"Plug and play" logic gates based on fluorescence switching regulated by self-assembly of nucleotide and lanthanide ions

Exploring the time-dependent and wavelength-guided tunable binary and ternary logic behaviours of a charge-transfer probe

This study presents the development of a novel time-dependent logic behaviour system and a state-of-the-art inter-switchable ternary molecular logic system, comprising 3-input INHIBIT and 3-input TRANSFER logic gates driven by elementary chemical interactions. The absorption spectra of the probe molecule underwent versatile time-dependent changes upon the individual and simultaneous addition of two analytes, namely F- and CN-, leading to alterations in the logic behaviour observed at both the 295 nm (from AND to TRANSFER) and 400 nm bands (from OR to INHIBIT). Additionally, we explored the creation of wavelength-guided molecular logic systems that leverage reversible (F- and H2O) and irreversible (CN- and H2O) chemical interactions. By employing CN- and H2O as dual chemical inputs, we derived binary TRANSFER, 2-input PASS 0, and binary COMPLEMENT logic gates based on the opto-chemical responses at 295 nm, 400 nm, and 500 nm, respectively. Lastly, we introduced an innovative inter-switchable ternary molecular logic system, involving 3-input INHIBIT and 3-input TRANSFER logic gates, using F-, CN-, and H2O as ternary chemical inputs, capitalizing on the probes' versatile and distinct absorption responses at varying wavelengths (400 and 295 nm, respectively).

Advancing Molecular-Scale Logic Devices through Multistage Switching in a Luminescent Bimetallic Ru(II)-Terpyridine Complex

Stimuli-responsive multistep switching phenomena of a luminescent bimetallic Ru(II) complex are employed herein to fabricate multiple configurable logic devices. The complex exhibits "off-on" and "on-off" emission switching upon alternative treatment with visible and UV light. Additionally, remarkable augmentation of the rate as well as quantum yield of photoisomerization was achieved via the use of a chemical oxidant (Ce4+) as well as a reductant (metallic sodium). Upon exploiting the emission spectral response of the complex, several advanced Boolean logic functions, including IMPLICATION as well as 2-input 2-output and 3-input 2-output complex combinational logic gates, are successfully implemented. Additionally, by utilizing the vast efficacy of Python, a novel "logic_circuit" model is devised that is capable of making accurate decisions under the influence of various input combinations. This model transcends traditional Boolean logic gates, offering flexibility and intuition to design logical functions tailored to specific chemical contexts. By integrating principles of logic circuits with chemical processes, this innovative approach enables structure determination of the chemical states based on input conditions, thereby unlocking avenues for exploring intricate interactions and reactions beyond conventional Boolean logic paradigms.

Ratiometric fluorescence detection of sulfide ions based on lanthanide coordination polymer using guanosine diphosphate as ligand

The efficiency of energy transfer from guanine nucleotide to terbium ion (Tb³⁺) is affected by the phosphate group significantly. Compared with the biomolecules 5'-GMP (guanosine monophosphate), guanosine diphosphate (GDP) exhibits better sensitize ability to Tb³⁺ ions luminescence. Assisted with the carboxycoumarin ligand, we synthesized a more stable optical Coumarin@GDP-Tb polymer with the characteristic emission peaks located on 440 nm and 545 nm in this work. The Coumarin@GDP-Tb polymer is not only rich in metal binding sites, but also maintains a moderate ionic binding force, which helps metal ions to bind or leave it easily. Experiment result shows that Coumarin@GDP-Tb polymer has the appropriate binding force for Fe²⁺ ions, which can be destroyed by sulfur ions (S^2-) as the formation of FeS precipitation. Based on this, Coumarin@GDP-Tb was designed as the ratio fluorescence probe for sulfur ions detection, where the fluorescence at 545 nm can be selectively quenched by Fe²⁺ ions, while that at 440 nm was unaffected, in the presence of S^2- ions, the quenched fluorescence can be recovered remarkably. With the increasing S^2- ions from 0.1-45 μM, the ratio of fluorescence intensity at 545 nm to 440 nm (F₅₄₅/F₄₄₀) is linear to S^2- concentration, and the detection limit of S^2- was calculated to be 0.073 μM. Contrast to those fluorescence probes with single wavelength emission, Coumarin@GDP-Tb displays a comparable sensitivity, the introduced self-adjust wavelength improved the detection accuracy efficiently. The above 98.1 % recovery rates of S^2- ions in the actual water sample demonstrated the practicability of Coumarin@GDP-Tb fluorescence probe.

