Bioelectronic Interface Connecting Reversible Logic Gates Based on Enzyme and DNA Reactions

It is believed that connecting biomolecular computation elements in complex networks of communicating molecules may eventually lead to a biocomputer that can be used for diagnostics and/or the cure of physiological and genetic disorders. Here, a bioelectronic interface based on biomolecule‐modified electrodes has been designed to bridge reversible enzymatic logic gates with reversible DNA‐based logic gates. The enzyme‐based Fredkin gate with three input and three output signals was connected to the DNA‐based Feynman gate with two input and two output signals—both representing logically reversible computing elements. In the reversible Fredkin gate, the routing of two data signals between two output channels was controlled by the control signal (third channel). The two data output signals generated by the Fredkin gate were directed toward two electrochemical flow cells, responding to the output signals by releasing DNA molecules that serve as the input signals for the next Feynman logic gate based on the DNA reacting cascade, producing, in turn, two final output signals. The Feynman gate operated as the controlled NOT gate (CNOT), where one of the input channels controlled a NOT operation on another channel. Both logic gates represented a highly sophisticated combination of input‐controlled signal‐routing logic operations, resulting in redirecting chemical signals in different channels and performing orchestrated computing processes. The biomolecular reaction cascade responsible for the signal processing was realized by moving the solution from one reacting cell to another, including the reacting flow cells and electrochemical flow cells, which were organized in a specific network mimicking electronic computing circuitries. The designed system represents the first example of high complexity biocomputing processes integrating enzyme and DNA reactions and performing logically reversible signal processing.     

INHIBIT‐Inspired Two‐Output DNA Logic Gates Based on Surface‐Enhanced Raman Scattering

Herein, we presented a novel logic gate based on an INHIBITION gate that performs parallel readouts. Logic gates performing INHIBITION and YES/OR were constructed using surface‐enhanced Raman scattering as optical outputs for the first time. The strategy allowed for simultaneous reading of outputs in one tube. The applicability of this strategy has been successfully exemplified in the construction of half‐adder using the two‐output logic gates as reporting gates. This reporting strategy provides additional design flexibility for dynamic DNA devices.     

A Reversible Multi‐Stimuli‐Responsive Fluorescence Probe and the Design for Combinational Logic Gate Operations

Here, a novel multi‐stimuli‐responsive fluorescence probe is developed by incorporating spiropyran group into the coumarin‐substituted polydiacetylene (PDA) vesicles. The fluorescence of PDA can be turned on upon heating, and can be quenched upon exposure to UV light irradiation or pH stimuli owing to the fluorescene resonance energy transfer (FRET) between the red‐phase PDA and the open merocyanine (MC) form of spiropyran. Moreover, we have designed and experimentally realized a set of logic gate operations for the first time based on the fluorescence modulation of the designed system upon thermal, photo, and pH stimuli. This novel type of resettable logic gates augur well for practical applications in information storage, optical recording, and sensing in complicated microenvironments.

     

Label‐Free Logic Modules and Two‐Layer Cascade Based on Stem‐Loop Probes Containing a G‐Quadruplex Domain

A simple, versatile, and label‐free DNA computing strategy was designed by using toehold‐mediated strand displacement and stem‐loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two‐layer logic cascade were constructed. The probes contain a G‐quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light‐up fluorescent signal of G‐quadruplex/NMM complex was used as the output readout. The inputs are the disease‐specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label‐free and modular strategy might be adapted in multi‐target diagnosis through DNA hybridization and aptamer‐target interaction.     

Controlled Logic Gates—Switch Gate and Fredkin Gate Based on Enzyme‐Biocatalyzed Reactions Realized in Flow Cells

Controlled logic gates, where the logic operations on the Data inputs are performed in the way determined by the Control signal, were designed in a chemical fashion. Specifically, the systems where the Data output signals directed to various output channels depending on the logic value of the Control input signal have been designed based on enzyme biocatalyzed reactions performed in a multi‐cell flow system. In the Switch gate one Data signal was directed to one of two possible output channels depending on the logic value of the Control input signal. In the reversible Fredkin gate the routing of two Data signals between two output channels is controlled by the third Control signal. The flow devices were created using a network of flow cells, each modified with one enzyme that biocatalyzed one chemical reaction. The enzymatic cascade was realized by moving the solution from one reacting cell to another which were organized in a specific network. The modular design of the enzyme‐based systems realized in the flow device allowed easy reconfiguration of the logic system, thus allowing simple extension of the logic operation from the 2‐input/3‐output channels in the Switch gate to the 3‐input/3‐output channels in the Fredkin gate. Further increase of the system complexity for realization of various logic processes is feasible with the use of the flow cell modular design.     

