A Molecular Keypad Lock: A Photochemical Device Capable of Authorizing Password Entries

Construction of HaloTag-based macromolecular probe for multiple logic gates and photoactivatable bioimaging

Protein bioconjugation has emerged as one of the most valuable tools for the development of protein-based biochemical assays. Herein, we report a fluorescent macromolecular probe RF12_POI, in which the coumarin derivative RF12 is specifically conjugated onto the HaloTag fused protein of interest (POI) to achieve a dual stimuli-mediated fluorescence response. RF12 is first obtained by installing a photo-cleavable 1-ethyl-2-nitrobenzyl group onto the C7 hydroxy moiety of coumarin fluorophore with a HaloTag ligand attaching to the acid-labile 1,3-dioxane moiety. Upon stimulation, RF12_Halo exhibits a sequential fluorescence response to photon/H+ on both liquid and solid interfaces. Through the conjugation of RF12 onto the GFP_Halo protein, RF12_GFP_Halo presents a fluorescence resonance energy transfer (FRET) from photo-cleaved RF12 to GFP in the protein complex. Furthermore, by utilizing the stimuli-responsive fluorescence characteristics of coumarin derivatives RF12 (photon/H+) and RF16 (H2O2/H+), we construct RF12/RF16_POI based protein films and achieve multiple applications of logic circuits, including AND, OR, XOR, INHIBIT, Half-adder or Half-subtractor. In these circuits, the output value of I/I0 is dependent on the input sequence of photon, H2O2, and H+. Additionally, we evaluate the fluorescence labeling ability of RF12 to intracellular IRE1_Halo protein and demonstrate that RF12 containing the HaloTag ligand could be precisely retained in cells to track IRE1_Halo protein. Hence, we provide a unique structural design strategy to construct fluorescence dual-responsive macromolecules for information encryption and cellular protein visualization.

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.

Enhancing Control Over Nitric Oxide Photorelease via a Molecular Keypad Lock

Based on Boolean logic, molecular keypad locks secure molecular information, typically with an optical output. Here we investigate a rare example of a molecular keypad lock with a chemical output. To this end, the light-activated release of biologically important nitric oxide from a ruthenium complex is studied, using proton concentration and photon flux as inputs. In a pH-dependent equilibrium, a nitritoruthenium(II) complex is turned into a nitrosylruthenium(II) complex, which releases nitric oxide under irradiation with visible light. The precise prediction of the output nitric oxide concentration as function of the pH and photon flux is achieved with an artificial intelligence approach, namely the adaptive neuro-fuzzy inference system. In this manner an exceptionally high level of control over the output concentration is obtained. Moreover, the provided concept to lock a chemical output as well as the output prediction may be applied to other (photo)release schemes.

Spatially Mediated Paper Reactors for On-Site Multicoded Encryption

This report develops a point-of-use chemical trigger and applies it to a dual-functional chemical encryption chip that enables manual and digital identification with enhanced coding security levels suitable for on-site information verification. The concept relies on conducting continuous chemical synthesis and chromatographic separation of specified compounds on a paper device in a straightforward sketch. In addition to single-step chemical reactions, cascade syntheses and operations involving components of distinct mobilities are also demonstrated. The condensation of dione and hydrazine is first demonstrated on a linear paper reactor, where precursors can mix to react, followed by final product separation under optimized conditions. This linear paper reactor design can also support a multistep cascade Wittig reaction by controlling the relative mobility of reactants, intermediates, and final products. Furthermore, a three-dimensional paper reactor with appropriate mobile phases helps to initiate complex solvent system-driven azide-alkyne cycloaddition. By the use of a three-dimensional device design for spatially limited interdevice reactant transportation, reactants crossing designated boundaries trigger confined chemical reactions at specific positions. Accumulation of repetitive reactions leads to successful product gradient generation and mixing effects, representing a fully controllable intersubstrate chemical operation on the platform. Standing on initiating desired chemical reactions at particular interface regions, integration of appropriate selective reaction area, numerical digits overlay, color diversity, and mobile recognition realizes this dual-functional multicoding encryption process.

