Photonic Boolean logic gates based on DNA aptamers

We designed a pair of DNA-based logic gates that sense single-stranded DNAs and aptamer ligands to produce fluorescence outputs according to Boolean logic functions AND and OR.     

Molecular-scale logic gates

Currently available approaches to molecular-scale logic gates are summarized and compared. These include: chemically-controlled fluorescent and transmittance-based switches concerned with small molecules, DNA oligonucleotides with fluorescence readout, oligonucleotide reactions with DNA-based catalysts, chemically-gated photochromics, reversibly denaturable proteins, molecular machines with optical and electronic signals, two-photon fluorophores and multichromophoric transient optical switches. The photochemical principles of electron and energy transfer are involved in several of these approaches. More complex molecular logic systems with reconfigurability and superposability provide contrasts with current semiconductor electronics. Integration of simple logic functions to produce more complex ones is also discussed in terms of recent developments.     

Deoxyribozyme-based logic gates

We report herein a set of deoxyribozyme-based logic gates capable of generating any Boolean function. We construct basic NOT and AND gates, followed by the more complex XOR gate. These gates were constructed through a modular design that combines molecular beacon stem-loops with hammerhead-type deoxyribozymes. Importantly, as the gates have oligonucleotides as both inputs and output, they open the possibility of communication between various computation elements in solution. The operation of these gates is conveniently connected to a fluorescent readout.     

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.     

Microfluidic logic gates and timers

We use surface tension-based passive pumping and fluidic resistance to create a number of microfluidic analogs to electronic circuit components. Three classes of components are demonstrated: (1) OR/AND, NOR/NAND, and XNOR digital microfluidic logic gates; (2) programmable, autonomous timers; and (3) slow, perfusive flow rheostats. The components can be implemented with standard pipettes and provide a means of non-electronic and autonomous preprogrammed control with potential utility in cell studies and high throughput screening applications.     

Unprecedented gas-phase chiroselective logic gates

The gas-phase encounters between 2-aminobutane and proton-bound chiral resorcin[4]arene/nucleoside complexes behave in the gas phase as supramolecular "chiroselective logic gates" by releasing the nucleoside depending on the resorcin[4]arene and the 2-aminobutane configurations.     

Molecular logic gates based on pentacyanoferrate complexes: from simple gates to three-dimensional logic systems

The article presents new aspects of reactivity of two pentacyanoferrates: [Fe(CN)5NO]2- and [Fe(CN)5N(O)SR]3-. The dependence of thermodynamic functions on cations was found for the reaction between nitroprusside and thiolate. The thermodynamic data are interpreted in terms of ion pairing and changes in the solvation shell of the cations. It was found that the reaction enthalpies and entropies depend strongly on the cation radius. The reaction volume in turn is strongly affected by the structure and properties of the hydration shell. Careful data analysis allowed the contribution of partial cation dehydration to the total reaction volume to be determined. The experimental results were also interpreted in terms of chemical logic gates. Complex logic systems were built from a number of cells containing a switching compound arranged in different geometric patterns. Increasing the dimensionality of these arrangements leads to really complex logic systems containing up to 20 AND and OR logic gates. The system is capable of processing up to 16 bits of input data.     

Endonuclease-based logic gates and sensors using magnetic force-amplified readout of DNA scission on cantilevers

The endonuclease scission of magnetic particles functionalized with sequence-specific DNAs, which are associated on cantilevers, is followed by the magnetic force-amplified readout of the reactions by the nano-mechanical deflection/retraction of the cantilevers. The systems are employed to develop AND or OR logic gates and to detect single base mismatch specificity of the endonucleases. The two endonucleases EcoRI (E(A)) and AscI (E(B)) are used as inputs. The removal of magnetic particles linked to the cantilever by the duplexes 1/1a and 2/2a via the simultaneous cleavage of the DNAs by E(A) and E(B) leads to the retraction of the magnetically deflected cantilever and to the establishment of the "AND" gate. The removal of the magnetic particles linked to the cantilevers by the duplex 3/3a by either E(A) or E(B) leads to the retraction of the magnetically deflected cantilever and to the establishment of the "OR" gate. The magnetic force-amplified readout of endonuclease activities is also employed to reveal single base mismatch specificity of the biocatalysts.     

