Computing Arithmetic Functions Using Immobilised Enzymatic Reaction Networks

Living systems use enzymatic reaction networks to process biochemical information and make decisions in response to external or internal stimuli. Herein, we present a modular and reusable platform for molecular information processing using enzymes immobilised in hydrogel beads and compartmentalised in a continuous stirred tank reactor. We demonstrate how this setup allows us to perform simple arithmetic operations, such as addition, subtraction and multiplication, using various concentrations of substrates or inhibitors as inputs and the production of a fluorescent molecule as the readout.

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.

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

An enzyme-based 1:2 demultiplexer is designed in a flow system composed of three cells where each one is modified with a different enzyme: hexokinase, glucose dehydrogenase and glucose-6-phosphate dehydrogenase. The Input signal activating the biocatalytic cascade is represented by glucose, while the Address signal represented by ATP is responsible for directing the Input signal to one of the output channels, depending on the logic value of the Address. The biomolecular 1:2 demultiplexer is extended to include two electrochemical actuators releasing entrapped DNA molecules in the active output channel. The modular design of the system allows for easy exchange and extension of the functional elements. The present demultiplexer can be easily integrated in various biomolecular logic systems, including different logic gates based on the enzyme- or DNA-based reactions, as well as containing different chemical actuators, for example, with a biomolecular release function.

An unusual highly emissive water-soluble iridium lissamine-alanine complex and its use in a molecular logic gate

The interaction of iridium(iii) with a new lissamine rhodamine B sulfonyl derivative, bearing alanine as a building block, (1) with an orange emission in water results in a green highly emissive Ir@1 complex at room temperature. The new Ir@1 complex can sense the toxic Hg(2+) metal ion and cysteine. Based on such properties, a new sophisticated molecular logic gate with three inputs was designed.

An Enzyme-Based Half-Adder and Half-Subtractor with a Modular Design

A half-adder and a half-subtractor have been realized using enzymatic reaction cascades performed in a flow cell device. The individual cells were modified with different enzymes and assembled in complex networks to perform logic operations and arithmetic functions. The modular design of the logic devices allowed for easy re-configuration, enabling them to perform various functions. The final output signals, represented by redox species [Fe(CN)6 ](3-/4-) or NADH/NAD(+) , were analyzed optically to derive the calculation results. These output signals might be applicable in the future for actuation processes, for example, substance release activated by logically processed signals.

Biophotonic logic devices based on quantum dots and temporally-staggered Förster energy transfer relays

Integrating photonic inputs/outputs into unimolecular logic devices can provide significantly increased functional complexity and the ability to expand the repertoire of available operations. Here, we build upon a system previously utilized for biosensing to assemble and prototype several increasingly sophisticated biophotonic logic devices that function based upon multistep Förster resonance energy transfer (FRET) relays. The core system combines a central semiconductor quantum dot (QD) nanoplatform with a long-lifetime Tb complex FRET donor and a near-IR organic fluorophore acceptor; the latter acts as two unique inputs for the QD-based device. The Tb complex allows for a form of temporal memory by providing unique access to a time-delayed modality as an alternate output which significantly increases the inherent computing options. Altering the device by controlling the configuration parameters with biologically based self-assembly provides input control while monitoring changes in emission output of all participants, in both a spectral and temporal-dependent manner, gives rise to two input, single output Boolean Logic operations including OR, AND, INHIBIT, XOR, NOR, NAND, along with the possibility of gate transitions. Incorporation of an enzymatic cleavage step provides for a set-reset function that can be implemented repeatedly with the same building blocks and is demonstrated with single input, single output YES and NOT gates. Potential applications for these devices are discussed in the context of their constituent parts and the richness of available signal.

Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors

Right out of the (logic) gate: Logic gates made from 3D DNA nanotetrahedra were constructed that are responsive to various ions, small molecules, and short strands of DNA. By including dynamic sequences in one or more edges of the tetrahedra, a FRET signal can be generated in the manner of AND, OR, XOR, and INH logic gates, as well as a half-adder circuit. These DNA logic gates were also applied to intracellular detection of ATP.

Encoded multichromophore response for simultaneous label-free detection

The self-assembly of molecularly precise nanostructures is widely expected to form the basis of future high-speed integrated circuits, but the technologies suitable for such circuits are not well understood. In this work, DNA self-assembly is used to create molecular logic circuits that can selectively identify specific biomolecules in solution by encoding the optical response of near-field coupled arrangements of chromophores. The resulting circuits can detect label-free, femtomole quantities of multiple proteins, DNA oligomers, and small fragments of RNA in solution via ensemble optical measurements. This method, which is capable of creating multiple logic-gate-sensor pairs on a 2 x 80 x 80-nm DNA grid, is a step toward more sophisticated nanoscale logic circuits capable of interfacing computers with biological processes.

All-optical integrated logic operations based on chemical communication between molecular switches

Molecular logic gates process physical or chemical "inputs" to generate "outputs" based on a set of logical operators. We report the design and operation of a chemical ensemble in solution that behaves as integrated AND, OR, and XNOR gates with optical input and output signals. The ensemble is composed of a reversible merocyanine-type photoacid and a ruthenium polypyridine complex that functions as a pH-controlled three-state luminescent switch. The light-triggered release of protons from the photoacid is used to control the state of the transition-metal complex. Therefore, the two molecular switching devices communicate with one another through the exchange of ionic signals. By means of such a double (optical-chemical-optical) signal-transduction mechanism, inputs of violet light modulate a luminescence output in the red/far-red region of the visible spectrum. Nondestructive reading is guaranteed because the green light used for excitation in the photoluminescence experiments does not affect the state of the gate. The reset is thermally driven and, thus, does not involve the addition of chemicals and accumulation of byproducts. Owing to its reversibility and stability, this molecular device can afford many cycles of digital operation.

An Ionically Driven Molecular IMPLICATION Gate Operating in Fluorescence Mode

An asymmetrically core-extended boron-dipyrromethene (BDP) dye was equipped with two electron-donating macrocyclic binding units with different metal ion preferences to operate as an ionically driven molecular IMPLICATION gate. A Na(+)-responsive tetraoxa-aza crown ether (R(2)) was integrated into the extended pi system of the BDP chromophore to trigger strong intramolecular charge transfer (ICT(2)) fluorescence and guarantee cation-induced spectral shifts in absorption. A dithia-oxa-aza crown (R(1)) that responds to Ag(+) was attached to the meso position of BDP in an electronically decoupled fashion to independently control a second ICT(1) process of a quenching nature. The bifunctional molecule is designed in such a way that in the absence of both inputs, ICT(1) does not compete with ICT(2) and a high fluorescence output is obtained (In(A)=In(B)=0-->Out=1). Accordingly, binding of only Ag(+) at R(1) (In(A)=1, In(B)=0) as well as complexation of both receptors (In(A)=In(B)=1) also yields Out=1. Only for the case in which Na(+) is bound at R(2) and R(1) is in its free state does quenching occur, which is the distinguishing characteristic for the In(A)=0 and In(B)=1-->Out=0 state that is required for a logic IMPLICATION gate and Boolean operations such as IF-THEN or NOT.

Chemical Approaches to Molecular Logic Elements for Addition and Subtraction

Molecular and supramolecular logic gates are candidates for computation at the nanoscale level. Nowadays all common logic operations can be mimicked with molecular devices based on chemical approaches. One step further towards molecular systems with increased logic capabilities is the addition or subtraction of binary digits. This Minireview describes recent developments to attain this goal, including bioinspired systems based on DNA and enzymes. Furthermore, chemical molecular logic gates are discussed and compared critically with regard to alternative concepts.