Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Enzyme Inhibition by a Substrate

Experimental Realization of a High-Quality Biochemical XOR Gate

We report an experimental realization of a biochemical XOR gate function that avoids many of the pitfalls of earlier realizations based on biocatalytic cascades. Inputs-represented by pairs of chemicals-cross-react to largely cancel out when both are nearly equal. The cross-reaction can be designed to also optimize gate functioning for noise handling. When not equal, the residual inputs are further processed to result in the output of the XOR type, by biocatalytic steps that allow for further gate-function optimization. The quality of the realized XOR gate is theoretically analyzed.

Enzyme-based logic gates and circuits-analytical applications and interfacing with electronics

The paper is an overview of enzyme-based logic gates and their short circuits, with specific examples of Boolean AND and OR gates, and concatenated logic gates composed of multi-step enzyme-biocatalyzed reactions. Noise formation in the biocatalytic reactions and its decrease by adding a "filter" system, converting convex to sigmoid response function, are discussed. Despite the fact that the enzyme-based logic gates are primarily considered as components of future biomolecular computing systems, their biosensing applications are promising for immediate practical use. Analytical use of the enzyme logic systems in biomedical and forensic applications is discussed and exemplified with the logic analysis of biomarkers of various injuries, e.g., liver injury, and with analysis of biomarkers characteristic of different ethnicity found in blood samples on a crime scene. Interfacing of enzyme logic systems with modified electrodes and semiconductor devices is discussed, giving particular attention to the interfaces functionalized with signal-responsive materials. Future perspectives in the design of the biomolecular logic systems and their applications are discussed in the conclusion. Graphical Abstract Various applications and signal-transduction methods are reviewed for enzyme-based logic systems.

Enzyme-based logic gates switchable between OR, NXOR and NAND Boolean operations realized in a flow system

The enzyme-based system performing a biocatalytic cascade reaction was realized in a flow device and was used to mimic Boolean logic operations. Chemical inputs applied to the system resulted in the activation of additional reaction steps, allowing the reversible switch of the logic operations between OR, NXOR and NAND gates for processing of two other biomolecular inputs.

Bridging the Two Worlds: A Universal Interface between Enzymatic and DNA Computing Systems

Molecular computing based on enzymes or nucleic acids has attracted a great deal of attention due to the perspectives of controlling living systems in the way we control electronic computers. Enzyme-based computational systems can respond to a great variety of small molecule inputs. They have the advantage of signal amplification and highly specific recognition. DNA computing systems are most often controlled by oligonucleotide inputs/outputs and are capable of sophisticated computing as well as controlling gene expressions. Here, we developed an interface that enables communication of otherwise incompatible nucleic-acid and enzyme-computational systems. The enzymatic system processes small molecules as inputs and produces NADH as an output. The NADH output triggers electrochemical release of an oligonucleotide, which is accepted by a DNA computational system as an input. This interface is universal because the enzymatic and DNA computing systems are independent of each other in composition and complexity.

Retropath: automated pipeline for embedded metabolic circuits

Metabolic circuits are a promising alternative to other conventional genetic circuits as modular parts implementing functionalities required for synthetic biology applications. To date, metabolic design has been mainly focused on production circuits. Emergent applications such as smart therapeutics, however, require circuits that enable sensing and regulation. Here, we present RetroPath, an automated pipeline for embedded metabolic circuits that explores the circuit design space from a given set of specifications and selects the best circuits to implement based on desired constraints. Synthetic biology circuits embedded in a chassis organism that are capable of controlling the production, processing, sensing, and the release of specific molecules were enumerated in the metabolic space through a standard procedure. In that way, design and implementation of applications such as therapeutic circuits that autonomously diagnose and treat disease, are enabled, and their optimization is streamlined.

