An Ionically Driven Molecular IMPLICATION Gate Operating in Fluorescence Mode

Nanoclusters with specific DNA overhangs: modifying configurability, engineering contrary logic pairs and the parity generator/checker for error detection

The most promising alternative for next-generation molecular computers is biocomputing, which uses DNAs as its primary building blocks to perform a Boolean operation. DNA nanoclusters (NCs) have emerged as promising candidates for biosensing applications due to their unique self-assembly properties and programmability. It has been demonstrated that adding DNA overhangs to DNA NCs improves their adaptability in identifying specific biomolecular interactions. A recent proposal in DNA computing is the concept of "contrary logic pairs (CLPs)" executed by employing a DNA hybrid architecture as a universal platform. We have designed thymine overhang-modified DNA-templated NCs (T-Au/Ag NCs). These NCs serve as a chemosensing ensemble platform, where the presence of HgII ions mediates the formation of M-Au/Ag NCs. The resulting NCs exhibit the capability to drive elementary CLPs (YES, NOT, OR, NOR, INH and IMP) as well as complex logic operations (XOR and XNOR). Additionally, they can be utilized for advanced non-arithmetic DNA logic devices like a parity generator (pG) and a parity checker (pC) for "error detection". Bit errors are an unavoidable and common occurrence during any computing. A cascade of XOR operations was used to evaluate these errors by introducing the pG and pC at the transmitting (TX) and receiving (RX) ends in binary transmission, respectively, which has devastating implications for reliable logic circuits, especially in advanced logic computation. Moreover, an even/odd natural number from 0 to 9 distinguishable pC was designed based on a dual-source responsive computing platform. This work offers inspiring avenues for a cost-effective strategy to construct highly-intelligent DNA computing devices by enhancing the multi-input responsive single DNA platform concept.

Multi-Light-Responsive Upconversion-and-Downshifting-Based Circularly Polarized Luminescent Switches in Chiral Metal-Organic Frameworks

Metal-organic frameworks (MOFs) have attracted tremendous attention for several novel applications. However, functional MOFs with light-responsive circularly polarized luminescence (CPL) are not examined in detail. Therefore, a dual CPL switch exhibiting both upconversion (UC) and downshifting (DS) CPL in the solid state is constructed by loading a luminescent diarylethene derivative (DAEC) and UC nanoparticles (UCNPs) into chiral MOFs. The chiral MOF⊃DAEC composites exhibit both photoswitchable luminescence and DS-CPL properties under alternating UV and visible light irradiation. Additionally, a reversible UC-CPL switch is realized using near-infrared (NIR) and visible light irradiation by introducing energy-level-matched UCNPs and DAEC into the chiral MOFs. The dissymmetry factor (g_lum ) of UC-CPL is noted to be significantly amplified through energy transfer compared to that of DS-CPL, which indicates that the information on circular polarization can be manipulated by altering the incident light. A chiroptical logic circuit with a 2D information output is designed with UV, visible, and NIR light as inputs by setting a rational threshold.

Multiple chiroptical switches and logic circuit based on salicyl‒ imine‒chitosan hydrogel

A chitosan-based chiral hydrogel was fabricated by grafting achiral salicylaldehyde (SA) on chitosan chains, followed by supramolecular assembly (CS-SA hydrogel hereafter). The structures and properties of the CS-SA hydrogel were characterized and investigated. The results indicated that the swelling ability of the CS-SA hydrogel depended on the medium pH and crosslinking degree. Circular dichroism measurements revealed that the chiral information of the chitosan was successfully transcribed to the achiral salicylic chromophores through imine bonds. Chiroptical switches based on acid-base responses of the imine bond and the OH fragment of SA and the swelling properties of the CS-SA hydrogel were fabricated, which is first reported for a chitosan-based hydrogel. In addition, a gel film showed good fatigue resistance under external stimuli. IMPLICATION, INHIBIT, and PASS logic gates and a logic circuit based on the chiroptical switches were successfully designed. This study suggests a new method of constructing biobased chiral functional materials.

