Molecular Logic Circuits Research Articles

Construction of dual-output molecular logic circuit based on bovine serum albumin loaded with two fluorescent compounds

Construction of dual-output molecular logic circuit based on bovine serum albumin loaded with two fluorescent compounds

A DNA Molecular Logic Circuit for Precise Tumor Identification.

Tumor-associated antigens (TAAs) are not exclusively expressed in cancer cells, inevitably causing the "on target, off tumor" effect of molecular recognition tools. To achieve precise recognition of cancer cells, by using protein tyrosine kinase 7 (PTK7) as a model TAA, a DNA molecular logic circuit Aisgc8 was rationally developed by arranging H+-binding i-motif, ATP-binding aptamer, and PTK7-targeting aptamer Sgc8c in a DNA sequence. Aisgc8 output the conformation of Sgc8c to recognize PTK7 on cells in a simulated tumor microenvironment characterized by weak acidity and abundant ATP, but not in a simulated physiological environment. Through in vitro and in vivo results, Aisgc8 demonstrated its ability to precisely recognize cancer cells and, as a result, displayed excellent performance in tumor imaging. Thus, our studies produced a simple and efficient strategy to construct DNA logic circuits, opening new possibilities to develop convenient and intelligent precision diagnostics by using DNA logic circuits.

Sequence-Unconstrained DNA Computing: DSN cycling and PER circuitry for dynamic miRNAs analysis and multifunctional logic operations

DNA strand displacement and enzyme-driven catalysis are pivotal in regulating molecular interactions and constructing molecular logic circuits. However, their application in intricate hierarchical cascading networks has been hindered by sequence crosstalk restrictions on the multiple inputs and outputs. In this study, we present a sequence-unconstrained strategy to implement versatile molecular logic circuits, relying on duplex-specific nuclease (DSN)-assisted cycling and primer exchange reaction (PER) amplification circuitry (DSN-PER). Employing linear capture probe (CP) conjugated with magnetic beads (MBs) significantly minimizes crosstalk reactions compared to the previous molecular beacon probe (MBP) for DNA barcoding. Importantly, the sequence design of “barcodes” is fully independent of target binding sites on MBs, allowing for the sensitive detection of a broad range of microRNAs (miRNAs) using the DSN-PER method. Specifically, this platform supports the programming of common logic computations (YES, NOT, OR, INHIBIT, AND, and NOR) and hierarchical circuit operation (OR-AND) in response to a specific pattern of varying miRNAs. These versatile logic circuits offer unique features with flexible sequence design, potentially broadening the applications of dynamic nucleic acid nanotechnologies in multiplexed bio-computation, intelligent diagnostics, and sophisticated DNA nanodevices.

Breast Tumor Diagnosis Based on Molecular Learning Vector Quantization Neural Networks.

DNA nanotechnology plays a crucial role in precise cancer medicine. Currently, molecular logic circuits are applied to detect tumor-specific biomarkers and control the release of therapeutic drugs. However, these systems lack self-learning capabilities for intelligent diagnostics in biological samples, and their data processing capabilities are limited. Here, a molecular learning vector quantization neural network (LVQNN) model based on DNA strand displacement (DSD) technology for breast tumor diagnosis is developed. Compared to previous work, the molecular LVQNN boasts powerful computing abilities, handling high-dimensional data for intelligent cancer diagnosis. To verify the feasibility and versatility of the network, two distinct typical datasets are selected: one from a single source with cell morphology data from 569 cases, and a more extensive one spanning different populations and ages, with miRNA gene expression data from 1881 cases. By using the molecular LVQNN, diagnostic experiments are conducted on 50 and 120 public individuals from these two datasets, respectively, achieving accuracy rates of 94% and 97.5%. This study demonstrates that the LVQNN model exhibits significant advantages in breast cancer diagnosis and enhances diagnostic accuracy while introducing new approaches for intelligent cancer diagnosis, anticipated to bring significant breakthroughs and application prospects to precise cancermedicine.

