Manufacturing Reusable NAND Logic Gates and Their Initial Circuits for DNA Nanoprocessors

DNA-based computers can potentially analyze complex sets of biological markers, thereby advancing diagnostics and the treatment of diseases. Despite extensive efforts, DNA processors have not yet been developed due, in part, to limitations in the ability to integrate available logic gates into circuits. We have designed a NAND gate, which is one of the functionally complete set of logic connectives. The gate's design avoids stem-loop-folded DNA fragments, and is capable of reusable operations in RNase H-containing buffer. The output of the gate can be translated into RNA-cleaving activity or a fluorescent signal produced either by a deoxyribozyme or a molecular beacon probe. Furthermore, three NAND-gate-forming DNA strands were crosslinked by click chemistry and purified in a simple procedure that allowed ≈10¹³ gates to be manufactured in 16 h, with a hands-on time of about 30 min. Two NAND gates can be joined into one association that performs a new logic function simply by adding a DNA linker strand. Approaches developed in this work could contribute to the development of biocompatible DNA logic circuits for biotechnological and medical applications.     

Towards a DNA Nanoprocessor: Reusable Tile‐Integrated DNA Circuits

Modern electronic microprocessors use semiconductor logic gates organized on a silicon chip to enable efficient inter‐gate communication. Here, arrays of communicating DNA logic gates integrated on a single DNA tile were designed and used to process nucleic acid inputs in a reusable format. Our results lay the foundation for the development of a DNA nanoprocessor, a small and biocompatible device capable of performing complex analyses of DNA and RNA inputs.     

The Construction of DNA Logic Gates Restricted to Certain Live Cells Based on the Structure Programmability and Aptamer-Cell Affinity of G-Quadruplexes

DNA computation is considered a fascinating alternative to silicon-based computers; it has evoked substantial attention and made rapid advances. Besides realizing versatile functions, implementing spatiotemporal control of logic operations, especially at the cellular level, is also of great significance to the development of DNA computation. However, developing simple and efficient methods to restrict DNA logic gates performing in live cells is still a challenge. In this work, a series of DNA logic gates was designed by taking full advantage of the diversity and programmability of the G-quadruplex (G4) structure. More importantly, by further using the high affinity and specific endocytosis of cells to aptamer G4, an INHIBIT logic gate has been realized whose operational site is precisely restricted to specific live cells. The design strategy might have great potential in the field of molecular computation and smart bio-applications.     

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.     

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.     

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.     

Recent Progress in Fluorescence Signal Design for DNA-Based Logic Circuits

DNA-based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA′s advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA-based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA-based logic circuit construction. Although work on sequence and structure design for DNA-based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA-based logic circuits. Several basic strategies are summarized and a few designs for developing multi-output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.     

Highly Sensitive INHIBIT and XOR Logic Gates Based on ICT and ACQ Emission Switching of a Porphyrin Derivative

Fluorescence‐switch‐based logic devices are very sensitive compared with most of the reported devices based on UV/Vis absorption systems. Herein, we demonstrate that a simple molecule, 5,10,15,20‐tetra‐(4‐aminophenyl)porphyrin (TAPP), shows protonation‐induced multiple emission switches through intramolecular charge transfer and/or aggregation‐caused quenching. Highly sensitive INHIBIT and XOR logic gates can be achieved by combining the intermolecular assembly with the intramolecular photoswitching of diprotonated TAPP (TAPPH₂²⁺). In addition, molecular simulations have been performed by DFT for a better understanding of the emission‐switching processes.     

Rhodamine-Appended Bipyridine: XOR and OR Logic Operations Integrated in an Example of Controlled Metal Migration

A new bipyridyl derivative 1 bearing rhodamine B as visible fluorophore was designed, synthesized and characterized as a fluorescent and colorimetric sensor for metal ions. Interaction with Cu²⁺, Zn²⁺, Cd²⁺, Hg⁺, and Hg²⁺ ions was followed by UV/Vis and emission spectroscopy. Upon addition of these metal ions, different colorimetric and fluorescent responses were observed. “Off-on-off” (Cu²⁺, Zn²⁺, and Hg²⁺) and “off-on” (Hg⁺ and Cd²⁺) systems were obtained. Probe 1 was explored to mimic XOR and OR logic operations for the simultaneous detection of Hg⁺–Cu²⁺ and Hg⁺–Zn²⁺ pairs, respectively. DFT calculations were also performed to gain insight into the lowest-energy gas-phase conformation of free receptor 1 as well as the atomistic details of the coordination modes of the various metal ions.     

