Bioelectronic Interface Connecting Reversible Logic Gates Based on Enzyme and DNA Reactions

Abstract

It is believed that connecting biomolecular computation elements in complex networks of communicating molecules may eventually lead to a biocomputer that can be used for diagnostics and/or the cure of physiological and genetic disorders. Here, a bioelectronic interface based on biomolecule-modified electrodes has been designed to bridge reversible enzymatic logic gates with reversible DNA-based logic gates. The enzyme-based Fredkin gate with three input and three output signals was connected to the DNA-based Feynman gate with two input and two output signals-both representing logically reversible computing elements. In the reversible Fredkin gate, the routing of two data signals between two output channels was controlled by the control signal (third channel). The two data output signals generated by the Fredkin gate were directed toward two electrochemical flow cells, responding to the output signals by releasing DNA molecules that serve as the input signals for the next Feynman logic gate based on the DNA reacting cascade, producing, in turn, two final output signals. The Feynman gate operated as the controlled NOT gate (CNOT), where one of the input channels controlled a NOT operation on another channel. Both logic gates represented a highly sophisticated combination of input-controlled signal-routing logic operations, resulting in redirecting chemical signals in different channels and performing orchestrated computing processes. The biomolecular reaction cascade responsible for the signal processing was realized by moving the solution from one reacting cell to another, including the reacting flow cells and electrochemical flow cells, which were organized in a specific network mimicking electronic computing circuitries. The designed system represents the first example of high complexity biocomputing processes integrating enzyme and DNA reactions and performing logically reversible signal processing.

Enzyme‐Based Logic Gates and Networks with Output Signals Analyzed by Various Methods

“…The electroanalytical methods used in such applications could be similar to those used in electrochemical biosensors. Various electroanalytical methods, including chronoamperometry and potentiometry, can be employed for detecting the output signals. The potentiometry methods can be extended to the use of ion‐selective and pH‐sensing electrodes, thus extending the output signal measurements to the analysis of various species that are not necessary redox active.…”

“…Figure C shows the potential produced on the PQQ‐modified sensing electrode at different combinations of the variable logic inputs (16 variants), for which only one input combination ( 1 , 1 , 1 , 1 ) resulted in the high negative potential corresponding to the NADH production in the biocatalytic cascade, as expected for the system mimicking three concatenated AND gates. Similar potentiometric measurements have been used for transduction of NADH formation to the electronic output in other logic systems of high complexity …”

An Enzyme‐based 1:2 Demultiplexer Interfaced with an Electrochemical Actuator

“…The important feature of the designed demultiplexer is production of NADH as the output signals in the Output1 or Output2 channels. As it has been already shown, the biocatalytically produced NADH is able to generate a negative potential on an electrode, while being electrocatalytically oxidized by pyrroloquinoline quinone (PQQ) immobilized on an electrode surface. PQQ is a well‐known electrocatalyst for the NADH oxidation, particularly when it is used in biofuel cells .…”

“…PQQ is a well‐known electrocatalyst for the NADH oxidation, particularly when it is used in biofuel cells . It should be noted that the NADH oxidation electrocatalyzed by PQQ proceeds without the application of an external potential and the process proceeds spontaneously resulting in the formation of a negative potential of ca.‐60 mV (vs. Ag/AgCl reference; the same reference was used in all other electrochemical experiments) on the electrode . This negative potential was used in our previous studies to dissolve electrochemically an Fe 3+ ‐crosslinked alginate gel thin film on a connected electrode, resulting in the release of biomolecules entrapped in the alginate gel .…”

“…Upon further investigation, an increase in the system's complexity is easily possible. Indeed, the input signals, Glc and ATP, can be biochemically produced through various logic gates and circuits, while the released DNA can be included in different logic operations based on various DNA or DNAzymes systems . Importantly, the modular design of the flow system should not be overlooked as it allows an easy method for the connections to the input and output channels, their extensions and variations.…”