Elucidating sensing mechanisms of a pyrene excimer-based calix[4]arene for ratiometric detection of Hg(ii) and Ag(i) and chemosensor behaviour as INHIBITION or IMPLICATION logic gates

This article reports the synthesis and characterisation of two lower rim calix[4]arene derivatives with thiourea as spacer and pyrene or methylene-pyrene as fluorophore. Both derivatives exhibit a fluorimetric response towards Hg²⁺, Ag⁺ and Cu²⁺. Only methylene-pyrenyl derivative 2 allows for selective detection of Hg²⁺ and Ag⁺ by enhancement or decrease of excimer emission, respectively. The limits of detection of 2 are 8.11 nM (Hg²⁺) and 2.09 nM (Ag⁺). DFT and TD-DFT computational studies were carried out and used to identify possible binding modes that explain the observed response during fluorescence titrations. Calculations revealed the presence of different binding sites depending on the conformation of 2, which suggest a reasonable explanation for non-linear changes in fluorescence depending on the physical nature of the interaction between metal centre and conformer. INHIBITION and IMPLICATION logic gates have also been generated monitoring signal outputs at pyrene monomer (395 nm) and excimer (472 nm) emission, respectively. Thus 2 is a potential primary sensor towards Ag⁺ and Hg²⁺ able to configure two different logic gate operations.

Illuminating Diverse Concomitant DNA Logic Gates and Concatenated Circuits with Hairpin DNA-Templated Silver Nanoclusters as Universal Dual-Output Generators

Exquisite administration of a new type of hairpin DNA-templated silver nanoclusters (H-AgNCs) as universal dual-output generators in DNA-based logic systems is reported. Diverse concomitant contrary logic gates (CCLGs) with opposite functions (YES^{^} NOT, OR^{^} NOR, INHIBIT^{^} IMPLICATION, XOR^{^} XNOR, and MAJORITY^{^} MINORITY) and extended concatenated logic circuits are presented and some of them perform specific functions, such as parity generators and checkers. The introduction of H-AgNCs as noncovalent signal reporters avoids tedious and high-cost labeling procedures. Of note, the concomitant feature of CCLGs attributed to the dual-emitter AgNCs conduces to reducing the time and cost to devise multiple logic gates. As compared to previous ones, this design eliminates numerous substances (e.g., organic dyes) and unstable components (hydrogen peroxide), which not only decreases the complexity of logic performs and improves repeatability of operation, but also makes it convenient to connect distinct DNA-based logic gates. It is worthy to anticipate that the cost-effective strategy will inspire researchers to develop much more complex logic systems and contribute to the field of molecular computing.

A selective chemosensor and fluorescence probe for relay recognition of cations and fluoride ions in aqueous media with logic gate function

Cation to anion relay recognition was studied for the first time with sequential specificity (Cu²⁺ → F^- or Co²⁺ → F^-) using a fluorescence "ON-OFF-ON" mechanism. L₁ is a receptor with high selectivity for F^-, Cu²⁺ and Co²⁺ ions in the solution of DMSO/H₂O with a 9:1 vol ratio. Absorption and fluorescence spectra were used to investigate the sensing process. Fluorescent emission intensity of L₁ at 324 is quenched (switch-Off) after the addition of Cu²⁺ and Co²⁺. Surprisingly, complex L₁ + Cu²⁺ or L₁ + Co²⁺ is restored with addition of F^- into the compound (switch-On). Consequently, implication (from emission) and inhibit (from absorption) logic gates are constructed at molecular level. The gates operate in fluorescence and absorption modes when Cu²⁺ and F^- or Co²⁺ and F^- are used as input materials and the fluorescence intensity signal as outputs. Based on reversible and reproducible system, a sequential memory unit with integrated ''Writing-Reading-Erasing-Reading'' behavior, is developed.