Majority and minority gates realized in enzyme-biocatalyzed systems integrated with logic networks and interfaced with bioelectronic systems

Biocatalytic reactions operating in parallel and resulting in reduction of NAD(+) or oxidation of NADH were used to mimic 3-input majority and minority logic gates, respectively. The substrates corresponding to the enzyme reactions were used as the input signals. When the input signals were applied at their high concentrations, defined as logic 1 input values, the corresponding biocatalytic reactions were activated, resulting in changes of the NADH concentration defined as the output signal. The NADH concentration changes were dependent on the number of parallel reactions activated by the input signals. The absence of the substrates, meaning their logic 0 input values, kept the reactions mute with no changes in the NADH concentration. In the system mimicking the majority function, the enzyme-biocatalyzed reactions resulted in a higher production of NADH when more than one input signal was applied at the logic 1 value. Another system mimicking the minority function consumed more NADH, thus leaving a smaller residual output signal, when more than one input signal was applied at the logic 1 value. The performance of the majority gate was improved by processing the output signal through a filter system in which another biocatalytic reaction consumed a fraction of the output signal, thus reducing its physical value to zero when the logic 0 value was obtained. The majority gate was integrated with a preceding AND logic gate to illustrate the possibility of complex networks. The output signal, NADH, was also used to activate a process mimicking drug release, thus illustrating the use of the majority gate in decision-making biomedical systems. The 3-input majority gate was also used as a switchable AND/OR gate when one of the input signals was reserved as a command signal, switching the logic operation for processing of the other two inputs. Overall, the designed majority and minority logic gates demonstrate novel functions of biomolecular information processing systems.

Design of synthetic biological logic circuits based on evolutionary algorithm

The construction of an artificial biological logic circuit using systematic strategy is recognised as one of the most important topics for the development of synthetic biology. In this study, a real-structured genetic algorithm (RSGA), which combines general advantages of the traditional real genetic algorithm with those of the structured genetic algorithm, is proposed to deal with the biological logic circuit design problem. A general model with the cis-regulatory input function and appropriate promoter activity functions is proposed to synthesise a wide variety of fundamental logic gates such as NOT, Buffer, AND, OR, NAND, NOR and XOR. The results obtained can be extended to synthesise advanced combinational and sequential logic circuits by topologically distinct connections. The resulting optimal design of these logic gates and circuits are established via the RSGA. The in silico computer-based modelling technology has been verified showing its great advantages in the purpose.

Logical regulation of the enzyme-like activity of gold nanoparticles by using heavy metal ions

In this study we employed self-deposition and competitive or synergistic interactions between metal ions and gold nanoparticles (Au NPs) to develop OR, AND, INHIBIT, and XOR logic gates through regulation of the enzyme-like activity of Au NPs. In the presence of various metal ions (Ag(+), Bi(3+), Pb(2+), Pt(4+), and Hg(2+)), we found that Au NPs (13 nm) exhibited peroxidase-, oxidase-, or catalase-like activity. After Ag(+), Bi(3+), or Pb(2+) ions had been deposited on the Au NPs, the particles displayed strong peroxidase-like activity; on the other hand, they exhibited strong oxidase- and catalase-like activities after reactions with Ag(+)/Hg(2+) and Hg(2+)/Bi(3+) ions, respectively. The catalytic activities of these Au NPs arose mainly from the various oxidation states of the surface metal atoms/ions. Taking advantage of this behavior, we constructed multiplex logic operations-OR, AND, INHIBIT, and XOR logic gates-through regulation of the enzyme-like activity after the introduction of metal ions into the Au NP solution. When we deposited Hg(2+) and/or Bi(3+) ions onto the Au NPs, the catalase-like activities of the Au NPs were strongly enhanced (>100-fold). Therefore, we could construct an OR logic gate by using Hg(2+)/Bi(3+) as inputs and the catalase-like activity of the Au NPs as the output. Likewise, we constructed an AND logic gate by using Pt(4+) and Hg(2+) as inputs and the oxidase-like activity of the Au NPs as the output; the co-deposition of Pt and Hg atoms/ions on the Au NPs was responsible for this oxidase-like activity. Competition between Pb(2+) and Hg(2+) ions for the Au NPs allowed us to develop an INHIBIT logic gate-using Pb(2+) and Hg(2+) as inputs and the peroxidase-like activity of the Au NPs as the output. Finally, regulation of the peroxidase-like activity of the Au NPs through the two inputs Ag(+) and Bi(3+) enabled us to construct an XOR logic gate.