Intelligent monitoring of the available lead (Pb) and cadmium (Cd) in soil samples based on half adder and half subtractor molecular logic gates

The available heavy metals in soil samples can cause the direct toxicity on ecosystems, plants, and human health. Traditional chemical extraction and recombinant bacterial methods for the available heavy metals assay often suffer from inaccuracy and poor specificity. In this work, we construct half adder and half subtractor molecular logic gates with molecular-level biocomputation capabilities for the intelligent sensing of the available lead (Pb) and cadmium (Cd). The available Pb and Cd can cleave DNAzyme sequences to release the trigger DNA, which can activate the hairpin probe assembly in the logic system. This multifunctional logic system can not only achieve the intelligent recognition of the available Pb and Cd according to the truth tables, but also can realize the simultaneous quantification with high sensitivity, with the detection limits of 2.8 pM and 25.6 pM, respectively. The logic biosensor is robust and has been applied to determination of the available Pb and Cd in soil samples with good accuracy and reliability. The relative error (Re) between the logic biosensor and the DTPA + ICP-MS method was from -8.1 % to 7.9 %. With the advantages of programmability, scalability, and multicomputing capacity, the molecular logic system can provide a simple, rapid, and smart method for intelligent monitoring of the available Pb and Cd in environmental samples.

A Tb3+ ion encapsulated anionic indium-organic framework as logical probe for distinguishing quenching Fe3+ and Cu2+ ions

We successfully synthesized a stable anionic microporous metal-organic framework (MOF) HDU-1 ([Me2NH2]2In2[(TATAB)4(DMF)4](DMF)4(H2O)4) and constructed a fluorescent probe Tb@HDU-1 by an exchange strategy. Because of its suspension distinct fluorescent response of Tb(III) characteristic transition and ligand emission, the Tb@HDU-1 can be used as fluorescent probe for sensing towards Fe3+ and Cu2+ ions. It is surprising that Tb@HDU-1 is used as a ratiometric fluorescent probe for Cu2+ ions while only single peak detection for Fe3+ ions, which describes a particular rare example of a sensor based on Ln-MOFs to distinguish quenching Fe3+ and Cu2+ ions. Hence we designed a molecular logic gate device for making the distinction of Fe3+ and Cu2+ ions more clearly and appropriately. In addition, the different quenching effect between Fe3+ and Cu2+ ions may be ascribed to the differences of competitive absorption and interaction between frameworks and metal ions.

Host-guest interaction aided Zinc carry and delivery by ESIPT active 2-(2'-hydroxyphenyl)benzoxazole

The effect of solvents and supramolecular hosts on the binding of metal ion with an excited state intramolecular proton transfer (ESIPT) active fluorophore 2-(2'-hydroxyphenyl)benzoxazole (HPBO) are investigated to scrutinize a possible metal ion carry and delivery system. The fluorophore forms strong fluorescent complex with Zn²⁺ ion. In aqueous medium, β-cyclodextrin (β-CD) breaks the HPBO-Zn²⁺ complex and encapsulate the freed fluorophore. Hence, the initially blocked ESIPT process is restored by forming an inclusion complex with the host molecules. However, in dimethyl sulphoxide (DMSO), β-CD does not break the complex. But cucurbit[7]uril (CB-7) breaks the complex in both DMSO and water. The tuned emission characteristics are considered for constructing different molecular logic gates. BUFFER, NOT, PASS, IMPLICATION and INHIBIT logic operations are substantiated based on Zn²⁺, CB-7 and β-CD response.