Photocleavable DNA Nanotube-Based Dual-Amplified Resonance Rayleigh Scattering System for MicroRNA Detection Incorporating Molecular Computing-Cascaded Keypad Lock Functionality

Cascade molecular events in complex systems are of vital importance for enhancing molecular diagnosis and information processing. However, the conversion of a cascaded biosensing system into a multilayer encrypted molecular keypad lock remains a significant challenge in the development of molecular logic devices. In this study, we present a photocleavable DNA nanotube-based dual-amplified resonance Rayleigh scattering (RRS) system for detecting microRNA-126 (miR-126). The cascading dual-amplification biosensing system provides a multilayer-encrypted prototype with the functionality of a molecular computing cascade keypad lock. RRS signals were greatly amplified by using photocleavable DNA nanotubes and enzyme-assisted strand displacement amplification (SDA). In the presence of miR-126, enzyme-assisted SDA produced numerous identical nucleotide fragments as the target, which were then specifically attached to magnetic beads through the DNA nanotube by using a Y-shaped DNA scaffold. Upon ultraviolet irradiation, the DNA nanotube was released into the solution, resulting in an increase in the intensity of the RRS signal. This strategy demonstrated a low limit of detection (0.16 fM) and a wide dynamic range (1 fM to 1 nM) for miR-126. Impressively, the enzyme-assisted SDA offers a molecular computing model for generating the target pool, which serves as the input element for unlocking the system. By cascading the molecular computing process, we successfully constructed a molecular keypad lock with a multilevel authentication technique. The proposed system holds great potential for applications in molecular diagnosis and information security, indicating significant value in integrating molecular circuits for intelligent sensing.

Recent progress in the development of small-molecule double-locked logic gate fluorescence probes

Various bioactive substances are simultaneously involved in physiological processes, and research on the synergistic effect of them can promote the study of pathological mechanisms. To achieve this purpose, several small-molecule double-locked logic gate fluorescence probes have been developed recently. They overcome many shortcomings of the traditional "single-signal" fluorescent probes, with fluorescence that can be activated by two analytes of interest order-independently or order-dependently with one output. In this review, we summarize recently published small-molecule double-locked logic gate probes for the optical detection of two bioactive substances in living systems. We envision that this review will attract significant attention from researchers to exploit more powerful functional double-locked logic gate probes.

Molecules that Generate Fingerprints: A New Class of Fluorescent Sensors for Chemical Biology, Medical Diagnosis, and Cryptography

ConspectusFluorescent molecular sensors, often referred to as "turn-on" or "turn-off" fluorescent probes, are synthetic agents that change their fluorescence signal in response to analyte binding. Although these sensors have become powerful analytical tools in a wide range of research fields, they are generally limited to detecting only one or a few analytes. Pattern-generating fluorescent probes, which can generate unique identification (ID) fingerprints for different analytes, have recently emerged as a new class of luminescent sensors that can address this limitation. A unique characteristic of these probes, termed ID-probes, is that they integrate the qualities of conventional small-molecule-based fluorescent sensors and cross-reactive sensor arrays (often referred to as chemical, optical, or electronic noses/tongues). On the one hand, ID-probes can discriminate between various analytes and their combinations, akin to array-based analytical devices. On the other hand, their minute size enables them to analyze small-volume samples, track dynamic changes in a single solution, and operate in the microscopic world, which the macroscopic arrays cannot access.Here, we describe the principles underlying the ID-probe technology, as well as provide an overview of different ID-probes that have been developed to date and the ways they can be applied to a wide range of research fields. We describe, for example, ID-probes that can identify combinations of protein biomarkers in biofluids and in living cells, screen for several protein inhibitors simultaneously, analyze the content of Aβ aggregates, as well as ensure the quality of small-molecule and biological drugs. These examples highlight the relevance of this technology to medical diagnosis, bioassay development, cell and chemical biology, and pharmaceutical quality assurance, among others. ID-probes that can authorize users and protect secret data are also presented and the mechanisms that enable them to hide (steganography), encrypt (cryptography), and prevent access to (password protection) information are discussed.The versatility of this technology is further demonstrated by describing two types of probes: unimolecular ID-probes and self-assembled ID-probes. Probes from the first type can operate inside living cells, be recycled, and their initial patterns can be more easily obtained in a reproducible manner. The second type of probes can be readily modified and optimized, allowing one to prepare various different probes from a much wider range of fluorescent reporters and supramolecular recognition elements. Taken together, these developments indicate that the ID-probe sensing methodology is generally applicable, and that such probes can better characterize analyte mixtures or process chemically encoded information than can the conventional fluorescent molecular sensors. We therefore hope that this review will inspire the development of new types of pattern-generating probes, which would extend the fluorescence molecular toolbox currently used in the analytical sciences.