Molecular logic gates using surface-enhanced Raman-scattered light

A voltage-activated molecular-plasmonics device was created to demonstrate molecular logic based on resonant surface-enhanced Raman scattering (SERS). SERS output was achieved by a combination of chromophore-plasmon coupling and surface adsorption at the interface between a solution and a gold nanodisc array. The chromophore was created by the self-assembly of a supramolecular complex with a redox-active guest molecule. The guest was reversibly oxidized at the gold surface to the +1 and +2 oxidation states, revealing spectra that were reproduced by calculations. State-specific SERS features enabled the demonstration of a multigate logic device with electronic input and optical output.     

Design of multiplex logic gates: Combining regulation of DNA structure with logical calculation

In this paper, we proposed a facile and accurate way for controlling multiplex fluorescent logic gates through changing the exciting and the observing wavelengths. As proof-of-principle, a Pb²⁺-specific DNAzyme probe and a thymine (T)-rich DNA probe were introduced to a double-stranded (ds-) DNA. The addition style of the two ions served as the four inputs by changing the distance of the three fluorophores, 6-carboxyfluorescein (FAM), ALEXA 532 (ALEXA) and carboxytetramethylrhodamine (TAMRA), all of which were modified on the dsDNA probe. Compared with the previous methods, the present approach needed neither different inputs nor the change of sequence of the probe to achieve multiplex logic gates. Furthermore, the modularity of the strategy may allow it to be extended to other types of logic gates.     

Colorimetric logic gates based on aptamer-crosslinked hydrogels

We have developed a novel molecular logic gate system based on the incorporation of aptamer-crosslinked hydrogels. Modified gold nanoparticles are used as the output signal, which is visible to the naked eye. This system is designed for AND and OR operations using two chemicals as stimulus inputs.     

Deoxyribozyme-based ligase logic gates and their initial circuits

A complete set (YES, NOT, AND, and ANDNOT) of molecular scale logic gates based on ligase deoxyribozymes was constructed. The activity of these gates was visualized through the formation of cascades with downstream phosphodieseterase YES gates, which performed fluorogenic cleavage.     

Light-driven OR and XOR programmable chemical logic gates

Photoelectrodes made of nanocrystalline titanium dioxide modified with various pentacyanoferrates exhibit unique photoelectrochemical properties; photocurrent direction can be switched from anodic to cathodic and vice versa upon changes in photoelectrode potential and incident light wavelength (PhotoElectrochemical Photocurrent Switching, PEPS effect). At certain potentials, anodic photocurrent generated upon UV irradiation has the same intensity as the cathodic photocurrent generated upon visible irradiation. Under these conditions, simultaneous irradiation with UV and visible light results in compensation of anodic and cathodic photocurrents, and zero net photocurrent is observed. This process can be used for construction of unique light-driven chemical logic gates.     

Modular multi-level circuits from immobilized DNA-based logic gates

One of the fundamental goals of molecular computing is to reproduce the tenets of digital logic, such as component modularity and hierarchical circuit design. An important step toward this goal is the creation of molecular logic gates that can be rationally wired into multi-level circuits. Here we report the design and functional characterization of a complete set of modular DNA-based Boolean logic gates (AND, OR, and AND-NOT) and further demonstrate their wiring into a three-level circuit that exhibits Boolean XOR (exclusive OR) function. The approach is based on solid-supported DNA logic gates that are designed to operate with single-stranded DNA inputs and outputs. Since the solution-phase serves as the communication medium between gates, circuit wiring can be achieved by designating the DNA output of one gate as the input to another. Solid-supported logic gates provide enhanced gate modularity versus solution-phase systems by significantly simplifying the task of choosing appropriate DNA input and output sequences used in the construction of multi-level circuits. The molecular logic gates and circuits reported here were characterized by coupling DNA outputs to a single-input REPORT gate and monitoring the resulting fluorescent output signals.     

Molecular logic gates based on 2-tyrylquinoline derivatives

Various logical operations can be performed by molecular logic gates (MLG) based on 2-styrylquinoline derivatives using irradiation with light and protonation as input signals and absorbance (optical density) as output signal. The MLG operation type (“INH”, “OR”, “AND”) depends on the observation wavelength.     

Quantum design rules for single molecule logic gates

Recent publications have demonstrated how to implement a NOR logic gate with a single molecule using its interaction with two surface atoms as logical inputs [W. Soe et al., ACS Nano, 2011, 5, 1436]. We demonstrate here how this NOR logic gate belongs to the general family of quantum logic gates where the Boolean truth table results from a full control of the quantum trajectory of the electron transfer process through the molecule by very local and classical inputs practiced on the molecule. A new molecule OR gate is proposed for the logical inputs to be also single metal atoms, one per logical input.