An indicator displacement assay-based optical chemosensor for heparin with a dual-readout and a reversible molecular logic gate operation based on the pyranine/methyl viologen

We have reported an optical indicator displacement assay (IDA) for heparin with a UV-vis absorbance and fluorescence dual-readout based on pyranine/methyl viologen (MV²⁺). Upon introducing heparin, pyranine/MV²⁺ shows a clearly observable increase in UV-vis absorbance and a turn-on of the fluorescence signal. We have demonstrated that the ionic nature of buffers significantly affects the pyranine displacement and the zwitterionic HEPES was most suitable for heparin sensing. After careful screening of experimental conditions, the pyranine/MV²⁺-based optical chemosensor exhibits a fast, sensitive, and selective response toward heparin. It shows dynamic linear concentration of heparin in the ranges of 0.1-40 U·mL^-1 and 0.01-20 U·mL^-1 for the absorptive and fluorescent measurements, respectively, which both cover the clinically relevant levels of heparin. As with the animal experiments, the optical chemosensor has been demonstrated to be selective and effective for heparin level qualification in rat plasma. The chemosensor is readily accessible, cost-effective, and reliable, which holds a great promise for potential application on clinical and biological studies. Furthermore, this IDA system can serve as an IMPLICATION logic gate with a reversible and switchable logical manner.

Designed multifunctional ratiometric fluorescent probe for directly detecting fluoride ion/ dichromate and indirectly monitoring urea

UiO-66-NH₂@eosin Y composite was obtained by confining eosin Y (EY) into the cavities of Zr-MOF and could emit two fluorescence peaks at 453 and 543 nm at an excitation wavelength of 355 nm. This multi-responsive and multifunctional ratiometric fluorescent nanoprobe not only enable directly distinct detection of F^-/Cr₂O₇^2- with ultra-high selectivity and sensitivity, but also could indirectly monitor the concentration of urea based on unique enzymatic hydrolysis reaction. The multifunctional probe was utilized for fluorescence labeling F-/Cr₂O₇^2- in sweat latent fingerprint through an environmentally friendly powder strategy and exhibited obvious luminescence visualization changes. Notably, the corresponding portable on-line test strips of probe for detection of F^- and Cr₂O₇^2- were made for monitoring the levels of F^- and Cr₂O₇^2-. Furthermore, the probe was applied to evaluate the degrees of F^-/Cr₂O₇^2- in HepG-2 cell and urea in serum with superior results,which indicate the potential application of the as-synthesized UiO-66-NH₂@EY as multifunctional probe for the detection of F^-, Cr₂O₇^2- and urea in biological samples. Finally, in order to extend the device-based applications of probe, an AND-OR-coupled molecular logic gate was put on agenda.

Simultaneous sensing γ-glutamyl transpeptidase and alkaline phosphatase by robust dual-emission carbon dots

Rapid, convenient, sensitive and simultaneous detection of distinct enzymes is urgently needed for diagnosis, therapeutics and prognostic of related diseases. Here, a new strategy for simultaneous monitoring γ-glutamyl transpeptidase (GGT) and alkaline phosphatase (ALP) activity has been fabricated based on dual-emission carbon dots (CDs). CDs were prepared by solvothermal treatment of Actinidia chinensis, which presents two fluorescent emissions at 471 nm (blue channel) and 671 nm (red channel). GGT and ALP activity can be detected based on inner filter effect (IFE) and static quenching effect (SQE) of blue and red channels of CDs, respectively. Linear ranges were 2.5-90 U L^-1 and 5-200 U L^-1, and limit of detection (LOD) were 0.71 U L^-1 and 1.2 U L^-1 for GGT and ALP, respectively. Developed CDs can monitor GGT and ALP activity in human serum samples with satisfied recoveries (99.3%-108.6% for GGT, 98.4%-105.4% for ALP). Furthermore, the combination of CDs to sense GGT and ALP activity with OR logic gate can predict human health status. The design and application of dual-emission CDs can also be extended as promising tools to detect multianalytes using different channel signals.

"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.