Multi‐Level Logic Gate Operation Based on Amplified Aptasensor Performance

Conventional electronic circuits can perform multi‐level logic operations; however, this capability is rarely realized by biological logic gates. In addition, the question of how to close the gap between biomolecular computation and silicon‐based electrical circuitry is still a key issue in the bioelectronics field. Here we explore a novel split aptamer‐based multi‐level logic gate built from INHIBIT and AND gates that performs a net XOR analysis, with electrochemical signal as output. Based on the aptamer–target interaction and a novel concept of electrochemical rectification, a relayed charge transfer occurs upon target binding between aptamer‐linked redox probes and solution‐phase probes, which amplifies the sensor signal and facilitates a straightforward and reliable diagnosis. This work reveals a new route for the design of bioelectronic logic circuits that can realize multi‐level logic operation, which has the potential to simplify an otherwise complex diagnosis to a “yes” or “no” decision.     

Reversible Logic Gates Based on Enzyme‐Biocatalyzed Reactions and Realized in Flow Cells: A Modular Approach

Reversible logic gates, such as the double Feynman gate, Toffoli gate and Peres gate, with 3‐input/3‐output channels are realized using reactions biocatalyzed with enzymes and performed in flow systems. The flow devices are constructed using a modular approach, where each flow cell is modified with one enzyme that biocatalyzes one chemical reaction. The multi‐step processes mimicking the reversible logic gates are organized by combining the biocatalytic cells in different networks. This work emphasizes logical but not physical reversibility of the constructed systems. Their advantages and disadvantages are discussed and potential use in biosensing systems, rather than in computing devices, is suggested.     

Two‐Photon Absorption and the Design of Two‐Photon Dyes

Two photons are better than one : This principle applies to a wide range of applications, ranging from engineering to physiology. Recent advances in our understanding of the phenomenon of two‐photon absorption (see picture) and in the design of two‐photon dyes are rapidly increasing the scope of this field.

     

Stimuli-Triggered Strand Displacement-Based Multifunctional Gene Detection Platform Controlled By A Multi-Input DNA Logic Gate

Highly sensitive detection of various cancer related genes is of great significance in a number of biomedical applications. Here we describe a logic-controlled multifunctional platform that is capable of detecting two kinds of gene sequences with a 2-aminopurine (2-AP) as a quencher-free fluorescent probe, the fluorescence of which dramatically increases when it loops out the DNA helices. This detection platform is assembled from the split ATP aptamer, G-quadruplex, and the antisense strands of the P53 and K-ras genes, together with their complementary components. It is selectively activated by ATP and K⁺ via the target-induced DNA strand displacement, enabling the exposure of two long toehold regions that allow the P53 and K-ras genes to trigger the next DNA strand displacements. A hairpin DNA containing a looped-out 2-AP in the stem is finally released, accompanying with a significant increase of fluorescence intensity. The whole process behaves as a four-input AND logic gate. Such a logic-controlled gene detection platform is able to convert the external stimulation of ions and biomolecules into a detectable fluorescence output and functions well in gene detection.     

N‐Annulated Perylene‐Substituted and Fused Porphyrin Dimers with Intense Near‐Infrared One‐Photon and Two‐Photon Absorption

Fusion of two N‐annulated perylene (NP) units with a fused porphyrin dimer along the S₀–S₁ electronic transition moment axis has resulted in new near‐infrared (NIR) dyes 1 a / 1 b with very intense absorption (ε>1.3×10⁵ M ^?1 cm^?1) beyond 1250 nm. Both compounds displayed moderate NIR fluorescence with fluorescence quantum yields of 4.4×10^?6 and 6.0×10^?6 for 1 a and 1 b , respectively. The NP‐substituted porphyrin dimers 2 a / 2 b have also been obtained by controlled oxidative coupling and cyclodehydrogenation, and they showed superimposed absorptions of the fused porphyrin dimer and the NP chromophore. The excited‐state dynamics of all of these compounds have been studied by femtosecond transient absorption measurements, which revealed porphyrin dimer‐like behaviour. These new chromophores also exhibited good nonlinear optical susceptibility with large two‐photon absorption cross‐sections in the NIR region due to extended π‐conjugation. Time‐dependent density functional theory calculations have been performed to aid our understanding of their electronic structures and absorption spectra.     