Regulation of light-harvesting antenna based on silver ion-enhanced emission of dye-doped coordination polymer nanoparticles

The design and construction of artificial light-harvesting systems for solar energy conversion to chemical energy has been an active research field. A variety of molecules and materials have been used to mimic the function of the light-harvesting antenna. However, the improvement or regulation of the antenna effect of the existing artificial light-harvesting systems is less explored. Coordination polymers have aroused extensive concern due to their applications in light-harvesting and energy conversion. Herein, it is found that silver ion can dramatically enhance the emission of dye encapsulated in the coordination polymer nanoparticles (CPNs). The mechanism of Ag⁺-induced fluorescence enhancement is elucidated. Taking advantage of the effect of Ag⁺ ions, the regulation of CPN-based light-harvesting system by Ag⁺ is achieved for the first time. The antenna effect could be up to 2.3 times the original value by adding Ag⁺ ions. The present work provides a new approach to regulate the antenna effect of the light-harvesting system with the advantages of convenience, rapidity, low cost, and flexibility.

Fluorescence for biological logic gates

Biological logic gates are smart probes able to respond to biological conditions in behaviors similar to computer logic gates, and they pose a promising challenge for modern medicine. Researchers are creating many kinds of smart nanostructures that can respond to various biological parameters such as pH, ion presence, and enzyme activity. Each of these conditions alone might be interesting in a biological sense, but their interactions are what define specific disease conditions. Researchers over the past few decades have developed a plethora of stimuli-responsive nanodevices, from activatable fluorescent probes to DNA origami nanomachines, many explicitly defining logic operations. Whereas many smart configurations have been explored, in this review we focus on logic operations actuated through fluorescent signals. We discuss the applicability of fluorescence as a means of logic gate implementation, and consider the use of both fluorescence intensity as well as fluorescence lifetime.

"Plug and Play" logic gate construction based on chemically triggered fluorescence switching of gold nanoparticles conjugated with Cy3-tagged aptamer

Gold nanoparticles (AuNPs) conjugated with Cy3-tagged aptamer which can specifically recognize chloramphenicol (CAP) (referred to as AuNPs-AptCAP) are described. CAP can trigger the configuration change of CAP binding aptamer, and thus switching the fluorescence of AuNPs-AptCAP through changing the efficiency of the fluorescence resonance energy transfer (FRET) system with Cy3 as donors and AuNPs as recipients. AuNPs-AptCAP exhibits a linear range of CAP concentrations from 26.0 to 277 μg L^-1 with a limit of detection of 8.1 μg L^-1 when Cy3 was excited at 530 nm and emission was measured at 570 nm. More importantly, AuNPs-AptCAP can be utilized as signal transducers for the build-up of a series of logic gates including YES, PASS 0, INH, NOT, PASS 1, and NAND. Utilizing the principle of a metal ion-mediated fluorescence switch together with a strong metal ion chelator, the fluorescence of AuNPs-AptCAP could be modulated by adding metal ions and EDTA sequentially. Therefore, a "Plug and Play" logic system based on AuNPs-AptCAP has been realized by simply adding other components to create new logic functions. This work highlights the advantages of simple synthesis and facile fluorescence switching properties, which will provide useful knowledge for the establishment of molecular logic systems. Graphical abstract.