An optical keypad lock with high resettability based on a quantum dot-porphyrin FRET nanodevice

Due to their appealing properties, nanomaterials have become ideal candidates for the implementation of computing systems. Herein, an optical keypad lock based on a Förster resonance energy transfer (FRET) nanodevice is developed. The nanodevice is composed of a green-emission quantum dot with a thick silica shell (gQD@SiO2) and peripheric blue-emission quantum dots with ultrathin silica spacer (bQD@SiO2), on which 5,10,15,20-tetrakis(4-sulfophenyl)porphyrin (TSPP) is covalently linked. The nanodevice outputs dual emission-based ratiometric fluorescence, depending on the FRET efficiency of bQD-porphyrin pairs, which is highly sensitive to the metalation of TSPP: values are 59.7%, 44.8%, and 10.1% for bQD-Zn(ii)TSPP, bQD-TSPP, and bQD-Fe(iii)TSPP pairs, respectively. As such, by using the competitive chelation-induced transmetalation of TSPP, the nanodevice is capable of implementing a 3-input keypad lock that is unlocked only by the correct input order of Zn(ii) chelator, iron ions, and UV light. Interestingly, the reversible transmetalation of TSPP permits the reset (lock) operation of the keypad lock with the correct input order of ascorbic acid, Zn(ii), and UV light. Application of the nanodevice is exemplified by the construction of paper and cellular keypad locks, respectively, both of which feature signal readability and/or high resettability, showing high potential for personal information identification and bio-encryption applications.

Human brain-inspired chemical artificial intelligence tools for the analysis and prediction of the anion-sensing characteristics of an imidazole-based luminescent Os(II)-bipyridine complex

Neural network and decision tree-based soft computing techniques are implemented in this work for the thorough analysis of the multichannel anion-sensing characteristics of an Os(II)-bipyridine complex derived from imidazole-4,5-bis(benzimidazole) ligand. With the aid of three imidazole NH protons in its outer coordination sphere, a substantial change in the spectral response as well as Os^II/Os^III potential is made possible upon treating with anions of varying basicity. Initial hydrogen bonding between NH protons and anions and thereafter complete proton transfer from the complex backbone probably take place in the process. The deprotonation of the complex by specific anions and restoration to its original form by acid is also reversible. The responsiveness of the new compound is complex enough to imitate multiple sophisticated binary and ternary Boolean logic (BL) functions (NOT logic, combinational logic, traffic signal, set-reset flip-flop logic, and ternary NOR logic) by employing its spectral and redox outputs upon the action of suitable anions and acid in a proper sequence. Executing sensing investigations on altering the amount of the anions within a widespread range is often time-consuming and tedious. To overcome the lacuna, we implemented multiple soft computing techniques, viz., fuzzy logic (FL), artificial neural networks (ANNs), adaptive neuro-fuzzy inference system (ANFIS), and decision tree (DT) regression, for the thorough analysis and prediction of the experimentally observed results. The outcomes obtained from different techniques were compared among themselves as well as with the experimental data and utilized for the proper modeling of the anion-sensing behaviors of the complex.

Colorimetric multi-channel sensing of metal ions and advanced molecular information protection based on fish scale-derived carbon nanoparticles

Some nanosystems based on carbon nanomaterials have been used for fluorescent chemical/biosensing, elementary information processing, and textual coding. However, little attention has been paid to utilizing biowaste-derived carbon nanomaterials for colorimetric multi-channel sensing and advanced molecular information protection (including text and pattern information). Herein, fish scale-derived carbon nanoparticles (FSCN) were prepared and used for colorimetric detection of metal ions, encoding, encrypting and hiding text- and pattern-based information. The morphology and composition of FSCN were analyzed by TEM, XRD, FTIR, and XPS, and it was found that the FSCN-based multi-channel colorimetric sensing system can detect Cr⁶⁺ (detection limit of 56.59 nM and 13.32 nM) and Fe³⁺ (detection limit of 81.55 nM) through the changes of absorption intensity at different wavelengths (272, 370, and 310 nm). Moreover, the selective responses of FSCN to 20 kinds of metal ions can be abstracted into a series of binary strings, which can encode, hide, and encrypt traditional text-based and even two-dimensional pattern-based information. The preparation of carbon nanomaterials derived from waste fish scales can stimulate other researcheres' enthusiasm for the development and utilization of wastes and promoting resource recycling. Inspired by this work, more researches will continue to explore the world of molecular information technology.

