DNA logic gates

A conceptually new logic gate based on DNA has been devised. Methoxybenzodeazaadenine ((MD)A), an artificial nucleobase which we recently developed for efficient hole transport through DNA, formed stable base pairs with T and C. However, a reasonable hole-transport efficiency was observed in the reaction for the duplex containing an (MD)A/T base pair, whereas the hole transport was strongly suppressed in the reaction using a duplex where the base opposite (MD)A was replaced by C. The influence of complementary pyrimidines on the efficiency of hole transport through (MD)A was quite contrary to the selectivity observed for hole transport through G. The orthogonality of the modulation of these hole-transport properties by complementary pyrimidine bases is promising for the design of a new molecular logic gate. The logic gate system was executed by hole transport through short DNA duplexes, which consisted of the "logic gate strand", containing hole-transporting nucleobases, and the "input strand", containing pyrimidines which modulate the hole-transport efficiency of logic bases. A logic gate strand containing multiple (MD)A bases in series provided the basis for a sharp AND logic action. On the other hand, for OR logic and combinational logic, conversion of Boolean expressions to standard sum-of-product (SOP) expressions was indispensable. Three logic gate strands were designed for OR logic according to each product term in the standard SOP expression of OR logic. The hole-transport efficiency observed for the mixed sample of logic gate strands exhibited an OR logic behavior. This approach is generally applicable to the design of other complicated combinational logic circuits such as the full-adder.     

Lineal DNA logic gate for microRNA diagnostics with strand displacement and fluorescence resonance energy transfer

Designing molecular logic gates to operate programmably for molecular diagnostics in molecular computing still remains challenging. Here, we designed a novel linear DNA logic gates for microRNA analysis based on strand displacement and fluorescence resonance energy transfer (FRET). Two labeled strands closed each other produce to FRET through hybridization with a complementary strand to form a basic work unit of logic gate. Two indicators of heart failure (microRNA-195 and microRNA-21) were selected as the logic inputs and the fluorescence mode was used as the logic output. We have demonstrated that the molecular logic gate mechanism worked well with the construction of YES and AND gates.     

DNA computation: a photochemically controlled AND gate

DNA computation is an emerging field that enables the assembly of complex circuits based on defined DNA logic gates. DNA-based logic gates have previously been operated through purely chemical means, controlling logic operations through DNA strands or other biomolecules. Although gates can operate through this manner, it limits temporal and spatial control of DNA-based logic operations. A photochemically controlled AND gate was developed through the incorporation of caged thymidine nucleotides into a DNA-based logic gate. By using light as the logic inputs, both spatial control and temporal control were achieved. In addition, design rules for light-regulated DNA logic gates were derived. A step-response, which can be found in a controller, was demonstrated. Photochemical inputs close the gap between DNA computation and silicon-based electrical circuitry, since light waves can be directly converted into electrical output signals and vice versa. This connection is important for the further development of an interface between DNA logic gates and electronic devices, enabling the connection of biological systems with electrical circuits.     

Molecular Processors: From Qubits to Fuzzy Logic

Single molecules or their assemblies are information processing devices. Herein it is demonstrated how it is possible to process different types of logic through molecules. As long as decoherent effects are maintained far away from a pure quantum mechanical system, quantum logic can be processed. If the collapse of superimposed or entangled wavefunctions is unavoidable, molecules can still be used to process either crisp (binary or multi‐valued) or fuzzy logic. The way for implementing fuzzy inference engines is declared and it is supported by the examples of molecular fuzzy logic systems devised so far. Fuzzy logic is drawing attention in the field of artificial intelligence, because it models human reasoning quite well. This ability may be due to some structural analogies between a fuzzy logic system and the human nervous system.     

Array-enhanced Logical Stochastic Resonance in Coupled Bistable Systems

We investigate the impact of coupling on the reliability of the logic system as well as the logical stochastic resonance (LSR) phenomenon in the coupled logic gates system. It is found that compared with single logic gate, the coupled system could yield reliable logic outputs in a much wider noise region, which means coupling can obviously improve the reliability of the logic system and thus enhance the LSR effect. Moreover, we find that the enhancement is larger for larger system size, whereas for large enough size the enhancement seems to be saturated. Finally, we also examine the effect of coupling strength, it can be observed that the noise region where reliable logic outputs can be obtained evolves non-monotonically as the coupling strength increases, displaying a resonance-like effect.     