An orange light emitting 'off–on-off' fluorogenic probe for consecutive detection of Al3+ ions and 2,4,6-trinitrophenol

A simple, orange light emitting 'off–on-off' fluorogenic sensor, (E)-4-(((2-hydroxy-4-nitrophenyl) imino) methyl) naphthalene-3-ol (HNMN), has been introduced for the successive recognition of Al3+ ions and 2, 4, 6-trinitrophenol respectively, utilizing the photoluminescence 'off–on-off' mechanism. A significant enhancement in the photoluminescence of HNMN is found at 558 nm, attributed to the chelation of Al3+ ions, resulting in a visible orange-colored photoluminescence under a handy 365 nm UV light illumination. Among the different tested nitroaromatic compounds (NACs), 2, 4, 6-trinitrophenol, namely picric acid (PA), selectively quenches the orange photoluminescence caused by Al3+ on the HNMN complex. The stoichiometric ratio for the complex formation between HNMN and aluminum ion is determined to be 1:1, with an estimated limit of detection (LOD) and quantification (LOQ) found to be 8.6 nM and 28.4 nM respectively in DMF medium. Different spectroscopic analyses have elucidated the mechanistic features of identifying Al3+ ions. A test kit–based experiment is performed with the HNMN-coated filter paper to detect Al3+ ions and PA sequentially & selectively. Based on the chemical inputs and optical output, we have framed the INHIBIT molecular logic circuit. The present report evokes a facile approach for the design and molecular development of highly red-shifting fluorosensors from the non-fluorophore moieties to avoid false signaling during the detection of target analytes.

Designing Unconventional Molecular Ternary INHIBIT Logic Gate and Crafting Multifunctional Molecular Logic Systems.

The paper describes an improved method for building flexible interswitchable logic gates such as rare-type molecular ternary INHIBIT and combinational logic circuits using a specially designed pyridine-end oligo-p-phenylenevinylene compound featuring alkyl substituents (-C16H33) in a THF medium. The probe molecule showed distinct opto-chemical signals upon interaction with Cu(II) and Hg(II) in THF medium. It is interesting to note that the presence of certain anions (S2-, I-, and CN-) could specifically mask the interaction of either of these metal ions or both. The most exciting thing is that we used a completely new gate design technique to construct a rare-type ternary INHIBIT logic gate using Cu(II), Hg(II), and CN- ions as three chemical inputs. With the identical set of chemical inputs, two more ternary combinational logic circuits were created out of these case-specific, independent reversible and irreversible spectroscopic studies. Finally, we were able to design adaptive molecular logic systems composed of several logic gates, including NOR, AND, IMPLICATION, INHIBIT, TRANSFER, and COMPLEMENT, that in this specific situation change the sort of logic sense by effortless optical toggling.

Ferrocene-based chemosensor creates molecular logic circuit for selective detection of Hg2+ and Cu2+

A cation sensor, R, with multi-channel signaling was developed by creating a covalent connection between a ferrocene unit and pyridyl-pyrazole rings. Spectroscopic techniques and single-crystal X-ray diffraction were employed to characterize sensor R. The examination revealed a dihedral angle of 140.09° for the pyridyl-pyrazole rings. The receptor R functions as a highly selective multi-channel chemosensor, exhibiting chromogenic, fluorogenic, and electrochemical capabilities. In a CH3CN/water (9:1) solvent mixture, receptor R operates as a multi-channel signaling chemosensor, selectively detecting Hg2+ and Cu2+ ions in water. The original pale-yellow solution turned orange upon Hg2+ addition and green upon Cu2+ addition. A new low energy (LE) band at 460 nm was detected after adding one equivalent of Hg2+. In cyclic voltammetry (CV), the half-wave potential (E1/2) of 462 mV shifted to 622 mV, whereas in differential pulse voltammogram (DPV), the oxidation peak underwent an anodic shift (ΔE1/2 = 155 mV). The maximum emission at 423 nm was lowered by more than 90 % when the concentration of Hg2+ ions reached one equivalent. One equivalent addition of Cu2+ results in a new LE band at 740 nm. Cu2+ ions suppress the oxidation peak current in both the CV and DPV of R. It also demonstrates chelation-enhanced fluorescence effect (CHEF) with Cu2+. The interaction between cations and R was elucidated through 13C NMR titration. DFT calculations revealed the binding mode. Its distinctive fluorescence demonstrates a 'turn-on' response to Cu2+ and a 'turn-off' response to Hg2+ with selectivity. This concept has been applied to create a molecular combinatorial logic circuit.