Facile Label-Free Three-Input Molecular Keypad Lock

Featured with molecule-level data encryption, molecular keypad locks show attractive merits in information security. Most of the previous multiple-input locks use fluorescence as output but are impeded by inefficient/labile prequenching or highly synthetic complexity/difficulty of the fluorophore-containing processor molecules. We herein propose a facile three-input molecular keypad lock, which is simple in synthesis and label free but capable of in situ generation of a fluorescent moiety (dityrosine) for background-free fluorescence readout. A nonfluorescent ("Locked") tyrosine derivate _zY_pc was easily synthesized as the processor. The correct "password" (i.e., UV → ALP → TYR, ABC) stepwise converted _zY_pc to a dityrosine-containing product, exhibiting a bright blue fluorescence output ("Open"). In contrast, wrongly permutated inputs failed to open this lock. This device shows potential to be extended as a more advanced keypad lock with better security.

Nitrogen, sulfur, and phosphorus Co-doped carbon dots-based ratiometric chemosensor for highly selective sequential detection of Al3+ and Fe3+ ions in logic gate, cell imaging, and real sample analysis

Heteroatom-doped photoluminescent (PL) carbon dots (CDs) have recently gained attention as optical sensors due to their excellent tunable properties. In this work, we propose a one-pot hydrothermal synthesis of PL nitrogen (N), sulfur (S), and phosphorus (P) co-doped carbon dots (NSP-CDs) using glutathione and phosphoric acid (H₃PO₄) as precursors. The synthesized NSP-CDs were characterized using different spectroscopic and microscopic techniques, including ultraviolet-visible (UV-Vis) spectroscopy, fluorescence spectroscopy, Fourier-transform infrared (FTIR), X-ray powder diffraction (XRD), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS) analysis. The NSP-CDs exhibited excellent PL properties with green emission at 492 nm upon excitation at 417 nm, a high quantum yield of 26.7%, and dependent emission behavior. The as-prepared NSP-CDs were spherical with a well-monodispersed average particle size of 5.2 nm. Moreover, NSP-CDs demonstrate high PL stability toward a wider pH, high salt ionic strength, and various solvents. Furthermore, the NSP-CDs showed a three-state "off-on-off" PL response upon the sequential addition of Al³⁺ and Fe³⁺ ions, with a low limit of detection (LOD) of 10.8 nM for Al³⁺ and 50.7 nM for Fe³⁺. The NSP-CD sensor can construct an INHIBIT logic gate with Al³⁺ and Fe³⁺ ions as the chemical inputs and emissions as the output mode. Owing to an excellent tunable PL property and biocompatibility, the NSP-CDs were applied for sensing Al³⁺ and Fe³⁺ ions as well as live cell imaging. Furthermore, NSP-CDs were designed as PL sensors for detecting Al³⁺ and Fe³⁺ ions in real water show their potential application.

Neural network and decision tree-based machine learning tools to analyse the anion-responsive behaviours of emissive Ru(ii)–terpyridine complexes

Artificial neural network, adaptive neuro-fuzzy inference and decision tree regression are implemented to analyse the anion-responsive behaviours of emissive Ru(ii)–terpyridine complexes.

Specific ultralow level chemo-recognition using Graphene-fluorophore supramolecular assembly: Fine-tuning the fluorophore framework

The non-covalent interactions between graphene and aromatic fluorophores have generated highly sensitive fluorimetric turn-on sensors for various significant analytes. Herein, the supramolecular interaction between reduced graphene oxide and 7-Hydroxy-4-Methyl-8-Amino Coumarin is made use of for tracing Cu²⁺ at sub-zeptomole level with excellent selectivity among a collection of nineteen metal ions. The system enables quantification of the analyte in a commendably wide range, from micromolar to zeptomolar, a feature that almost all-optical sensors lack. Handy solid-state sensor strip fabricated using the above-mentioned supramolecular combination enabled visual recognition of Cu²⁺ions at the molecular level. Based on the chemo recognition ability of the fluorophore, multiple Boolean logic devices operating at the molecular level are proposed. By screening pertinent coumarin derivatives, it is demonstrated that the selectivity and sensitivity of the sensors of this sort are decided by the number of π- interaction centers of the fluorophores and the strength by which they interact with graphene, respectively, which will enable identification and modification of proper fluorophores for ultra-trace detection of contaminants of environmental relevance from aqueous solutions.

