Fluorescence-Based Multimodal DNA Logic Gates

The use of DNA structures in creating multimodal logic gates bears high potential for building molecular devices and computation systems. However, due to the complex designs or complicated working principles, the implementation of DNA logic gates within molecular devices and circuits is still quite limited. Here, we designed simple four-way DNA logic gates that can serve as multimodal platforms for simple to complex operations. Using the proximity quenching of the fluorophore-quencher pair in combination with the toehold-mediated strand displacement (TMSD) strategy, we have successfully demonstrated that the fluorescence output, which is a result of gate opening, solely relies on the oligonucleotide(s) input. We further demonstrated that this strategy can be used to create multimodal (tunable displacement initiation sites on the four-way platform) logic gates including YES, AND, OR, and the combinations thereof. The four-way DNA logic gates developed here bear high promise for building biological computers and next-generation smart molecular circuits with biosensing capabilities.

Design, synthesis, and biological evaluation of some 2-(3-oxo-5,6-diphenyl-1,2,4-triazin-2(3H)-yl)-N-phenylacetamide hybrids as MTDLs for Alzheimer's disease therapy

Inspite of established symptomatic relief drug targets, a multi targeting approach is highly in demand to cure Alzheimer's disease (AD). Simultaneous inhibition of cholinesterase (ChE), β secretase-1 (BACE-1) and Dyrk1A could be promising in complete cure of AD. A series of 18 diaryl triazine based molecular hybrids were successfully designed, synthesized, and tested for their hChE, hBACE-1, Dyrk1A and Aβ aggregation inhibitory potentials. Compounds S-11 and S-12 were the representative molecules amongst the series with multi-targeted inhibitory effects. Compound S-12 showed hAChE inhibition (IC50 value = 0.486 ± 0.047 μM), BACE-1 inhibition (IC50 value = 0.542 ± 0.099 μM) along with good anti-Aβ aggregation effects in thioflavin-T assay. Only compound S-02 of the series has shown Dyrk1A inhibition (IC50 value = 2.000 ± 0.360 μM). Compound S-12 has also demonstrated no neurotoxic liabilities against SH-SY5Y as compared to donepezil. The in vivo behavioral studies of the compound S-12 in the scopolamine- and Aβ-induced animal models also demonstrated attanuation of learning and memory functions in rats models having AD-like characteristics. The ex vivo studies, on the rat hippocampal brain demonstrated reduction in certain biochemical markers of the AD brain with a significant increase in ACh level. The Western blot and Immunohistochemistry further revealed lower tau, APP and BACE-1 molecular levels. The drosophilla AD model also revealed improved eyephenotype after treatment with compound S-12. The molecular docking studies of the compounds suggested that compound S-12 was interacting with the ChE-PAS & CAS residues and catalytic dyad residues of the BACE-1 enzymes. The 100 ns molecular dynamics simulation studies of the ligand-protein complexed with hAChE and hBACE-1 also suggested stable ligand-protein confirmation throughout the simulation run.

Design and development of benzyl piperazine linked 5-phenyl-1,2,4-triazole-3-thione conjugates as potential agents to combat Alzheimer's disease

Our present work demonstrates the molecular hybridization-assisted design, synthesis, and biological evaluation of 22 benzylpiperazine-linked 1,2,4-triazole compounds (PD1-22) as AD modifying agents. All the compounds were tested for their in vitro hChEs, hBACE-1, and Aβ-aggregation inhibition properties. Among them, compound PD-08 and PD-22 demonstrated good hChE and hBACE-1 inhibition as compared to standards donepezil and rivastigmine. Both compounds displaced PI from PAS at 50 µM concentration which was comparable to donepezil and also demonstrated anti-Aβ aggregation properties in self- and AChE-induced thioflavin T assay. Both compounds have shown excellent BBB permeation via PAMPA-BBB assay and were found to be non-neurotoxic at 80 µM concentration against differentiated SH-SY5Y cell lines. Compound PD-22 demonstrated an increase in rescued eye phenotype in Aβ-phenotypic drosophila AD model and amelioration of behavioral deficits in the Aβ-induced rat model of AD. The in-silico docking studies of compound PD-22 revealed a good binding profile towards CAS and PAS residues of AChE and the catalytic dyad of the BACE-1. The 100 ns molecular dynamics simulation studies of compound PD-22 complexed with AChE and BACE-1 enzymes suggested stable ligand-protein complex throughout the simulation run. Based on our findings compound PD-22 could further be utilized as a lead to design a promising candidate for AD therapy.