An Adenine‐Based Chromone‐Coupled ‘Off‐On‐Off’ Fluorogenic Dyad for Cascade Detection of Zn2+ and HSO₄− Ions or Zn2+ Ions and Picric Acid

AbstractA chromone‐coupled adenine‐based fluorogenic chemosensor (BD1) has been introduced for cascade detection of Zn2+ and HSO4−ions or Zn2+ and picric acid (PA) based on the fluorescence ‘OFF‐ON‐OFF’ mechanism. A momentous fluorescence improvement has been observed due to the accumulation of Zn2+ ions in the BD1 solution because of the formation of the Zn2+ chelated BD1 complex. A cyan color fluorescence enhancement is visible under the exposure of a 365 nm UV lamp, which is also manifested in the CIE diagram. The detection limit of our developed sensor BD1 and Zn2+−BD1 complex towards the identification of Zn2+ and HSO4− ions are in the nM and μM range, respectively, in the solution phase. Among the several explosive nitroaromatic compounds (NACs), only PA quenches the fluorescence of the Zn2+ chelated BD1 complex, and the nature of quenching is both static and dynamic. A paper strips‐based test kit experiment is performed for on‐spot identification of Zn2+ ions and PA. Based on these chemically encoded inputs and the fluorescence intensity as optical output, we have constructed an INHIBIT molecular logic circuit. The present report evokes a new approach for the development of new chemosensors from bioinspired materials such as adenine, a purine nucleobase.

A Simple and Rapid Quinoline Schiff Base as a Fluorescent Probe for Zn2+ and Its Application in Test Strips

AbstractA simple fluorescent probe, (E)‐N‐(3‐methoxy‐4‐methylphenyl)‐1‐(quinolin‐2‐yl)methanimine (L), was synthesized via Schiff base condensation reaction between quinoline‐2‐carboxaldehyde and 3‐methoxy‐4‐methylaniline. L can be used as a ′turn‐on′ fluorescent probe for the selective and sensitive detection of Zn2+ ions in a CH3OH/HEPES medium. The detection limit was 1.04×10−7 M. Job plot analysis shows that the binding stoichiometry of L and Zn2+ is 1 : 1, further verified by the single crystal structure. The fluorescence‐enhanced response of L towards Zn2+ ions may be related to the chelation‐enhanced fluorescence (CHEF) supported by theoretical calculations. By adding EDTA, the reversibility of the probe binding to Zn2+ ions is demonstrated, enabling the construction of a functional molecular logic circuit. In addition, probe L was successfully incorporated into test strips for the quantitative detection of Zn2+.

Molecular circuit for exponentiation based on the domain coding strategy.

DNA strand displacement (DSD) is an efficient technology for constructing molecular circuits. However, system computing speed and the scale of logical gate circuits remain a huge challenge. In this paper, a new method of coding DNA domains is proposed to carry out logic computation. The structure of DNA strands is designed regularly, and the rules of domain coding are described. Based on this, multiple-input and one-output logic computing modules are built, which are the basic components forming digital circuits. If the module has n inputs, it can implement 2n logic functions, which reduces the difficulty of designing and simplifies the structure of molecular logic circuits. In order to verify the superiority of this method for developing large-scale complex circuits, the square root and exponentiation molecular circuits are built. Under the same experimental conditions, compared with the dual-track circuits, the simulation results show that the molecular circuits designed based on the domain coding strategy have faster response time, simpler circuit structure, and better parallelism and scalability. The method of forming digital circuits based on domain coding provides a more effective way to realize intricate molecular control systems and promotes the development of DNA computing.

Diaminomaleonitrile Schiff base with phenothiazine aldehyde as multimode chemosensor for copper ions and its application

A diaminomaleonitrile and phenothiazine coupled probe P was synthesized and structurally characterized by FTIR, NMR, mass, and single-crystal X-ray diffraction analysis. The probe P crystallizes in a monoclinic P21/c space group and is very selective to Cu2+ ions in ACN: H2O (8:2, v/v). Probe P exhibits a visible color change from yellow-orange to colorless and turn-on blue fluorescence with Cu2+ ions. The probe P could form a 1:1 stoichiometry complex with Cu2+ ions with an estimated binding constant of 3.24 × 104 M−1. The binding mechanism was studied using the EPR, FTIR, ESI-mass, and DFT/TD-DFT calculations. The multimode probe P could detect Cu2+ ions down to 0.86 µM, 1.45 µM, and 5.68 nM by spectrophotometry, smartphone-integrated RGB, and spectrofluorometry methods, respectively. The probe P-loaded silica test strips were used qualitatively to recognize Cu2+ ions in a water medium. The dynamic response of probe P with Cu2+ and Na2EDTA was used to construct the molecular logic circuit. Also, probe P was used to detect Cu2+ ions in the DrG cell line and zebrafish larvae.