Synthetic DNA applications in information technology

Synthetic DNA is a growing alternative to electronic-based technologies in fields such as data storage, product tagging, or signal processing. Its value lies in its characteristic attributes, namely Watson-Crick base pairing, array synthesis, sequencing, toehold displacement and polymerase chain reaction (PCR) capabilities. In this review, we provide an overview of the most prevalent applications of synthetic DNA that could shape the future of information technology. We emphasize the reasons why the biomolecule can be a valuable alternative for conventional electronic-based media, and give insights on where the DNA-analog technology stands with respect to its electronic counterparts.

Multifunctional Carbon Nanocomposites as Nanoneurons from Multimode and Multianalyte Sensing to Molecular Logic Computing, Steganography, and Cryptography

Inspired by information exchange and logic functions of life based on molecular recognition and interaction networks, ongoing efforts are directed toward development of molecular or nanosystems for multiplexed chem/biosensing and advanced information processing. However, because of their preparation shortcomings, poor functionality, and limited paradigms, it is still a big challenge to develop advanced nanomaterials-based systems and comprehensively realize neuron-like functions from multimode sensing to molecular information processing and safety. Herein, using fish scales derived carbon nanoparticles (FSCN) as a reducing agent and stabilizer, a simple one-step synthesis method of multifunctional silver-carbon nanocomposites (AgNPs-FSCN) is developed. The prepared AgNPs-FSCN own wide antibacterial and multisignal response abilities in five channels (including color, Tyndall, absorption and fluorescence intensities, and absorption wavelength) for quantitative colorimetric and fluorescence sensing of H₂ O₂ , ascorbic acid, and dopamine. Benefiting from its multicoding stimuli-responsive ability, molecular concealment, and programmability, AgNPs-FSCN can be abstracted as nanoneurons for implementing batch and parallel molecular logic computing, steganography, and cryptography. This research will promote the preparation of advanced multifunctional nanocomposites and the development of their multipurpose applications, including the multireadout-guided multianalyte intelligent sensing and sophisticated molecular computing, communication, and security.

Unlocking Chemically Encrypted Information Using Three Types of External Stimuli

Encryption is critical to information security; however, existing chemical-based information encryption strategies are still in their infancy. We report here a new approach to chemical encryption involving a supramolecular gel QR (quick response) code with multiple encryption functions. Three color "turn-on" supramolecular polymer gels, G1-G3, were prepared that produce pink, purple, and yellow colors when subject to treatment with acetic acid vapor, UV light, and methanolic FeCl₃, respectively. As the result of hydrogen-bonding interactions at the gel interfaces, the three gels can be assembled to produce gel G4. Engraving a QR code pattern onto G4 then gave gel G5. When one or two stimuli are applied to the individual pieces corresponding to the QR engraved versions of the gels G1-G3 making up G5, a complete scannable pattern is not displayed, and the stored information cannot be recognized. Only when three different stimuli are applied at the same time does G5 give a complete recognizable pattern allowing the stored information to be retrieved. This strategy was applied to the decryption-based opening of a coded lock.

Concise Modular Synthesis and NMR Structural Determination of Gallium Mycobactin T

A modular synthesis of mycobactin T and its N-acetyl analogue is reported in a route that facilitates permutation of the lipid tails. A key feature is the generation of N(α)-Cbz-N(ε)-benzyloxy-N(ε)-Boc-lysine (A4) with methyl(trifluoromethyl)dioxirane in 59% yield. Selective hydroxamate N-acylation was achieved with acyl fluorides, enabling installation of lipids tails in the final step. O-Benzyl-dehydrocobactin T (B4) was prepared by modifying a known five-step sequence with an overall yield of 49%. 2-Hydroxyphenyl-4-carboxyloxazoline (C3) was prepared from 2-hydroxybenzoic acid and l-serine methyl ester in three steps with an overall yield of 55%. Ester coupling of A4 and B4 with EDCI afforded MbI-1 in 73% yield. Catalytic hydrogenation with Pd/BaSO₄ and 50 psi of H₂ simultaneously effected alkene reduction and debenzylation to afford MbI-2 in 96% yield. Fragment C3 was converted into acyl fluoride C4, which coupled with MbI-2 to afford MbI-3 in 51% yield. Finally, Boc-removal with HCl/EtOAc and treatment of the resultant hydroxylamine with stearyl fluoride furnished mycobactin T in 65% yield. Overall, the yield is 4% over 14 steps. The gallium mycobactin T-N-acetyl derivative (GaMbT-NAc) structure was determined by ¹H NMR. The structure shows an octahedral Ga and two internal hydrogen bonds between peptidic N-Hs and two of the oxygen atoms coordinating Ga.

