An enzyme-based reversible CNOT logic gate realized in a flow system (ESI) (original) (raw)

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An enzyme-based reversible CNOT logic gate realized in a flow system

The Analyst, 2014

An enzyme system organized in a flow device was used to mimic a reversible Controlled NOT (CNOT) gate with two input and two output signals. Reversible conversion of NAD + and NADH cofactors was used to perform a XOR logic operation, while biocatalytic hydrolysis of p-nitrophenyl phosphate resulted in an Identity operation working in parallel. The first biomolecular realization of a CNOT gate is promising for integration into complex biomolecular networks and future biosensor/biomedical applications.

Two-Input Enzymatic Logic Gates Made Sigmoid by Modifications of the Biocatalytic Reaction Cascade

Computing based on biochemical processes is a newest rapidly developing field of unconventional information and signal processing. In this paper we present results of our research in the field of biochemical computing and summarize the obtained numerical and experimental data for implementations of the standard two-input OR and AND gates with double-sigmoid shape of the output signal. This form of response was obtained as a function of the two inputs in each of the realized biochemical systems. The enzymatic gate processes in the first system were activated with two chemical inputs and resulted in optically detected chromogen oxidation, which happens when either one or both of the inputs are present. In this case, the biochemical system is functioning as the OR gate. We demonstrate that the addition of a "filtering" biocatalytic process leads to a considerable reduction of the noise transmission factor and the resulting gate response has sigmoid shape in both inputs. The second system was developed for functioning as an AND gate, where the output signal was activated only by a simultaneous action of two enzymatic biomarkers. This response can be used as an indicator of liver damage, but only if both of these of the inputs are present at their elevated, pathophysiological values of concentrations. A kinetic numerical model was developed and used to estimate the range of parameters for which the experimentally realized logic gate is close to optimal. We also analyzed the system to evaluate its noise-handling properties. 348 vladimir privman et al.

Concatenated logic gates using four coupled biocatalysts operating in series

Proceedings of the National Academy of Sciences, 2006

The assembly of three concatenated enzyme-based logic gates consisting of OR, AND, XOR is described. Four biocatalysts, acetylcholine esterase, choline oxidase, microperoxidase-11, and the NAD ؉ -dependent glucose dehydrogenase, are used to assemble the gates. Four inputs that include acetylcholine, butyrylcholine, O2, and glucose are used to drive the concatenated-gates system. The cofactor NAD ؉ , and its reduced 1,4-dihydro form, NADH, are used as a reporter couple, and these provide an optical output for the gates. The modulus of the absorbance changes of NADH is used as a readout signal.

Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Signal Change

The Journal of Physical Chemistry B, 2010

We consider a realization of the XOR logic gate in a process biocatalyzed by an enzyme which can be inhibited by a substrate when the latter is inputted at large enough concentrations. A model is developed for describing such systems in an approach suitable for evaluation of the analog noise amplification properties of the gate. The obtained data are fitted for gate quality evaluation within the developed model, and we discuss aspects of devising XOR gates for functioning in "biocomputing" systems utilizing biomolecules for information processing.

Two-Input Enzymatic Logic Gates Made Sigmoid by Modifications of the Biocatalytic Reaction Cascades

2013

Computing based on biochemical processes is a newest rapidly developing field of unconventional information and signal processing. In this paper we present results of our research in the field of biochemical computing and summarize the obtained numerical and experimental data for implementations of the standard two-input OR and AND gates with double-sigmoid shape of the output signal. This form of response was obtained as a function of the two inputs in each of the realized biochemical systems. The enzymatic gate processes in the first system were activated with two chemical inputs and resulted in optically detected chromogen oxidation, which happens when either one or both of the inputs are present. In this case, the biochemical system is functioning as the OR gate. We demonstrate that the addition of a "filtering" biocatalytic process leads to a considerable reduction of the noise transmission factor and the resulting gate response has sigmoid shape in both inputs. The second system was developed for functioning as an AND gate, where the output signal was activated only by a simultaneous action of two enzymatic biomarkers. This response can be used as an indicator of liver damage, but only if both of these of the inputs are present at their elevated, pathophysiological values of concentrations. A kinetic numerical model was developed and used to estimate the range of parameters for which the experimentally realized logic gate is close to optimal. We also analyzed the system to evaluate its noise-handling properties.

Integration of biomolecular logic gates with field-effect transducers

Electrochimica Acta, 2011

The integration of biomolecular logic gates with field-effect devices -the basic element of conventional electronic logic gates and computing -is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO 2 -Ta 2 O 5 structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta 2 O 5 ) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

Catalyst-Based Biomolecular Logic Gates

Catalysts

Regulatory processes in biology can be re-conceptualized in terms of logic gates, analogous to those in computer science. Frequently, biological systems need to respond to multiple, sometimes conflicting, inputs to provide the correct output. The language of logic gates can then be used to model complex signal transduction and metabolic processes. Advances in synthetic biology in turn can be used to construct new logic gates, which find a variety of biotechnology applications including in the production of high value chemicals, biosensing, and drug delivery. In this review, we focus on advances in the construction of logic gates that take advantage of biological catalysts, including both protein-based and nucleic acid-based enzymes. These catalyst-based biomolecular logic gates can read a variety of molecular inputs and provide chemical, optical, and electrical outputs, allowing them to interface with other types of biomolecular logic gates or even extend to inorganic systems. Conti...

Switchable electrode controlled by Boolean logic gates using enzymes as input signals

Bioelectrochemistry, 2009

Application of Boolean logic operations performed by enzymes to control electrochemical systems is presented. Indium-tin oxide (ITO) electrodes with the surface modified with poly-4-vinyl pyridine (P4VP) brush were synthesized and used as switchable electrochemical systems. The switch ON and OFF of the electrode activity were achieved by pH changes generated in situ by biocatalytic reactions in the presence of enzymes used as input signals. Two logic gates operating as AND/OR Boolean functions were designed using invertase and glucose oxidase or esterase and glucose oxidase as input signals, respectively. The electrode surface coated with a shrunk P4VP polymer at neutral pH values was not electrochemically active because of the blocking effect of the polymer film. The positive outputs of the logic operations yielded a pH drop to acidic conditions, resulting in the protonation and swelling of the P4VP polymer allowing penetration of a soluble redox probe to the conducting support, thus switching the electrode activity ON. The electrode interface was reset to the initial OFF state, with the inhibited electrochemical reaction, upon in situ pH increase generated by another enzymatic reaction in the presence of urease. Logically processed biochemical inputs of various enzymes allowed reversible activationinactivation of the electrochemical reaction.