Boolean Logic Gates that Use Enzymes as Input Signals

Network analysis of biochemical logic for noise reduction and stability: a system of three coupled enzymatic and gates

We develop an approach aimed at optimizing the parameters of a network of biochemical logic gates for reduction of the "analog" noise buildup. Experiments for three coupled enzymatic AND gates are reported, illustrating our procedure. Specifically, starch, one of the controlled network inputs, is converted to maltose by beta-amylase. With the use of phosphate (another controlled input), maltose phosphorylase then produces glucose. Finally, nicotinamide adenine dinucleotide (NAD(+)), the third controlled input, is reduced under the action of glucose dehydrogenase to yield the optically detected signal. Network functioning is analyzed by varying selective inputs and fitting standardized few-parameters "response-surface" functions assumed for each gate. This allows a certain probe of the individual gate quality, but primarily yields information on the relative contribution of the gates to noise amplification. The derived information is then used to modify our experimental system to put it in a regime of a less noisy operation.

Dual magnetobiochemical logic control of electrochemical processes based on local interfacial pH changes

An electrode surface modified with a pH-sensitive polymeric brush was reversibly activated by local pH changes produced in situ by glucose oxidase associated with magnetic nanoparticles confined at the surface in the presence of an external magnet. The system mimics Boolean AND logic gate, with the magnetic and chemical input signals stimulating the electrochemical reactions at the switchable interface. Biomedical applications of the "smart" interface controlled by enzymatic reactions through local pH changes are anticipated in various implantable biomedical devices.

Stimuli-responsive hydrogel membranes coupled with biocatalytic processes

A nanostructured signal-responsive thin hydrogel membrane was coupled with enzyme-based systems to yield "smart" multisignal-responsive hybrid systems with built-in "logic". The enzyme systems transduce biochemical input signals into structural changes of the membrane, thus resulting in the amplification of the biochemical signals and their transformation into the gated transport of molecules through the membrane. Coupling of the biocatalytic systems with a stimuli-responsive membrane is a promising approach for the development of materials that can regulate transport and release of chemicals/drugs by receiving and processing the biochemical information via biochemical reactions.

Enzyme-based logic systems and their applications for novel multi-signal-responsive materials

Recent advances in biochemical logic systems and their integration with signal-responsive materials to yield "smart" hybrid systems are briefly outlined in the paper.

Bioelectrocatalytic system coupled with enzyme-based biocomputing ensembles performing boolean logic operations: approaching "smart" physiologically controlled biointerfaces

The modified electrode for electrocatalytic oxidation of NADH was developed using a pH-switchable redox interface. The operation of the modified electrode was controlled by logic operations performed by enzyme systems processing biochemical input signals. The electrocatalytic oxidation of NADH was activated upon appropriate combinations of the signals processed by the AND/OR logic operations performed by the enzymes. The modified interface was reset in a mute nonactive state by another enzyme reaction. The coupling between the enzyme logic systems and the bioelectrocatalytic interface was achieved by pH changes produced in situ by the enzyme reactions, resulting in different protonation states of the polymeric matrix associated with the electrode surface. The bioelectrocatalytic system integrated with biochemical computing systems opens the way to novel "smart" interfaces for multisignal biosensors and signal-controlled biofuel cells. In a long perspective, this approach will allow physiological control of implantable bioelectronic devices.

Optoelectronic properties of nanostructured ensembles controlled by biomolecular logic systems

A nanostructured system composed of enzyme-functionalized silica microparticles, ca. 74 microm, and gold-coated magnetic nanoparticles, 18 +/- 3 nm, modified with pH-sensitive organic shells was used to process biochemical signals and transduce the output signal into the changes of the optoelectronic properties of the assembly. The enzymes (glucose oxidase, invertase, esterase) covalently bound to the silica microparticles performed Boolean logic operations AND/OR processing biochemical information received in the form of chemical input signals resulting in changes of the solution pH value. Dissociation state of the organic shells on the gold-coated magnetic nanoparticles was controlled by pH changes generated in situ by the enzyme logic systems. The charge variation on the organic shells upon the reversible protonation/dissociation process resulted in the changes of the gold layer localized surface plasmon resonance energy (LSPR), thus producing optical changes in the system. The proton transfer process allowed the functional coupling of the information processing enzyme systems with the signal transducing gold-coated magnetic nanoparticles providing their cooperative performance. Magnetic properties of the gold-coated magnetic nanoparticles allowed separation of the signal-transducing nanoparticles from the enzyme-modified signal processing silica microparticles. The reversible system operation was achieved by the Reset function, returning the pH value and optical properties of the system to the initial state. This process was biocatalyzed by another immobilized enzyme (urease) activated with a biochemical signal. The studied approach opens the way to novel optical biosensors logically processing multiple biochemical signals and "smart" multisignal responsive materials with logically switchable optical properties.

"Chemical transformers" from nanoparticle ensembles operated with logic

The pH-responsive nanoparticles were coupled with information-processing enzyme-based systems to yield "smart" signal-responsive hybrid systems with built-in Boolean logic. The enzyme systems performed AND/OR logic operations, transducing biochemical input signals into reversible structural changes (signal-directed self-assembly) of the nanoparticle assemblies, thus resulting in the processing and amplification of the biochemical signals. The hybrid system mimics biological systems in effective processing of complex biochemical information, resulting in reversible changes of the self-assembled structures of the nanoparticles. The bioinspired approach to the nanostructured morphing materials could be used in future self-assembled molecular robotic systems.