2-Nitro- and 4-fluorocinnamaldehyde based receptors as naked-eye chemosensors to potential molecular keypad lock

New-generation chemosensors desire small organic molecules that are easy to synthesise and cost-effective. As a new interdisciplinary area of research, the integration of these chemosensors into keypad locks or other advanced communication protocols is becoming increasingly popular. Our lab has developed new chemosensor probes that contain 2-nitro- (1-3) and 4-fluoro-cinnamaldehyde (4-6) and applied them to the anion recognition and sensing process. Probes 1-6 are colorimetric sensors for naked-eye detection of AcO-/CN-/F-, while probes 4-6 could differentiate between F- and AcO-/CN- anions in acetonitrile. Using the density functional theory (DFT), it was found that probes 1-6 acted as effective chemosensors. By using Probe 5 as a chemosensor, we explored colorimetric recognition of multiple anions in more detail. Probe 5 was tested in combination with a combinatorial approach to demonstrate pattern-generation capability and its ability to distinguish among chemical inputs based on concentration. After pattern discrimination using principal component analysis (PCA), we examined anion selectivity using DFT computation. In our study, probe 5 demonstrates excellent performance as a chemosensor and shows promise as a future molecular-level keypad lock system.

Light and Cation-Driven Optical Switch based on a Stilbene-Appended Terpyridine System for the Design of Molecular-Scale Logic Devices

A molecular system comprising a terpyridine moiety capable of coordinating with different cations and a photoswitchable stilbene unit has been utilized here for the fabrication of multiply configurable logic systems. Incorporation of a substituted stilbene unit into the terpyridine motif generates an intraligand charge-transfer-sensitive module whose absorption and emission spectral properties are highly sensitive to light as well as cations. On the basis of the optical response profile of the receptor in the presence of selected cations as well as light of a specific wavelength, we are able to demonstrate multiple Boolean logic functions such as INHIBIT, IMPLICATION, OR, NOR, and NAND, as well as various combinations of them. Of particular interest, we utilized the present system for the construction of security keypad locks and memory devices by maintaining a proper sequence of the stimuli and monitoring either absorption or emission spectral response at a specific wavelength as the output signal. In addition to various Boolean logic functions, the present system has also the ability to mimic fuzzy logic operations for generating an infinite-valued logic scheme depending on its emission spectral responses upon varying the concentration of cationic (Fe²⁺ and/or Zn²⁺) and anionic (CN^-) inputs.

A therapeutic keypad lock decoded in drug resistant cancer cells

A molecular keypad lock that displays photodynamic activity when exposed to glutathione (GSH), esterase and light in the given order, is fabricated and its efficacy in drug resistant MCF7 cancer cells is investigated. The first two inputs are common drug resistant tumor markers. GSH reacts with the agent and shifts the absorption wavelength. Esterase separates the quencher from the structure, further activating the agent. After these sequential exposures, the molecular keypad lock is exposed to light and produces cytotoxic singlet oxygen. Among many possible combinations, only one 'key' can activate the agent, and initiate a photodynamic response. Paclitaxel resistant MCF7 cells are selectively killed. This work presents the first ever biological application of small molecular keypad locks.

Toward Smart Information Processing with Synthetic DNA Molecules

DNA, a biological macromolecule, is a naturally evolved information material. From the structural point of view, an individual DNA strand can be considered as a chain of data with its bases working as single units. For decades, due to the high biochemical stability, large information storage capacity, and high recognition specificity, DNA has been recognized as an attractive material for information processing. Especially, the chemical synthesis strategies and DNA sequencing techniques have been rapidly developed recently, further enabling encoding information with synthetic DNA molecules. Herein, recent progresses are summarized on information processing based on synthetic DNA molecules from three aspects including information storage, computation, and encryption, and proposed the challenges and future development directions.

A naked-eye colorimetric sensor based on chalcone for the sequential recognition of copper(ii) and sulfide ions in semi-aqueous solution: spectroscopic and theoretical approaches

A chalcone-based new colorimetric sensor A01 for the sequential detection of Cu²⁺ and S²⁻ ions.