Chromogenic, specific cascade detection of fluoride and alkaline earth metal ions

A salen-based colorimetric chemosensor (MM) has been designed and synthesized to selectively recognize F− and alkaline earth metal ions in solution and solid phase, respectively. A ratiometric UV–visible absorption spectral change with a colorimetric visualization from yellow to pink is observed in the presence of F− ions. The detection of F− ions is fully reversible in alkaline earth metal ions. The limit of detection (LOD) of F− ions by our as-prepared MM could be possible down to the μM range. A paper strips-based test kit has been fabricated to detect F− ions selectively by the naked eye. A smartphone-based assay analysis is also successfully performed to identify F− ions in the non-aqueous media. Such a dual ions sensing system with excellent reversibility and repeatability prompted us to consider probe MM a viable choice for fabricating molecular logic circuits and set-reset memorized molecular devices.

Modeling of molecular logic circuits using switching property of bipyridine–biborinine molecular diodes

Many researchers have focused on molecular electronics, and this field can progress faster by applying semiconductors to molecular modeling. In this work, two middle rings of a bipyridine–biborinine molecular diode are rotated from 25∘ to 90∘ such that the current along the molecule is reduced. The current is minimum and almost zero at 90∘, while it is maximum at 25∘. Accordingly, considering these two angles, the molecule can act as a switching device when the two middle rings are rotated. The bipyridine–biborinine molecular diode is modeled considering the effect of rotation by including two resistors in the model. Two parallel diodes are used in this modeling for pyridine and borinine rings. The ideality factors of these diodes are varied based on the electronegativity of pyridine and borinine rings. This model is then applied to consider different molecular logic gates such as NAND, NOR, NOT, OR and AND gates, as well as molecular logic circuits (half adder and full adder), using the unique capabilities of the LTspice software.

A Tutorial Review on the Fluorescent Probes as a Molecular Logic Circuit-Digital Comparator.

The rapid progress in the field of fluorescent probes and fluorescent sensing material extended this research area toward more complex molecular logic gates capable of carrying out a variety of sensing functions simultaneously. These molecules are able to calculate a composite result in which the analysis is not performed by a man but by the molecular device itself. Since the first report by de Silva of AND molecular logic gate, all possible logic gates have been achieved at the molecular level, and currently, utilization of more complicated molecular logic circuits is a major task in this field. Comparison between two digits is the simplest logic operation, which could be realized with the simplest logic circuit. That is why the right understanding of the applied principles during the implementation of molecular digital comparators could play a critical role in obtaining logic circuits that are more complicated. Herein, all possible ways for the construction of comparators on the molecular level were discussed, and recent achievements connected with these devices were presented.

Design of two different functional molecular logic devices based on hybrid fluorescence resonance­electron exchange energy transfer

Faster and more convenient construction of different functional multi-input–multi-output molecular logic devices has become a current research hotspot. In this study, a complex was synthesized using bovine serum albumin (BSA) and hydrazide dihydroxydisalicylaldehyde by a combinatorial approach. Then, the interaction mechanism was investigated by fluorescence spectroscopy and molecular simulation. Both methods revealed that the interaction between BSA and hydrazide dihydroxydisalicylaldehyde mainly occurred at site I of BSA. The main types of interactions included hydrogen bonding and van der Waals forces. Based on hybridized fluorescence resonance and electron exchange energy transfer, the complex generated two fluorescence emission peaks. Then, a digital comparator and a molecular logic circuit were designed using different metal ions or pH to modulate the output signals. Notably, the apparent increase in the fluorescence lifetime of the donor serves as an important basis for electron exchange between the donor and the acceptor.

Speed and Correctness Guarantees for Programmable Enthalpy-Neutral DNA Reactions†.

Molecular control circuits embedded within chemical systems to direct molecular events have transformative applications in synthetic biology, medicine, and other fields. However, it is challenging to understand the collective behavior of components due to the combinatorial complexity of possible interactions. Some of the largest engineered molecular systems to date have been constructed using DNA strand displacement reactions, in which signals can be propagated without a net change in base pairs (enthalpy neutral). This flexible and programmable component has been used for constructing molecular logic circuits, smart structures and devices, for systems with complex autonomously generated dynamics, and for diagnostics. Limiting their utility, however, strand displacement systems are susceptible to the spurious release of output in the absence of the proper combination of inputs (leak), as well as reversible unproductive binding (toehold occlusion) and spurious displacement that slow down desired kinetics. We systematize the properties of the simplest enthalpy-neutral strand displacement cascades (logically linear topology), and develop a taxonomy for the desired and undesired properties affecting speed and correctness, and trade-offs between them based on a few fundamental parameters. We also show that enthalpy-neutral linear cascades can be engineered with stronger thermodynamic guarantees to leak than non-enthalpy-neutral designs. We confirm our theoretical analysis with laboratory experiments comparing the properties of different design parameters. Our method of tackling the combinatorial complexity using mathematical proofs can guide the engineering of robust and efficient molecular algorithms.