A Schiff base receptor as a fluorescence turn-on sensor for Ni2+ ions in living cells and logic gate application

A new receptor (R) with easily available “off–on–off” colorimetric and fluorescent responses was synthesized and characterized using ¹H NMR, ¹³C NMR, and ESI-MS studies.

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.

Triplex DNA logic gate based upon switching on/off their structure by Ag(+)/cysteine

The formation of intramolecular triplex DNA can be regulated by Ag(+) and Cys (cysteine), which switch off/on the fluorescence of the oligonucleotides, 5'-TAMRA-TTC TCT TCC TCT TCC TTC TGA CGA CAG TTG ACT CTT CCT TCT CCT TCT CTT-BHQ-2-3' (Oligo 1) and 3'-GAA GGA AGA GGA AGA GAA-5' (Oligo 2). Based on this principle, sensors for Ag(+) and Cys are developed. The sensor for Ag(+) has a linear range of 2.5 nM-40 nM and a detection limit of 1.8 nM, whereas the sensor for Cys has a linear range of 10.0 nM-120.0 nM and a detection limit of 8.2 nM. Furthermore, the fluorescence is reversible with the alternate addition of Ag(+) and Cys. We constructed a DNA logic gate using Ag(+) and Cys as the input, and the fluorescence intensity as the output. The DNA logic gate is simple; moreover, it has a fast response and good reversibility.

A Chiroptical Logic Circuit Based on Self-Assembled Soft Materials Containing Amphiphilic Spiropyran

A chiral logic circuit is proposed based on the multiple chiroptical responsiveness of a supramolecular gel material. The gel is fabricated by mixing a chiral gelator and a spiropyran derivative. Chiral responsiveness including the chiral switch and the logic gate is realized through the combined chirality transfer, photochromism, and acidichromism of the system.

A highly efficient and selective coumarin based fluorescent probe for colorimetric detection of Fe3+and fluorescence dual sensing of Zn2+and Cu2+

A new coumarin based Schiff-base chemosensor was synthesized and evaluated. Based on Job’s plot,¹H NMR titration, ESI-MS and B-H plot, the structure of ligand and its metal ion is 1 : 1 stoichiometry. It also exhibits a binary logic function.

A dithienosilole-based fluorescent chemosensor for multiple logic operations at the molecular level

A chemosensor consisting of two terpyridines covalently linked to a dithienosilole unit (1) has been synthesized, and its optical and metal sensing properties have been investigated. Due to the metal-organic coordination function, 1 can bind with many transition metal ions and display different fluorescence responses that cause it to function as a "turn-off" fluorescent chemosensor. A significant bathochromic shift in the fluorescence spectra is observed in the presence of Zn(2+). Meanwhile, the emission of 1 is weakened upon exposure to Ag(+) and Fe(2+) and completely quenched by Ni(2+), Co(2+), and Cu(2+). Based on the observed results, several logic gates, such as XNOR, INHIBIT, and IMPLICATION, have been achieved by controlling the chemical inputs.

An efficient and ultrasensitive rhodamine B-based reversible colorimetric chemosensor for naked-eye recognition of molybdenum and citrate ions in aqueous solution: sensing behavior and logic operation

In this paper we manifest a novel rhodamine B (RhB) based colorimetric chemosensor for molybdenum and citrate ions (Cit(3-)) in an absolutely aqueous media. It has been identified as highly sensitive probe for Mo(6+) which responds at 4.0 nmol L(-1) concentration levels. RhB while combined with Mo(6+) in aqueous solution displays a color changing from pink to purple which could be quickly dissociated by the addition of citrate in this system so that reversible color changes from purple to pink can be achieved. The comparison of this method with some other methods for citrate indicates that this is the only method which can detect citrate in aqueous solution by color changes. This chemosensor can be applied for quantification of citrate with a linear range covering from 1.67×10(-7) to 1.22×10(-5) M and a detection limit of 2.0×10(-8) M. Moreover, the response of the chemosensor toward Mo(6+) and citrate is fast. In addition, based on above sensing mechanism, an IMPLICATION logic operation can be achieved using Mo(6+) ion and Cit(3-) as the inputs, making RhB a promising candidate for further applications in molecular logic devices and also indicates that RhB is suitable for the detection of Mo(6+) and Cit(3-) ions in real samples.

