is directly related to the degree of heterogeneity that exists on the surface for hybridization reactions. A proper study and one which would be of more value would be to collect data for a single chemistry of immobilization and detection and analyze this in terms of density and orientation at the surface.…”

“…In an initial analysis for hybridization binding kinetics Sadana and Vo-Dinh (24) recently showed that a single-fractal analysis is sufficient to adequately describe the hybridization of 10 nM 16 * CFl (oligonucleotide) to 16 * B immobilized to a biosensor surface via sulfosuccinimidyl-6-(biotinamido)-hexaonoate and streptavidin using chemical and thermal regeneration (25). Besides, for this system an increase in the fractal dimension, D f , leads to an increase in the binding rate coefficient, k. An example where a dual-fractal analysis is utilized is also given (24).…”

“…Besides, for this system an increase in the fractal dimension, D f , leads to an increase in the binding rate coefficient, k. An example where a dual-fractal analysis is utilized is also given (24). In this paper we extend the fractal analysis to the hybridization of more systems and further analyze the influence of the fractal dimension on the binding rate coefficient.…”

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

“…Recently, fractal analysis has been extended to include analyte-receptor and analyte-receptorless (protein) systems. These ideas have also been very recently extended to the single-strand (ss) RNA-ssDNA or ssDNA-ssDNA binding observed in hybridization kinetics (26). For example, only when the nucleotides on the single-strand ribonucleic acid (RNA) are complementary to their counterparts on the single-strand deoxyribonucleic acid (DNA) does the binding takes place.…”