Excitation wavelength as logic operator

Multiple molecular logic gates were harvested on a single synthesized material, (E)-2-(2-hydroxy-3-methoxybenzylideneamino)phenol (MBAP), by combining excitation wavelength dependent multi-channel fluorescence outputs and the same chemical inputs. Interestingly, the effortless switching of logic behavior was achieved by simply tweaking the excitation wavelength and sometimes the emission wavelengths with no alteration of chemical inputs and the main device molecule, MBAP. Additionally, new generation purely optically driven memory units were designed on the same system supporting an almost infinite number of write-erase cycles since inter-conversion of memory states was completely free from chemical interferences and impurity issues. Two-way memory functions ("erase-read-write-read" and "write-read-erase-read") worked simultaneously on the same system and could be accessed by simple optical switching between two excitation and emission wavelengths. Our optically switchable device might outperform traditional multifunctional logic gates and memory devices that generally employ chemical triggers to switch functionality and memory states. These optically switchable multifunctional molecular logic gates and memory systems might drive smart devices in the near future with high energy efficiency, extended life span, structural and functional simplicity, exclusive reversibility and enhanced data storage density.

Fluorescent Terpolymers via In Situ Allocation of Aliphatic Fluorophore Monomers: Fe(III) Sensor, High-Performance Removals, and Bioimaging

Herein, purely aliphatic intrinsically fluorescent terpolymers, i.e., 1 and 2, are synthesized through one-pot solution polymerization via N-H functionalized and multi C-C/C-N coupled in situ protrusion of fluorescent monomers using two nonemissive monomers. These scalable terpolymers are suitable for highly selective Fe(III) sensing, high-performance exclusion of Fe(III), logic function and the imaging of normal mammalian Madin-Darby canine kidney and human osteosarcoma cancer cell lines. The structures of terpolymers, in situ attachment of fluorescent monomers, clusteroluminescence, adsorption-mechanism, and cell-imaging abilities are understood via unadsorbed and/or adsorbed microstructural analyses using ¹ H/¹³ C NMR, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, UV-vis spectroscopy, atomic absorption spectroscopy, thermogravimetric analysis, high-resolution transmission electron microscopy, dynamic light scattering, fluorescence imaging, and fluorescence lifetime. The geometries, electronic structures, location of fluorophores, and singlet-singlet absorption and emission of terpolymers are examined using density functional theory (DFT) and time-dependent DFT. For the precise identification of fluorophores, transition from occupied natural transition orbitals (NTOs) to unoccupied NTOs is computed. For 1/2, limit of detection (LOD) values and adsorption capacities are 6.0 × 10^-7 /8.0 × 10^-7 m and 147.82/120.56 mg g^-1 at pH_i = 7.0 and 303 K, respectively. The overall properties of 1 are more advantageous compared to 2 in sensing, cell imaging, and adsorptive exclusion of Fe(III).

MIL-61 and Eu3+@MIL-61 as Signal Transducers To Construct an Intelligent Boolean Logical Library Based on Visualized Luminescent Metal-Organic Frameworks

MIL-61 and its postsynthesis product (Eu³⁺@MIL-61) are employed as signal transducers to construct a series of basic logic gates (NOT, NAND, INHIBIT, and XNOR) on account of their simple synthetic process and fascinating luminescent properties. Also, a two-output combinational logic gate and a cascaded logic gate can be constructed on these two signal transducers by changing the inputs. In this logic gate library system, the fluorescence of MIL-61 (λ_395nm) or Eu³⁺@MIL-61 (λ_615nm) is used as outputs with a threshold of 0.5. The advantage of this boolean logical library is that the two signal transducers are readily available and cost effective. In addition, the luminescence change is visible to the naked eye under a UV lamp, which is more convenient in application. More importantly, it presents a new route for the design of a molecular logic gate library based on luminescent metal-organic frameworks. And for further application, we experimentally construct two logic devices (a 4-to-2 encoder and a parity checker) based on Eu³⁺@MIL-61 to perform nonarithmetic information.