Integrated Molecular Logic Using a Multistate Electrochromic Platform

Herein, we present an approach that integrates molecular logic functions using surface-confined metallo-organic assemblies. These assemblies are electrochromic and mimic the behaviour of logic elements. The logic elements are addressed individually by electrochemical methods, and their outputs are simultaneously read-out optically by UV/Vis absorption spectroscopy. The versatility of our setup is demonstrated by the integration of two multi-component assemblies; each acting as ternary logic elements. We used also a laminated cell configuration to demonstrate color-to-color and color-to-transparent transitions. This concept offers a route for the future development of devices with multiple logic states.     

DNA-based photonic logic gates: AND,NAND, and INHIBIT

Conventional microprocessors use elementary logic gates to perform complex computational tasks. Mimicking such computational processes using purely molecular systems has been limited in most cases by the lack of design generality or potential addressability of existing molecular logic gates. Herein we report that by employing the universal recognition properties of DNA simple photonic logic gates can be created that are capable of AND, NAND, and INHIBIT logic operations.     

Connectable DNA Logic Gates: OR and XOR Logics

Modern computer processors are based on semiconductor logic gates connected to each other in complex circuits. This study contributes to the development of a new class of connectable logic gates made of DNA in which the transfer of oligonucleotide fragments as input/output signals occurs upon hybridization of DNA sequences. The DNA strands responsible for a logic function form associates containing immobile DNA four‐way junction structures when the signal is high and dissociate into separate strands when the signal is low. A basic set of logic gates (NOT, AND, and OR) was designed. Two NOT gates, two AND gates, and an OR gate were connected in a network that corresponds to an XOR logic function. The design of the logic gates presented here may contribute to the development of the first biocompatible molecular computer.     

A differential ICT based molecular probe for multi-ions and multifunction logic circuits

This paper presents anthraquinone and benzimidazole based hybrid molecular architect as the state of the art for multifunctional molecular logic circuits. The moleculator exhibits differential output behavior towards F(-), Zn(2+) and Cu(2+) ions to provide opportunities for elaboration of XOR, INHIBIT, XNOR, AND, OR, NOR, logic functions and their integrated logic functions half-adder, half-subtractor and comparator within a single molecule. These integral logic functions can be reprogrammed by self-annihilation or by another additional input in the same cell. This single molecule behaves uniquely where different logic functions can be operated and reset by using different inputs and outputs.     

DNA‐Based Adaptive Plasmonic Logic Gates

Self‐assembled plasmonic logic gates that read DNA molecules as input and return plasmonic chiroptical signals as outputs are reported. Such logic gates are achieved on a DNA‐based platform that logically regulate the conformation of a chiral plasmonic nanostructure, upon specific input DNA strands and internal computing units. With systematical designs, a complete set of Boolean logical gates are realized. Intriguingly, the logic gates could be endowed with adaptiveness, so they can autonomously alter their logics when the environment changes. As a demonstration, a logic gate that performs AND function at body temperature while OR function at cold storage temperature is constructed. In addition, the plasmonic chiroptical output has three distinctive states, which makes a three‐state molecular logic gate readily achievable on this platform. Such DNA‐based plasmonic logic gates are envisioned to execute more complex tasks giving these unique characteristics.     

DNA-Based Adaptive Plasmonic Logic Gates

Self-assembled plasmonic logic gates that read DNA molecules as input and return plasmonic chiroptical signals as outputs are reported. Such logic gates are achieved on a DNA-based platform that logically regulate the conformation of a chiral plasmonic nanostructure, upon specific input DNA strands and internal computing units. With systematical designs, a complete set of Boolean logical gates are realized. Intriguingly, the logic gates could be endowed with adaptiveness, so they can autonomously alter their logics when the environment changes. As a demonstration, a logic gate that performs AND function at body temperature while OR function at cold storage temperature is constructed. In addition, the plasmonic chiroptical output has three distinctive states, which makes a three-state molecular logic gate readily achievable on this platform. Such DNA-based plasmonic logic gates are envisioned to execute more complex tasks giving these unique characteristics.     