A hydrophilic naphthalimide-based fluorescence chemosensor forCu2+ ion: Sensing properties, cell imaging and molecular logic behavior

In this work, a hydrophilic naphthalimide-based fluorescence chemosensor (sensor 1) was synthesized for Cu²⁺ recognition, in which 2-(2-aminoethoxy)ethanol was introduced to improve the hydrophily and Schiff base acted as the multidentate ligand for Cu²⁺. The effect factors, sensing mechanism and regenerability of sensor 1 for Cu²⁺ sensing were systematically investigated. It was found that sensor 1 displayed a long emission wavelength of 532 nm upon excited in visible light region (436 nm), and the good water solubility made it utilized in aqueous media. It could selectively react with Cu²⁺ over other common metal ions to form a 2:1 complex within 1 min and result in significant fluorescence quench. The fluorescence change was linear to 0.5-10.0 μmol L^-1 of Cu²⁺ with a low detection limit of 3.74 × 10^-8 mol L^-1. Sensor 1 has been successfully utilized for analyzing Cu²⁺ in water samples as well as imaging cellular Cu²⁺. Moreover, in view of fluorescence "on-off-on" switches of sensor 1 induced by Cu²⁺ and EDTA, an IMPLICATION logic gate was constructed based on fluorescence mode with Cu²⁺ and EDTA as inputs.

Execution of julolidine based derivative as bifunctional chemosensor for Zn2+ and Cu2+ ions: Applications in bio-imaging and molecular logic gate

A simple julolidine based chemosensor (JT) was designed and synthesized by single condensation step. JT displayed excellent selectivity and sensitivity with on-off responses towards Zn²⁺ and Cu²⁺ over other biologically relevant metal ions in aqueous media. Upon addition of Zn²⁺ ions, JT exhibited a significant blue shift in emission followed by turn-on enhancement while with Cu²⁺, the fluorescence intensity of JT was completely vanished. The 1:1 binding affinity between JT and Zn²⁺/Cu²⁺ was proposed by Job's plot analysis. The detection limit for Zn²⁺ and Cu²⁺ ions reached at 3.5 × 10^-8 M and 1.46 × 10^-6 M, respectively. The sensing mechanism of JT with Zn²⁺/Cu²⁺ was supported by DFT calculations. Based on photophysical studies and its reversibility environment with EDTA, molecular logic gates were fabricated. Furthermore, JT was successfully established to detect intracellular Zn²⁺ ions in live cells by turn-on response.

A reversible and dual responsive sensing approach for determination of ascorbate ion in fruit juice, biological, and pharmaceutical samples by use of available triaryl methane dye and its application to constructing a molecular logic gate and a set/reset memorized device

Since dyes are available in huge quantities and have the well-established chemistry involved in their synthesis, their use in chemosensing could be continued. In the current study, a new and reversible colorimetric and fluorometric chemosensor based on available triaryl methane dye (brilliant green (BG)) - phosphotungstic acid (PTA) complex has been designed for determination of ascorbate (AscH^-1) ion in water/DMSO (90:10v/v, 1.0mmolL^-1 HEPES, pH7.0). The "ON-OFF" fluorescence and colorimetric responses of this ion association complex to AscH^-1 were based on a displacement mechanism. For the detection of AscH^-1, the linear ranges achieved for UV-Vis absorbance and fluorescence experiments were 3.9-62.6μmolL^-1 and 1.9-85.4μmolL^-1, respectively. The limits of detection for both of them were also calculated to be 0.4 and 0.2μmolL^-1. The proposed method was also successfully utilized for rapid recognition of ascorbate in juice samples, human serum, and the formulation of supplement products. Moreover, the proposed chemosensor capability of functioning as INHIBITION-type sensor with PTA and AscH^-1 as chemical inputs was indicated by the investigation of the molecular logic behavior of this chemosensor. Eventually, a sequential memory unit displaying "Write-Read-Erase-Read" function could be integrated based on the reversible and reproducible system.