Probe computing model based on small molecular switch

Background

DNA is a promising candidate for the construction of biological devices due to its unique properties, including structural simplicity, convenient synthesis, high flexibility, and predictable behavior. And DNA has been widely used to construct the advanced logic devices.

Results

Herein, a molecular probe apparatus was constructed based on DNA molecular computing to perform fluorescent quenching and fluorescent signal recovery, with an ’ ON/OFF’ switching function. In this study, firstly, we program the streptavidin-mediated fluorescent quenching apparatus based on short-distance strand migration. The variation of fluorescent signal is acted as output. Then DNAzyme as a switching controller was involved to regulate the fluorescent signal increase. Finally, on this base, a cascade DNA logic gate consists of two logic AND operations was developed to enrich probe machine.

Conclusion

The designed probe computing model can be implemented with readout of fluorescence intensity, and exhibits great potential applications in the field of bioimaging as well as disease diagnosis.

Studies on a multifunctional chromo-fluorogenic sensor for dual channel recognition of Zn2+ and CN− ions in aqueous media: mimicking multiple molecular logic gates and memory devices

A new effectual naphthalene-based azomethine receptor has been systematically designed and synthesized as a selective colorimetric and fluorescent chemosensor for dual channel detection of cations and anions in aqueous environments.

Nucleobases, nucleosides, and nucleotides: versatile biomolecules for generating functional nanomaterials

The incorporation of biomolecules into nanomaterials generates functional nanosystems with novel and advanced properties, presenting great potential for applications in various fields. Nucleobases, nucleosides and nucleotides, as building blocks of nucleic acids and biological coenzymes, constitute necessary components of the foundation of life. In recent years, as versatile biomolecules for the construction or regulation of functional nanomaterials, they have stimulated interest in researchers, due to their unique properties such as structural diversity, multiplex binding sites, self-assembly ability, stability, biocompatibility, and chirality. In this review, strategies for the synthesis of nanomaterials and the regulation of their morphologies and functions using nucleobases, nucleosides, and nucleotides as building blocks, templates or modulators are summarized alongside selected applications. The diverse applications range from sensing, bioimaging, and drug delivery to mimicking light-harvesting antenna, the construction of logic gates, and beyond. Furthermore, some perspectives and challenges in this emerging field are proposed. This review is directed toward the broader scientific community interested in biomolecule-based functional nanomaterials.

Solvent Polarity-Dependent Behavior of Aliphatic Thiols and Amines toward Intriguingly Fluorescent AuAgGSH Assembly

Highly stable fluorescent glutathione (GSH)-protected AuAg assembly has been synthesized in water under UV irradiation. The assembly is composed of small Ag₂/Ag₃ clusters. These clusters gain stability through synergistic interaction with Au(I) present within the assembly. This makes the overall assembly fluorescent. Here, GSH acts as a reducing as well as stabilizing agent. The assembly is so robust that it can be vacuum-dried to solid particles. The as-obtained solid is dispersible in nonaqueous solvents. The interaction between solvent and the assembly provides stability to the assembly, and the assembly shows fluorescence. It is interesting to see that the behavior of long-chain aliphatic thiols or amines toward the fluorescent assembly is altogether a different phenomenon in aqueous and nonaqueous mediums. The assembly gets ruptured in water due to direct interaction with long-chain thiols or amines, whereas in nonaqueous medium, solvation of added thiols or amines becomes pronounced, which hinders the interaction of solvent with the assembly. However, the fluorescence of the assembly is always quenched with thiols or amines no matter what the solvent medium is. In aqueous medium, the fluorescence quenching by aliphatic thiol or amine becomes pronounced with successive decrease in their chain length, whereas in nonaqueous medium, the trend is just reversed with chain length. The reasons behind such an interesting reversal of fluorescence quenching in aqueous and nonaqueous solvents have been discussed explicitly. Again, in organic solvents, thiol or amine-induced quenched fluorescence is selectively recovered by Pb(II) ion without any alteration of excitation and emission maxima. This phenomenon is not observed in water because of the ruptured fluorescent assembly. The fluorescence recovery by Pb(II) and unaltered emission peak only in nonaqueous solvent unequivocally prove the engagement of Pb(II) with thiols or amines, which in turn revert the original solvent-supported stabilization of the assembly.