A novel coumarin based molecular switch for dual sensing of Zn(ii) and Cu(ii)

New coumarin based molecular switch for Zn²⁺ and Cu²⁺ presents a tunable system comprising of two INHIBIT logic gates with Zn²⁺ and Cu²⁺ or Zn²⁺ and EDTA as chemical inputs. IMPLICATION logic gate is obtained with Cu²⁺ and EDTA as chemical inputs.

Interlocked DNA nanostructures controlled by a reversible logic circuit

DNA nanostructures constitute attractive devices for logic computing and nanomechanics. An emerging interest is to integrate these two fields and devise intelligent DNA nanorobots. Here we report a reversible logic circuit built on the programmable assembly of a double-stranded (ds) DNA [3]pseudocatenane that serves as a rigid scaffold to position two separate branched-out head-motifs, a bimolecular i-motif and a G-quadruplex. The G-quadruplex only forms when preceded by the assembly of the i-motif. The formation of the latter, in turn, requires acidic pH and unhindered mobility of the head-motif containing dsDNA nanorings with respect to the central ring to which they are interlocked, triggered by release oligodeoxynucleotides. We employ these features to convert the structural changes into Boolean operations with fluorescence labelling. The nanostructure behaves as a reversible logic circuit consisting of tandem YES and AND gates. Such reversible logic circuits integrated into functional nanodevices may guide future intelligent DNA nanorobots to manipulate cascade reactions in biological systems.

Sugar-based molecular computing by material implication

A method to integrate an (in principle) unlimited number of molecular logic gates to construct complex circuits is presented. Logic circuits, such as half- or full-adders, can be reinterpreted by using the functional completeness of the implication function (IMP) and the trivial FALSE operation. The molecular gate IMP is represented by a fluorescent boronic acid sugar probe. An external wiring algorithm translates the fluorescent output from one gate into a chemical input for the next gate on microtiter plates. This process is demonstrated on a four-bit full adder.

Fluorometric/colorimetric logic gates based on BODIPY-functionalized mesoporous silica

We have demonstrated that metal ions acting as modulators in BODIPY-functionalized SiO₂ nanoparticles can generate absorbance changes in accordance with the operation of a half-adder digital circuit.

Integration of the 1,2,3-triazole "click" motif as a potent signalling element in metal ion responsive fluorescent probes

In a systematic approach we synthesized a new series of fluorescent probes incorporating donor-acceptor (D-A) substituted 1,2,3-triazoles as conjugative π-linkers between the alkali metal ion receptor N-phenylaza-[18]crown-6 and different fluorophoric groups with different electron-acceptor properties (4-naphthalimide, meso-phenyl-BODIPY and 9-anthracene) and investigated their performance in organic and aqueous environments (physiological conditions). In the charge-transfer (CT) type probes 1, 2 and 7, the fluorescence is almost completely quenched by intramolecular CT (ICT) processes involving charge-separated states. In the presence of Na(+) and K(+) ICT is interrupted, which resulted in a lighting-up of the fluorescence in acetonitrile. Among the investigated fluoroionophores, compound 7, which contains a 9-anthracenyl moiety as the electron-accepting fluorophore, is the only probe which retains light-up features in water and works as a highly K(+)/Na(+)-selective probe under simulated physiological conditions. Virtually decoupled BODIPY-based 6 and photoinduced electron transfer (PET) type probes 3-5, where the 10-substituted anthracen-9-yl fluorophores are connected to the 1,2,3-triazole through a methylene spacer, show strong ion-induced fluorescence enhancement in acetonitrile, but not under physiological conditions. Electrochemical studies and theoretical calculations were used to assess and support the underlying mechanisms for the new ICT and PET 1,2,3-triazole fluoroionophores.