Nucleic Acid Driven DNA Machineries Synthesizing Mg2+‐Dependent DNAzymes: An Interplay between DNA Sensing and Logic‐Gate Operations

Polymerase/nicking enzymes and nucleic‐acid scaffolds are implemented as DNA machines for the development of amplified DNA‐detection schemes, and for the design of logic gates. The analyte nucleic acid target acts, also, as input for the logic gates. In the presence of two DNA targets, acting as inputs, and appropriate DNA scaffolds, the polymerase‐induced replication of the scaffolds, followed by the nicking of the replication products, are activated, leading to the autonomous synthesis of the Mg²⁺‐dependent DNAzyme or the Mg²⁺‐dependent DNAzyme subunits. These biocatalysts cleave a fluorophore/quencher‐functionalized nucleic‐acid substrate, thus providing fluorescence signals for the sensing events or outputs for the logic gates. The systems are used to develop OR, AND, and Controlled‐AND gates, and the DNA‐analyte targets represent two nucleic acid sequences of the smallpox viral genome.     

One‐ and Two‐Photon Absorption: Physical Principle and Applications

We introduce the principle and applications of one‐photon absorption (OPA) and two‐photon absorption (TPA) controlled by external electric fields. The physical mechanism of OPA and TPA are firstly introduced, which can visually promote thoroughly understanding of principle and physical analysis. Secondly, the applications of different molecules in OPA and TPA with and without external electric field are introduced in detail. The effect of the external electric field on the charge transfer during the absorption process is also exemplified. Furthermore, the external electric field on the molecular orbital wave function is visualized through the charge transfer process in the excited state transitions. The purpose of this review is to deepen the understanding of the types of charge transfer under linear and non‐linear absorption in different systems.     

Versatile and Homogeneous DNA Tetraplex Platform for Constructing Label-Free Logic Devices: From Design to Application

The design of DNA-based logic circuits has become an active research field in DNA nanotechnology and holds great potential in intelligent bioanalysis. To date, although many DNA-based logic systems have been realized, the implementation of advanced logic functions is still challenging, especially with simple and homogeneous compositions. Herein, by integrating two DNA tetraplex structures (G-quadruplex and i-motif), a completely label-free logic platform with high scalability was established, with which a series of advanced functions were realized, including arithmetic (adders and subtractors) and nonarithmetic ones (majority and dual-transfer gates). Furthermore, the platform was also applied as an intelligent biosensor to coanalyze two cancer-related micro-RNAs with high sensitivities and specificities. Considering the excellent versatility, expandability, and biocompatibility, the platform may promote the development of DNA computing and hold great potential in multiparameter sensing and medical diagnosis.     

Light‐Induced Protein Dimerization by One‐ and Two‐Photon Activation of Gibberellic Acid Derivatives in Living Cells

We developed a highly efficient system for light‐induced protein dimerization in live cells using photo‐caged derivatives of the phytohormone gibberellic acid (GA₃). We demonstrate the application of the photo‐activatable chemical inducer of dimerization (CID) for the control of protein translocation with high spatiotemporal precision using light as an external trigger. Furthermore, we present a new two‐photon (2P)‐sensitive caging group, whose exceptionally high two‐photon cross section allows the use of infrared light to efficiently unleash the active GA₃ for inducing protein dimerization in living cells.     

Theoretical Studies on the One‐ and Two‐Photon Absorption Properties of Double‐bis(styryl)benzene Derivatives

Two series of bis(styryl)benzene derivatives (BSBD), namely the single‐BSBD and the double‐BSBD, were investigated. The equilibrium geometries and electronic structures were obtained by using the density functional theory B3LYP and 6‐31G basis set. In succession, the one‐ and two‐photon absorption properties of all the molecules were studied theoretically with a ZINDO‐SOS (sum‐over‐states) method in detail. It can be seen that the double‐BSBDs have larger two‐photon absorption (TPA) cross sections in the visible‐IR range than the corresponding single‐BSBDs, demonstrating that increasing the molecular dimension is a very effective method to enhance the values of the TPA cross sections. On the other hand, it can be also noticed that the values of the TPA cross sections are correlative with the ability of donating (accepting) electrons of the terminal substituent groups R [N(CH₃)₂, CH₃, H and CF₃] in these molecules. That is, the intramolecular charge transfer is also a factor for the enhancement of the TPA efficiency. To sum up, the idea of increasing the molecular dimension to enhance the TPA cross section value is a helpful direction to explore better TPA materials for practical applications. And the double‐BSBD molecules are promising TPA materials for the further investigation from the standpoint of the high transparency and the larger TPA cross sections.