A label-free visual platform for self-correcting logic gate construction and sensitive biosensing based on enzyme-mimetic coordination polymer nanoparticles

In molecular logic gates, the occurrence of erroneous procedures is a frequently encountered and critical problem in data transmission, and thus it is highly desirable to develop novel logic systems with self-correction abilities. Herein, based on the horseradish peroxidase (HRP)-like activity of the novel metal coordination polymer nanoparticles formed between Cu²⁺ and guanosine monophosphate (GMP), denoted as Cu-GMP CPNs, a label-free visual platform was constructed and successfully utilized for both self-correcting logic gate construction and sensitive biosensing. The HRP-mimicking ability of Cu-GMP CPNs was verified and utilized for the sensitive detection of both H₂O₂ and glucose. More importantly, a set of logic gates (AND, OR, NOR, INHIBIT, and XNOR) were fabricated, in which two intermediate outputs, i.e., color change and precipitate formation, were combined in an "AND" mode to produce the final output, and thus the as-proposed logic system exhibited the self-correction ability to automatically correct the erroneous intermediate outputs induced by interfering substances such as HRP. Moreover, in addition to the unique feature of self-correction, the as-proposed logic system also exhibited the advantages of simple operation, rapid response and easy detection of the visual outputs by the naked eye, thus expanding its practical applications to a variety of fields. Therefore, the label-free visual platform we have proposed here offers a promising strategy for logic gate fabrication and may pave the way for the development of novel molecular computing with self-correction abilities.

Biocomputing nanoplatforms as therapeutics and diagnostics

Biocomputing nanoplatforms are designed to detect and integrate single or multiple inputs under defined algorithms, such as Boolean logic gates, and generate functionally useful outputs, such as delivery of therapeutics or release of optically detectable signals. Using sensing modules composed of small molecules, polymers, nucleic acids, or proteins/peptides, nanoplatforms have been programmed to detect and process extrinsic stimuli, such as magnetic fields or light, or intrinsic stimuli, such as nucleic acids, enzymes, or pH. Stimulus detection can be transduced by the nanomaterial via three different mechanisms: system assembly, system disassembly, or system transformation. The increasingly sophisticated suite of biocomputing nanoplatforms may be invaluable for a multitude of applications, including medical diagnostics, biomedical imaging, environmental monitoring, and delivery of therapeutics to target cell populations.

Chemically induced fluorescence switching of carbon-dots and its multiple logic gate implementation

Investigations were carried out on the carbon-dots (C-dots) based fluorescent off - on (Fe(3 + )- S2O3(2-)) and on - off (Zn(2 + )- PO4(3-)) sensors for the detection of metal ions and anions. The sensor system exhibits excellent selectivity and sensitivity towards the detection of biologically important Fe(3 + ), Zn(2 + ) metal ions and S2O3(2-), PO4(3-) anions. It was found that the functional group on the C-dots surface plays crucial role in metal ions and anions detection. Inspired by the sensing results, we demonstrate C-dots based molecular logic gates operation using metal ions and anions as the chemical input. Herein, YES, NOT, OR, XOR and IMPLICATION (IMP) logic gates were constructed based on the selection of metal ions and anions as inputs. This carbon-dots sensor can be utilized as various logic gates at the molecular level and it will show better applicability for the next generation of molecular logic gates. Their promising properties of C-dots may open up a new paradigm for establishing the chemical logic gates via fluorescent chemosensors.