Simple and universal platform for logic gate operations based on molecular beacon probes

A new platform technology is herein described with which to construct molecular logic gates by employing the hairpin-structured molecular beacon probe as a basic work unit. In this logic gate operation system, single-stranded DNA is used as the input to induce a conformational change in a molecular beacon probe through a sequence-specific interaction. The fluorescent signal resulting from the opening of the molecular beacon probe is then used as the output readout. Importantly, because the logic gates are based on DNA, thus permitting input/output homogeneity to be preserved, their wiring into multi-level circuits can be achieved by combining separately operated logic gates or by designing the DNA output of one gate as the input to the other. With this novel strategy, a complete set of two-input logic gates is successfully constructed at the molecular level, including OR, AND, XOR, INHIBIT, NOR, NAND, XNOR, and IMPLICATION. The logic gates developed herein can be reversibly operated to perform the set-reset function by applying an additional input or a removal strand. Together, these results introduce a new platform technology for logic gate operation that enables the higher-order circuits required for complex communication between various computational elements.

Input-dependent induction of oligonucleotide structural motifs for performing molecular logic

The K(+)-H(+)-triggered structural conversion of multiple nucleic acid helices involving duplexes, triplexes, G-quadruplexes, and i-motifs is studied by gel electrophoresis, circular dichroism, and thermal denaturation. We employ the structural interconversions for perfoming molecular logic operations, as verified by fluorimetry and colorimetry. Short G-rich and C-rich cDNA and RNA single strands are hybridized to produce four A-form and B-form duplexes. Addition of K(+) triggers the unwinding of the duplexes by inducing the folding of G-rich strands into DNA- or RNA G-quadruplex mono- and multimers, respectively. We found a decrease in pH to have different consequences on the resulting structural output, depending on whether the C-rich strand is DNA or RNA: while the protonated C-rich DNA strand folds into at least two isomers of a stable i-motif structure, the protonated C-rich RNA strand binds a DNA/RNA hybrid duplex to form a Y·RY parallel triplex. When using K(+) and H(+) as external stimuli, or inputs, and the induced G-quadruplexes as reporters, these structural interconversions of nucleic acid helices can be employed for performing logic-gate operations. The signaling mode for detecting these conversions relies on complex formation between DNA or RNA G-quadruplexes (G4) and the cofactor hemin. The G4/hemin complexes catalyze the H(2)O(2)-mediated oxidation of peroxidase substrates, resulting in a fluorescence or color change. Depending on the nature of the respective peroxidase substrate, distinct output signals can be generated, allowing one to operate multiple logic gates such as NOR, INH, or AND.

Labile zinc-assisted biological phosphate chemosensing and related molecular logic gating interpretations

Herein, molecular fluorescence 'OFF-ON' behavior with aqueous addition of biological phosphate and Zn(2+) is studied with Zn(2)(slys)(2)Cl(2) [H(2)slys = 6-amino-2-{(2-hydroxybenzylidene)amino}hexanoic acid], a fluorescent water-soluble complex, using various spectroscopic tools (e.g., (31)P NMR, UV-vis, emission, and CD spectroscopy) at the micromolar level. Adduct-dependent fluorescence intensity changes can be interpreted as a two-input (cation/anion) implication molecular logic gating system. A displacement study of PPi from the dizinc complex is also reported. Diphosphate and triphosphate addition/displacements were also studied. (31)P NMR spectroscopy shows gradual NMR peak shifts from bound ADP/GDP to free ADP/GDP with increasing [PPi]. In the emission spectrum, fluorescence quenching is shown: CD signal maxima decrease with addition of PPi. These displacement events are also tested with triphosphates (ATP, GTP), and their binding strength/displacement ability over ADP/GDP is quantified: PPi > ATP ≈ GTP (3.35 ± 0.77 × 10(4) M(-1) for PPi, 7.73 ± 1.79 × 10(3) M(-1) for ATP, 9.21 ± 2.88 × 10(3) M(-1) for GTP over 1·ADP). Many anions and cations were also screened for selectivity. Tubulin polymerization was assayed in the presence of 1 and its copper analogue which reflected a slight inhibition in polymerization.