DNA-based visual majority logic gate with one-vote veto function

A molecular logic gate is a basic element and plays a key role in molecular computing. Herein, we have developed a label-free and enzyme-free three-input visual majority logic gate which is realized for the first time according to DNA hybridization only, without DNA replacement and enzyme catalysis. Furthermore, a one-vote veto function was integrated into the DNA-based majority logic gate, in which one input has priority over other inputs. The developed system can also implement multiple basic and cascade logic gates.     

Implication and Inhibition Boolean Logic Gates Mimicked with Enzyme Reactions

The enzyme system mimicking Implication (IMPLY) and Inhibition (INHIB) Boolean logic gates has been designed. The same enzyme system was used to operate as the IMPLY or INHIB gate simply by reformulating the input signals. The optical analysis of the logic operation confirmed the output generation as expected for the studied logic gates. The conceptual approach to the IMPLY and INHIB logic gates allows their construction with many other enzymes operating in a similar way.     

Alert-type biological dosimeter based on enzyme logic system

A cooperative effect of two biomarkers, α-amylase and lactate dehydrogenase, was used to analyze radiation-caused tissue damage in vitro in model solutions of human serum. The analytical system was based on the recently emerged biocomputing concept applying biocatalytic cascades for logic processing of biochemical input signals. The studied system resembled a Boolean NAND logic gate in which the change of the optical output signal from a high level (logic value 1) to a low level (logic value 0) confirmed the presence of both biomarkers at pathological concentrations (1,1 input signals), thus yielding the conclusion about radiation tissue damage. The system operates in a digital YES/NO format as an alert-type biosensor with a built-in Boolean logic.     

Biofuel Cells for Self‐Powered Electrochemical Biosensing and Logic Biosensing: A Review

This article reviews recent advances and progress in developing electrochemical (EC) biosensing and logic biosensing systems based on self‐powered biofuel cells (BFCs). BFCs that exploit enzymes and microbes have attracted a considerable recent interest owing to their unique ability to provide sustainable energy from renewable fuel source under mild conditions. This review focuses on recently introduced novel concepts for using BFCs as the basic element for EC‐biosensing and especially EC‐logic biosensing applications. The fabrication and design of such self‐powered EC‐biosensing and EC‐logic biosensing are described along and different new approaches for BFCs‐based EC‐biosensing and EC‐logic biosensing involving substrate effects, inhibition effects, blocking effects and gene regulation effects. Latest advances in coupling a self‐powered diagnostic operation with logic‐activated drug release functionality are discussed. We conclude with the implications of the new self‐powered biosensing/logic‐biosensing platforms along with future prospects and challenges.     

All-photonic multifunctional molecular logic device

Photochromes are photoswitchable, bistable chromophores which, like transistors, can implement binary logic operations. When several photochromes are combined in one molecule, interactions between them such as energy and electron transfer allow design of simple Boolean logic gates and more complex logic devices with all-photonic inputs and outputs. Selective isomerization of individual photochromes can be achieved using light of different wavelengths, and logic outputs can employ absorption and emission properties at different wavelengths, thus allowing a single molecular species to perform several different functions, even simultaneously. Here, we report a molecule consisting of three linked photochromes that can be configured as AND, XOR, INH, half-adder, half-subtractor, multiplexer, demultiplexer, encoder, decoder, keypad lock, and logically reversible transfer gate logic devices, all with a common initial state. The system demonstrates the advantages of light-responsive molecules as multifunctional, reconfigurable nanoscale logic devices that represent an approach to true molecular information processing units.     

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.     

Molecular photonic logic gates

The possibility of performing logical operations at the molecular level is being actively investigated at present with the aim of developing molecular logic gates, which can be used in information technologies. In this minireview, the design algorithm of molecular logic gates is considered and the requirements on molecular systems for use as logic gates are specified. Examples of molecular logic gates performing different logical operations are given. Attention is focused on all-photonic molecular logic gates, in which light is used as an input signal for transferring the system from one state to another and for reading the output signal by absorption or luminescence. In addition, optoelectronic devices with light as the input signal and electric current as the output signal are briefly discussed.     

A set of logic gates fabricated with G-quadruplex assembled at an electrode surface

A G-quadruplex-hemin complex assembled at an electrode surface may exhibit "smart" behaviors under benign conditions, which can be further used in fabricating a set of logic gates. Desirably, these logic gates can be integrated into a logic network with the advantages of integrity, unification and reversibility.