Multifunctional Exo III-assisted scalability strategy for constructing DNA molecular logic circuits.

The construction of logic circuits is critical to DNA computing. Simple and effective scalability methods have been the focus of attention in various fields related to constructing logic circuits. We propose a double-stranded separation (DSS) strategy to facilitate the construction of complex circuits. The strategy combines toehold-mediated strand displacement with exonuclease III (Exo III), which is a multifunctional nuclease. Exo III can quickly recognize an apurinic/apyrimidinic (AP) site. DNA oligos with an AP site can generate an output signal by the strand displacement reaction. However, in contrast to traditional strand displacement reactions, the double-stranded waste from the strand displacement can be further hydrolysed by the endonuclease function of Exo III, thus generating an additional output signal. The DSS strategy allows for the effective scalability of molecular logic circuits, enabling multiple logic computing capabilities simultaneously. In addition, we succeeded in constructing a logic circuit with dual logic functions that provides foundations for more complex circuits in the future and has a broad scope for development in logic computing, biosensing, and nanomachines.

Designing three digital logic circuits based on two-component molecular systems of a combination of BSA and N, N′-bis(salicylidene) - ethylenediamine

A compound generally has only a single maximum emission wavelength. Therefore, it is relatively difficult to construct a dual-output molecular logic circuit. Herein, a novel fluorescent probe is designed by combining BSA and N, N′-bis(salicylidene)-ethylenediamine. The fluorescence intensity of the probe significantly fluorescence responses at 350 nm or 440 nm changed when stimulated with Zn2+, Fe2+, Cu2+, and EDTAH2Na2. Consequently, three different functional dual-output digit logic circuits are successfully designed in an aqueous solution. This combination is versatile with an additional advantage of water-solubility. Simultaneously, this combination provides a good reference model in exploring Dexter energy transfer in fluorescent experiments.

A new azo Schiff base probe for detection of Cr3+, HSO4−, and CN−: Computational studies, 4-to-2 encoder, and integrated molecular logic circuits

A novel azo Schiff base chemosensor was synthesized via condensation reaction of azo chromophore with benzylamine. This chemosensor as a highly sensitive and selective probe indicated colorimetric response toward Cr3+ (from yellow to colorless) as well as CN− and HSO4− anions (from yellow to orange and yellow to colorless, respectively). The sensory behavior of this probe was investigated in CH3CN: H2O (4: 1 v/v) solution. Via UV–vis titration and Benesi– Hildebrand method, the binding constants (Ka) were determined. The limit of detection for Cr3+, HSO4−, and CN− was 1.76 × 10−10, 1.01 × 10−10, and 5.24 × 10−6 M, respectively. The stoichiometry binding ratios of chemosensor to Cr3+, HSO4−, and CN− were 2: 1, 1: 1, and 1: 2, respectively. L as a colorimetric chemosensor could successfully detect CN− in apple seed samples. DFT and TD-DFT calculations were used to investigate the colorimetric mechanism which was in line with the experimental results. The combinatorial circuit was designed by three logic gates (NOT, OR, and AND) using different output signals towards CN−, HSO4−, and Cr3+. If the suitable experimental condition is selected, the molecule shows the truth table in accordance to the 4-to-2 encoder characteristics. In the 4-to-2 encoder, four chemical inputs are compacted into two photonic outputs, out1 and out2, with absorption at 340 nm and 500 nm, respectively.

DNA circuits compatible encoder and demultiplexer based on a single biomolecular platform with DNA strands as outputs.

A series of multiple logic circuits based on a single biomolecular platform is constructed to perform nonarithmetic and arithmetic functions, including 4-to-2 encoder, 1-to-2 demultiplexer, 1-to-4 demultiplexer, and multi-input OR gate. The encoder to a DNA circuit is the equivalent of a sensory receptor to a reflex arc. They all function to encode information from outside the pathway (DNA circuit or reflex arc) into a form that subsequent pathways can recognize and utilize. Current molecular encoders are based on optical or electrical signals as outputs, while DNA circuits are based on DNA strands as transmission signals. The output of existing encoders cannot be recognized by subsequent DNA circuits. It is the first time the DNA-based encoder with DNA strands as outputs can be truly applied to the DNA circuit, enabling the application of DNA circuits in non-binary biological environments. Another novel feature of the designed system is that the developed nanodevices all have a simple structure, low leakage and low crosstalk, which allows them to implement higher-level encoders and demultiplexers easily. Our work is based on the idea of complex functionality in a simple form, which will also provide a new route for developing advanced molecular logic circuits.