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.     

Tunable Molecular Logic Gates Designed for Imaging Released Neurotransmitters

Tunable dual‐analyte fluorescent molecular logic gates (ExoSensors) were designed for the purpose of imaging select vesicular primary‐amine neurotransmitters that are released from secretory vesicles upon exocytosis. ExoSensors are based on the coumarin‐3‐aldehyde scaffold and rely on both neurotransmitter binding and the change in environmental pH associated with exocytosis to afford a unique turn‐on fluorescence output. A pH‐functionality was directly integrated into the fluorophore π‐system of the scaffold, thereby allowing for an enhanced fluorescence output upon the release of labeled neurotransmitters. By altering the pH‐sensitive unit with various electron‐donating and ‐withdrawing sulfonamide substituents, we identified a correlation between the pK_a of the pH‐sensitive group and the fluorescence output from the activated fluorophore. In doing so, we achieved a twelvefold fluorescence enhancement upon evaluating the ExoSensors under conditions that mimic exocytosis. ExoSensors are aptly suited to serve as molecular imaging tools that allow for the direct visualization of only the neurotransmitters that are released from secretory vesicles upon exocytosis.     

Antibody Activation using DNA‐Based Logic Gates

Oligonucleotide‐based molecular circuits offer the exciting possibility to introduce autonomous signal processing in biomedicine, synthetic biology, and molecular diagnostics. Here we introduce bivalent peptide–DNA conjugates as generic, noncovalent, and easily applicable molecular locks that allow the control of antibody activity using toehold‐mediated strand displacement reactions. Employing yeast as a cellular model system, reversible control of antibody targeting is demonstrated with low nM concentrations of peptide–DNA locks and oligonucleotide displacer strands. Introduction of two different toehold strands on the peptide–DNA lock allowed signal integration of two different inputs, yielding logic OR‐ and AND‐gates. The range of molecular inputs could be further extended to protein‐based triggers by using protein‐binding aptamers.     

Fluorescent Logic Gates Chemically Attached to Silicon Nanowires

I′m in the mood for dansyl : A chemically controlled fluorescent logic gate was formed by grafting a dansyl unit onto silicon nanowires (SiNWs; see picture). The logic gate was operated by utilizing pH changes, Hg^II, and Cl^? or Br^? ions as inputs and the fluorescence of the modified SiNWs as output. The modified SiNWs could perform as a three‐input logic gate that combines the YES and INH operations.

     

Coherent Activation of DNA Tweezers: A “SET–RESET” Logic System

Open sesame : Aptamer–substrate complexes activate the coherent operation of two tweezers that act as a “SET–RESET” logic system. Each tweezer cycles between a fluorescent open state and a closed quenched state (Q=quencher, F=fluorophore) when triggered by adenosine monophosphate (AMP) and adenosine deaminase (AD).

     

Interfacing Synthetic DNA Logic Operations with Protein Outputs

DNA logic gates are devices composed entirely of DNA that perform Boolean logic operations on one or more oligonucleotide inputs. Typical outputs of DNA logic gates are oligonucleotides or fluorescent signals. Direct activation of protein function has not been engineered as an output of a DNA‐based computational circuit. Explicit control of protein activation enables the immediate triggering of enzyme function and could yield DNA computation outputs that are otherwise difficult to generate. By using zinc‐finger proteins, AND, OR, and NOR logic gates were created that respond to short oligonucleotide inputs and lead to the activation or deactivation of a split‐luciferase enzyme. The gate designs are simple and modular, thus enabling integration with larger multigate circuits, and the modular structure gives flexibility in the choice of protein output. The gates were also modified with translator circuits to provide protein activation in response to microRNA inputs as potential cellular cancer markers.