Networked Enzymatic Logic Gates with Filtering: New Theoretical Modeling Expressions and Their Experimental Application

We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic cascade. New theoretical expressions are derived to allow simple, few-parameter modeling of network components concatenated in such cascades, both with and without filtering. The derived expressions are tested against experimental data obtained for the realized networks responses, measured optically, to variations of its input chemicals concentrations with and without filtering processes. We also describe how the present modeling approach captures and explains several observations and features identified in earlier studies of enzymatic processes when they were considered as potential network components for multi-step information/signal processing systems.

Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid Filter Response

We report the first realization of a biomolecular AND gate function with double-sigmoid response (sigmoid in both inputs). Two enzyme biomarker inputs activate the gate output signal which can then be used as indicating liver injury, but only when both of these inputs have elevated pathophysiological concentrations, effectively corresponding to logic-1 of the binary gate functioning. At lower, normal physiological concentrations, defined as logic-0 inputs, the liver-injury output levels are not obtained. High-quality gate functioning in handling of various sources of noise, on time scales of relevance to potential applications is enabled by utilizing filtering effected by a simple added biocatalytic process. The resulting gate response is sigmoid in both inputs when proper system parameters are chosen, and the gate properties are theoretically analyzed within a model devised to evaluate its noise-handling properties.

Biomolecular Filters for Improved Separation of Output Signals in Enzyme Logic Systems Applied to Biomedical Analysis

Biomolecular logic systems processing biochemical input signals and producing digital outputs in the form of YES/NO were developed for analysis of physiological conditions characteristic of liver injury, soft tissue injury and abdominal trauma. Injury biomarkers were used as input signals for activating the logic systems. Their normal physiological concentrations were defined as logic-0 level, while their pathologically elevated concentrations were defined as logic-1 values. Since the input concentrations applied as logic 0 and 1 values were not sufficiently different, the output signals being at low and high values (0, 1 outputs) were separated with a short gap making their discrimination difficult. Coupled enzymatic reactions functioning as a biomolecular signal processing system with a built-in filter property were developed. The filter process involves a partial back-conversion of the optical-output-signal-yielding product, but only at its low concentrations, thus allowing the proper discrimination between 0 and 1 output values.