Encrypting messages with artificial bacterial receptors

A method for encrypting messages using engineered bacteria and different fluorescently labeled synthetic receptors is described. We show that the binding of DNA-based artificial receptors to E. coli expressing His-tagged outer membrane protein C (His-OmpC) induces a Förster resonance energy transfer (FRET) between the dyes, which results in the generation of a unique fluorescence fingerprint. Because the bacteria continuously divide, the emission pattern generated by the modified bacteria dynamically changes, enabling the system to produce encryption keys that change with time. Thus, this development indicates the potential contribution of live-cell-based encryption systems to the emerging area of information protection at the molecular level.

Homogeneous DNA-only keypad locks enable one-pot assay of multi-inputs

Homogeneous DNA-only keypad locks were built with multi-stranded scalable junction substrates and a series of double-stranded eliminators to differentially process correctly- and wrongly-added DNA inputs, respectively. Unlike conventional strategies that employed solid-phase platforms, one-pot assay of multiple DNA inputs was achieved, showing merits in fabricating complicated information security systems.

Demonstration of Arithmetic Calculations by DNA Tile-Based Algorithmic Self-Assembly

Owing to its high information density, energy efficiency, and massive parallelism, DNA computing has undergone several advances and made significant contributions to nanotechnology. Notably, arithmetic calculations implemented by multiple logic gates such as adders and subtractors have received much attention because of their well-established logic algorithms and feasibility of experimental implementation. Although small molecules have been used to implement these computations, a DNA tile-based calculator has been rarely addressed owing to complexity of rule design and experimental challenges for direct verification. Here, we construct a DNA-based calculator with three types of building blocks (propagator, connector, and solution tiles) to perform addition and subtraction operations through algorithmic self-assembly. An atomic force microscope is used to verify the solutions. Our method provides a potential platform for the construction of various types of DNA algorithmic crystals (such as flip-flops, encoders, and multiplexers) by embedding multiple logic gate operations in the DNA base sequences.

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.

Polymorphism-Dependent Dynamic Ultralong Organic Phosphorescence

Developing ultralong organic phosphorescence (UOP) materials with smart response to external stimuli is of great interest in photonics applications, whereas the manipulation of molecular stacking on tuning such dynamic UOP is still a formidable challenge. Herein, we have reported two polymorphs with distinct photoactivated dynamic UOP behavior based on a pyridine derivative for the first time. Our experiment revealed that the dynamic UOP behavior including photoactivation and deactivation feature is highly dependent on irradiation intensity and environmental atmosphere. Additionally, given the unique dynamic UOP feature, these phosphors have been successfully applied to phosphorescence-dependent molecular logic gate and timing data storage. This result not only paves a way to design smart functional materials but also expands the scope of the applications on organic phosphorescence materials.

Constructing a four-input molecular keypad lock with a multi-stimuli-responsive phthalocyanine

A novel phthalocyanine has been designed and synthesised whose response towards different stimuli can be manipulated to enable it to function as a four-input molecular keypad lock.

Engineering diformyl diaryldipyrromethane into a molecular keypad lock

A diaryldipyrromethane-based acyclic system acts as a photolabile sequential chemosensor for both anions and cations via ESIDPT and deprotonation, which is engineered into a fluorescent molecular keypad lock system.

DNA origami cryptography for secure communication

Biomolecular cryptography exploiting specific biomolecular interactions for data encryption represents a unique approach for information security. However, constructing protocols based on biomolecular reactions to guarantee confidentiality, integrity and availability (CIA) of information remains a challenge. Here we develop DNA origami cryptography (DOC) that exploits folding of a M13 viral scaffold into nanometer-scale self-assembled braille-like patterns for secure communication, which can create a key with a size of over 700 bits. The intrinsic nanoscale addressability of DNA origami additionally allows for protein binding-based steganography, which further protects message confidentiality in DOC. The integrity of a transmitted message can be ensured by establishing specific linkages between several DNA origamis carrying parts of the message. The versatility of DOC is further demonstrated by transmitting various data formats including text, musical notes and images, supporting its great potential for meeting the rapidly increasing CIA demands of next-generation cryptography.

Biomolecular cyptography that exploits specific interactions could be used for data encryption. Here the authors use the folding of M13 DNA to encrypt information for secure communication.

Growing prospects of DNA nanomaterials in novel biomedical applications

As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications.

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.