Dynamically NAND gate system on DNA origami template

Molecular logic gates play an important role in many fields and DNA-based logic gates are the basis of DNA computers. A dynamically NAND gate system on the DNA origami template is established in this paper. Naturally, the system is stable in solution without any reaction. Different logical values are mapped into different DNA input strands. When logical values are entered into the system, the corresponding DNA input strands undergo a directed hybridization chain reaction (HCR) at corresponding positions on the DNA origami template. The operation results are identified by disassembly between the nanogold particles (AuNPs) and DNA origami template. The nanogold particles remain on the DNA origami template, indicating that the result is true; The nanogold particles are dynamically separated from the DNA origami template, indicating that the result is false. The simulation of the system through Visual DSD shows that the reaction strictly followed the designed direction, and no error products are generated during the reaction. These simulation results show that the system has the advantages of feasibility, stability and intelligence.

Fluorescein derived Schiff base as fluorimetric zinc (II) sensor via 'turn on' response and its application in live cell imaging

A novel Schiff base L composed of fluorescein hydrazine and a phenol functionalized moiety has been designed and prepared via cost-effective condensation reaction. The L is utilized for selective sensing of Zn²⁺ over other environmental and biological relevant metal ions in aqueous alcoholic solution under physiological pH range. The binding of Zn²⁺ to the receptor L is found to causes ~23 fold fluorescence enhancement of L. The 1:1 binding mode of the metal complex is established by combined UV-Vis, fluorescence, and HRMS (high-resolution mass spectroscopy) spectroscopic methods. The binding constant (K_a) for complexation and the limit of detection (LOD) of Zn²⁺ is calculated to be 2.86 × 10⁴ M^-1 and 1.59 μM, respectively. Further photophysical investigations including steady-state, time-resolved fluorescence analysis and spectral investigations including NMR (nuclear magnetic resonance), IR (infrared spectroscopy) suggest introduction of CHEF (chelation enhance fluorescence) with the suppression of CN isomerization and PET (photo-induced electron transfer) mechanism for the strong fluorescent response towards Zn²⁺. Finally, the sensor L is successfully employed to monitor a real-time detection of Zn²⁺ by means of TLC (thin layer chromatography) based paper strip. The L is used in the cell imaging study using African green monkey kidney cells (Vero cells) for the determination of exogenous Zn²⁺ by Immunofluorescence Assay (IFA) process.

Development of three ways molecular logic gate based on water soluble phenazine fluorescent 'selective ion' sensor

New hydrophilic fluorescent selective ion sensor based on phenazine and phthalazine moieties, 1,1'-(phenazine-2,3-diyl)-bis(3-(1,4-dihydroxyphthalazin-6-yl)urea) (1), has been designed, synthesized and characterized. Interestingly, sensor 1 exhibits prominent "turn-on" and "turn-off" fluorogenic signaling at 580 nm towards Fe²⁺ & AcO^- and Sr²⁺ & Cu²⁺, respectively. The fluorescence titration experiments shed light on the nature of the interaction between 1 and guest molecules (Fe²⁺, Sr²⁺, Cu²⁺ and AcO^-), which divulge that 1 is flexible enough to orient itself according to the size of the guest molecule. Water mediated excited-state intramolecular proton transfer (ESIPT) and photo-induced electron transfer (PET) mechanisms are responsible for the dual behavior of 1, which binds with guest molecules in 1:1 stoichiometry. Based on the significant duplex fluorescence response of 1, a molecular logic gate keypad lock with sixteen "on" passwords for a storage system has been developed.

A highly selective and reversible fluorescence "OFF-ON-OFF" chemosensor for Hg2+ based on rhodamine-6G dyes derivative and its application as a molecular logic gate

A new rhodamine-6G-based chemosensor X was designed and synthesized for the colorimetric and fluorometric detection of Hg²⁺. The chemosensor X responsed to Hg²⁺ had good sensitivity, high selectivity and excellent reversibility in HEPES buffer (10 mM, pH 7.4)/CH₃CN (40:60, V/V). The recognition mechanism of X toward Hg²⁺ was evaluated by Job's plot, IR and MS. Meanwhile, X-Hg²⁺ fluorescence lifetime was also measured. It was interesting that X displayed favorable reversibility to form an "off-on-off" type signaling behavior with the Hg²⁺-induced emission spectra being quenched by I^-. Furthermore, it could be applied as a molecular logic gate and test strips based on X exhibited a good reversibility selectivity to Hg²⁺.