A reversible and efficient probe for dual mode recognition of Al3+ and Cu2+ with logic gate behaviour: Crystal structure, theoretical and in-vivo bio-imaging investigations

This work presents the synthesis, characterization, crystal structure and spectroscopic investigations of isophthalohydrazide based probe. Among various tested metal ions, the probe selectively detects Al³⁺ and Cu²⁺ in aqueous ethanol via fluorometric and colorimetric methods, respectively. It displays a fluorescence "turn-on" response with Al³⁺ and visual colour change from colourless to yellow with Cu²⁺. Sensing mechanism is explored with UV-Vis, fluorescence spectroscopy and ¹H NMR titration, and confirmed with computational results. Suppression of CN isomerization and photo-induced electron transfer (PET) along with chelation enhanced fluorescence emission (CHEF) result in "turn-on" fluorescence with Al³⁺ while ligand to metal charge transfer (LMCT) accounts for visual colour change with Cu²⁺. Job's plot and HRMS confirm 1:2 (L:M) stoichiometry. The probe also exhibits efficient reversibility and reproducibility with EDTA which are successfully mimicked with combinatorial logic gate and truth table. Additionally, solid state applications and bio-imaging investigation on gut tissue of Drosophila 3rd instar larvae are performed.

Advances in Applications of Molecular Logic Gates

Logic gates are devices that can perform Boolean logic operations and are the basic components of integrated circuits for information processing and storage. In recent years, molecular logic gates are gradually replacing traditional silicon-based electronic computers with their significant advantages and are used in research in water quality monitoring, heavy metal ion detection, disease diagnosis and treatment, food safety detection, and biological sensors. Logic gates at the molecular level have broad development prospects and huge development potential. In this review, the development and application of logic gates in various fields are used as the entry point to discuss the research progress of logic gates and logic circuits. At the same time, the application of logic gates in quite a few emerging fields is briefly summarized and predicted.

A Schiff base sensor for relay monitoring of In3+ and Fe3+ through “off–on–off” fluorescent signals

A Schiff base N′-(3-ethoxy-2-hydroxybenzylidene)-4,5-dihydronaphtho[1,2-b]thiophene-2-carbohydrazide (LB2) was designed and synthesized and could be used as a sensor to identify In³⁺ and Fe³⁺ through fluorescence ‘off–on–off’ behavior.

An ICT-based fluorescence enhancement probe for detection of Sn2+ in cancer cells

Development of a novel fluorescence enhancement probe for detection of Sn²⁺ in organisms, with high selectivity and sensitivity, is of great interest but remains a great challenge. Herein, an ICT-based fluorescence probe TPPB was rationally developed to act as an ‘enhancement’ luminescent and “naked-eye” indicator for Sn²⁺ detection. Importantly, spectroscopic studies indicated that TPPB was a fluorescence enhancement sensor for Sn²⁺ with rapid response, low detection limit (0.116 μM) and excellent binding constant (1.6 × 10⁴ M⁻¹). The mechanism of TPPB response to Sn²⁺ was further proved by ¹H NMR titration, and enhancement calculations. Furthermore, TPPB is applied as a fluorescence probe for imaging in Hela cells, indicated that it can be potentially applied for Sn²⁺ sensing in biological fields.

Development of a novel fluorescence enhancement probe for detection of Sn²⁺ in organisms, with high selectivity and sensitivity, is of great interest but remains a great challenge.

Synthesis, crystal structures, and luminescent properties of Zn(ii), Cd(ii), Eu(iii) complexes and detection of Fe(iii) ions based on a diacylhydrazone Schiff base

Acylhydrazone Schiff bases are rich in N and O atoms to coordinate with metal ions to form multidentate complexes.