Ion-tuned DNA/Ag fluorescent nanoclusters as versatile logic device

A novel kind of versatile logic device has been constructed utilizing ion-tuned DNA/Ag fluorescent nanoclusters, with K(+) and H(+) as two inputs. A well-chosen hairpin DNA with a poly-C loop serves as the template for synthesizing two species of Ag nanoclusters. Several G-tracts and C-tracts on its two terminals enable the hairpin DNA to convert into the G-quadruplex and/or i-motif structures upon input of K(+) and H(+). Such a structural change remarkably influences the spectral behaviors of Ag nanoclusters. In particular, different species of Ag nanoclusters have distinct fluorescence responses to the input of K(+) and H(+). These unique features of DNA/Ag nanoclusters enable multiple logic operations via multichannel fluorescence output, indicating the versatility as a molecular logic device. By altering the specific sequence of the hairpin DNA, more logic gates can be constructed utilizing Ag nanoclusters.

Ultra-sensitive fluorescent sensor for Hg2+ based on a donor-acceptor-donor framework

A new fluoroionophore [E-4,4'-di(N-(2-pyridyl)amino)stilbene, E1] with a donor-acceptor-donor framework, which features a central stilbene (acceptor) fluorophore and two terminal pyridylamino (donor) ionophores, is reported. The probe displays an ultrasensitive fluorescence quenching response toward Hg(2+) in H(2)O/THF. Coordination of Hg(2+) to E1 affords a 2:1 complex, enabling the detection of Hg(2+) at a concentration as low as 4.4 × 10(-14) M. The interactions between the two species have been thoroughly characterized with UV-vis absorption spectroscopy, fluorescence spectroscopy, and nuclear magnetic resonance spectroscopy. Density functional theory calculations provide further insights into the nature of the fluorescence quenching response. In contrast, a fluorescent molecule with the donor-acceptor architecture, E-4-(N-(2-pyridyl)amino)stilbene (E4), exhibits a greatly attenuated fluorescence quenching response toward Hg(2+).

A molecular half-subtractor with Zn2+ and UV-light as inputs

The salen-type Schiff base (2,2'-bis(2-hydroxybenzylideneamino)-1,1'-binaphthyl (BHB)) has been synthesized and characterized. Exhibiting absorption and fluorescence changes in the presence of Zn(2+) in chloroform and ethanol mixed solution, BHB could be used as a fluorescent chemosensor for the detection of Zn(2+). Furthermore, by monitoring the fluorescence and absorbance as output signals, BHB can function as a combinatorial logic circuit for a molecular half-subtractor with Zn(2+) and UV irradiation as input variables.

Potassium-lead-switched G-quadruplexes: a new class of DNA logic gates

A cation-driven allosteric G-quadruplex DNAzyme (PW17) was utilized to devise a conceptually new class of DNA logic gate based on cation-tuned ligand binding and release. K(+) favors the binding of hemin to parallel-stranded PW17, thereby promoting the DNAzyme activity, whereas Pb(2+) induces PW17 to undergo a parallel-to-antiparallel conformation transition and thus drives hemin to release from the G-quadruplex, deactivating the DNAzyme. Such a K(+)-Pb(2+) switched G-quadruplex, in fact, functions as a two-input INHIBIT logic gate. With the introduction of another input EDTA, this G-quadruplex can be further utilized to construct a reversibly operated IMPLICATION gate.