Multi-ion detection and molecular switching behaviour of reversible dual fluorescent sensor

The selective chemosensing behaviour of imidazole bisthiocarbohydrazone (IBTC) towards F^- and Cu²⁺ are studied via colorimetric, UV-Visible, fluorescence spectra studies, and binding constants were calculated. The ¹H NMR titration study strongly support that the deprotonation of IBTC followed by the hydrogen bond formation via N1H1 and N2H2 protons with fluoride ion. The fluorescence inactive IBTC-Cu complex became fluorescence active in the presence of perchlorate (ClO₄^-) ion. The selective detection of perchlorate ion was also explained. The F^- sensing mechanism of IBTC has been investigated by Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT) methods. The theoretical outcomes well reproduce the experimental results. And it concluded the NH protons, nearby the imine group was first captured by the added F^- ion and then deprotonation happened followed by the formation of hydrogen bond. The IBTC found good reversibility character with the alternative addition of Ca²⁺ and F^-. The multi-ion detection of IBTC was used to construct the NOR, OR and INHIBITION molecular logic gates.

Nanozyme-based bio-barcode assay for high sensitive and logic-controlled specific detection of multiple DNAs

Since HCV and HIV share a common transmission path, high sensitive detection of HIV and HCV gene is of significant importance to improve diagnosis accuracy and cure rate at early stage for HIV virus-infected patients. In our investigation, a novel nanozyme-based bio-barcode fluorescence amplified assay is successfully developed for simultaneous detection of HIV and HCV DNAs with excellent sensitivity in an enzyme-free and label-free condition. Here, bimetallic nanoparticles, PtAu_NPs, present outstanding peroxidase-like activity and act as barcode to catalyze oxidation of nonfluorescent substrate of amplex red (AR) into fluorescent resorufin generating stable and sensitive "Turn On" fluorescent output signal, which is for the first time to be integrated with bio-barcode strategy for fluorescence detection DNA. Furthermore, the provided strategy presents excellent specificity and can distinguish single-base mismatched mutant from target DNA. What interesting is that cascaded INHIBIT-OR logic gate is integrated with biosensors for the first time to distinguish individual target DNA from each other under logic function control, which presents great application in development of rapid and intelligent detection.

Sensing behavior and logic operation of a colorimetric fluorescence sensor for Hg(2+)/Cu(2+) ions

A BODIPY-based 1 as a colorimetric fluorescence sensor was synthesized, and its metal sensing property was investigated. 1 displayed high selectivity and sensitivity towards Hg(2+) and Cu(2+) ions among 15 different metal cations. The addition of Hg(2+) and Cu(2+) ions into 1 in CH3CN resulted in a significant bathochromic shift of the UV absorption spectra from 533nm to 560nm and 593nm, respectively, changing the corresponding colors from pink to purple and blue. When excited at 530nm, the fluorescence intensity of 1 was quenched over 75% upon addition of Hg(2+) ions, while 1 with Cu(2+) ions exhibited significant fluorescence enhancement with a 23nm red-shift. Based on these results, three logic gates (OR, IMPLICATION, and INHIBIT) were obtained by controlling the chemical inputs.

Development of a sensor to study the DNA conformation using molecular logic gates

This communication reports our investigations on the Fluorescence Resonance Energy Transfer (FRET) between two laser dyes Acriflavine and Rhodamine B in absence and presence of DNA at different pH. It has been observed that energy transfer efficiency is largely affected by the presence of DNA as well as the pH of the system. It is well known that with increase in pH, DNA conformation changes from double stranded to single stranded (denaturation) and finally form random coil. Based on our experimental results two different types of molecular logic gates namely, XOR and OR logic have been demonstrated which can be used to have an idea about DNA conformation in solution.