Graphene-Based Steganographically Aptasensing System for Information Computing, Encryption and Hiding, Fluorescence Sensing and in Vivo Imaging of Fish Pathogens

Inspired by information processing and communication of life based on complex molecular interactions, some artificial (bio)chemical systems have been developed for applications in molecular information processing or chemo/biosensing and imaging. However, little attention has been paid to simultaneously and comprehensively utilize the information computing, encoding, and molecular recognition capabilities of molecular-level systems (such as DNA-based systems) for multifunctional applications. Herein, a graphene-based steganographically aptasensing system was constructed for multifunctional application, which relies on specific molecular recognition and information encoding abilities of DNA aptamers ( Aeromonas hydrophila and Edwardsiella tarda-binding aptamers as models) and the selective adsorption and fluorescence quenching capacities of graphene oxide (GO). Although graphene-DNA systems have been widely used in biosensors and diagnostics, our proposed graphene-based aptasensing system can not only be utilized for fluorescence sensing and in vivo imaging of fish pathogens ( A. hydrophila and E. tarda), but can also function as a molecular-level logic computing system where the combination of matters (specific molecules or materials) as inputs produces the resulting product (matter level) or fluorescence (energy level) changes as two outputs. More importantly and interestingly, our graphene-based steganographically aptasensing system can also serve as a generally doubly cryptographic and steganographic system for sending different secret messages by using pathogen-binding DNA aptamers as information carriers, GO as a cover, and a pair of keys, that is, target pathogen as a public key, the encryption key used to encode or decode a message in DNA as a private key. Our study not only provides a novel nanobiosensing assay for rapid and effective sensing and in vivo imaging of fish pathogens, but also demonstrates a prototype of (bio)molecular steganography as an important and interesting extension direction of molecular information technology, which is helpful in probably promoting the development of multifunctional molecular-level devices or machines.

Sequential displacement strategy for selective and highly sensitive detection of Zn2+, Hg2+ and S2- ions: An approach toward a molecular keypad lock

A thiocarbonohydrazone locked salicylidene based macrocycle ligand L has been synthesized and its ion sensing properties were examined by UV-visible and fluorescence spectroscopy. The macrocycle serves as a highly selective colorimetric sensor for Hg²⁺ ions while it acts as an excellent fluorescent sensor for Zn²⁺ ions by exhibiting a green fluorescence at 498 nm even in the presence of interfering ions. A detailed analysis of binding characteristics such as complex stoichiometry, association constant and detection limits of L toward Hg²⁺ and Zn²⁺ ions were evaluated by UV-visible and fluorescence experiments which revealed a stronger binding affinity and higher detection limit of L toward the mercury ions. Further, the sequential displacement strategy for the chromofluorogenic detection of Zn²⁺, Hg²⁺ and S^2- ions by ligand L, has been studied comprehensively. Finally, the ion-responsive fluorescence output signal of L were employed to design a molecular keypad lock which could be accessible by two users having two different set of chemical passwords (inputs) through distinguishable optical trajectories.

Molecular memory with downstream logic processing exemplified by switchable and self-indicating guest capture and release

Molecular-logic based computation (MLBC) has grown by accumulating many examples of combinational logic gates and a few sequential variants. In spite of many inspirations being available in biology, there are virtually no examples of MLBC in chemistry where sequential and combinational operations are integrated. Here we report a simple alcohol-ketone redox interconversion which switches a macrocycle between a large or small cavity, with erect aromatic walls which create a deep hydrophobic space or with collapsed walls respectively. Small aromatic guests can be captured or released in an all or none manner upon chemical command. During capture, the fluorescence of the alcohol macrocycle is quenched via fluorescent photoinduced electron transfer switching, meaning that its occupancy state is self-indicated. This represents a chemically-driven RS Flip-Flop, one of whose outputs is fed into an INHIBIT gate. Processing of outputs from memory stores is seen in the injection of packaged neurotransmitters into synaptic clefts for onward neural signalling. Overall, capture-release phenomena from discrete supermolecules now have a Boolean basis.

Three-Input Molecular Keypad Lock Based on a Norbornadiene-Quadricyclane Photoswitch

The photo- and acidochromic properties of a new generation norbornadiene derivative have been harnessed for the realization of a three-input keypad lock, where a specific sequence of inputs induces a unique output. Reversible quadricyclane/norbornadiene photoisomerization is reported, and this rare feature allows the first example of a norbornadiene-based molecular logic system. The function of this system is clearly rationalized in terms of the interconversion scheme and the absorption spectra of the involved species.