Contrary Logic Pair Library, Parity Generator/Checker and Various Concatenated Logic Circuits Engineered by a Label-Free and Immobilization-Free Electrochemiluminescence Resonance Energy Transfer System

Empowering DNA-Based Information Processing: Computation and Data Storage

Information processing is a critical topic in the digital age, as silicon-based circuits face unprecedented challenges such as data explosion, immense energy consumption, and approaching physical limits. Deoxyribonucleic acid (DNA), naturally selected as a carrier for storing and using genetic information, possesses unique advantages for information processing, which has given rise to the emerging fields of DNA computing and DNA data storage. To meet the growing practical demands, a wide variety of materials and interfaces have been introduced into DNA information processing technologies, leading to significant advancements. This review summarizes the advances in materials and interfaces that facilitate DNA computation and DNA data storage. We begin with a brief overview of the fundamental functions and principles of DNA computation and DNA data storage. Subsequently, we delve into DNA computing systems based on various materials and interfaces, including microbeads, nanomaterials, DNA nanostructures, hydrophilic-hydrophobic compartmentalization, hydrogels, metal-organic frameworks, and microfluidics. We also explore DNA data storage systems, encompassing encapsulation materials, microfluidics techniques, DNA nanostructures, and living cells. Finally, we discuss the current bottlenecks and obstacles in the fields and provide insights into potential future developments.

Immobilization-free and label-free electrochemical DNA biosensing based on target-stimulated release of redox reporter and its catalytic redox recycling

Herein, we demonstrate a simple, homogenous and label-free electrochemical biosensing system for sensitive nucleic acid detection based on target-responsive porous materials and nuclease-triggered target recycling amplification. The Fe(CN)63- reporter was firstly sealed into the pores of Fe3O4 nanoparticles by probe DNA. Target DNA recognition triggered the controllable release of Fe(CN)63- for the redox reaction with the electron mediator of methylene blue enriched in the dodecanethiol assembled electrode and thereby generating electrochemical signal. The exonuclease III (Exo III)-assisted target recycling and the catalytic redox recycling between Fe(CN)63- and methylene blue contributed for the enhanced signal response toward target recognition. The low detection limit toward target was obtained as 478 fM and 1.6 pM, respectively, by square wave voltammetry and cyclic voltammetry methods. It also possessed a well-discrimination ability toward mismatched strands and high tolerance to complex sample matrix. The coupling of bio-gated porous nanoparticles, nuclease-assisted target amplification and catalytic redox recycling afforded the sensing system with well-controllable signal responses, sensitive and selective DNA detection, and good stability, reusability and reproducibility. It thus opens a new avenue toward the development of simple but sensitive electrochemical biosensing platform.

Logic Signal Amplification System for Sensitive Electrochemiluminescence Detection and Subtype Identification of Cancer Cells

Achieving sensitive detection and accurate identification of cancer cells is vital for diagnosing and treating the disease. Here, we developed a logic signal amplification system using DNA tetrahedron-mediated three-dimensional (3D) DNA nanonetworks for sensitive electrochemiluminescence (ECL) detection and subtype identification of cancer cells. Specially designed hairpins were integrated into DNA tetrahedral nanostructures (DTNs) to perform a catalytic hairpin assembly (CHA) reaction in the presence of target microRNA, forming hyperbranched 3D nanonetworks. Benefiting from the "spatial confinement effect," the DNA tetrahedron-mediated catalytic hairpin assembly (DTCHA) reaction displayed significantly faster kinetics and greater cycle conversion efficiency than traditional CHA. The resulting 3D nanonetworks could load a large amount of Ru(phen)32+, significantly enhancing its ECL signal, and exhibit detection limits for both miR-21 and miR-141 at the femtomolar level. The biosensor based on modular logic gates facilitated the distinction and quantification of cancer cells and normal cells based on miR-21 levels, combined with miR-141 levels, to further identify different subtypes of breast cancer cells. Overall, this study provides potential applications in miRNA-related clinical diagnostics.

A facile, low-cost bimetallic iron-nickel MOF nanozyme-propelled ratiometric fluorescent sensor for highly sensitive and selective uric acid detection and its smartphone application

As a kind of well-known disease biomarker, uric acid (UA) is closely associated with normal metabolism and health. Despite versatile nanozymes facilitating the analysis of UA, most previous works could only generate single-signal outputs with unsatisfactory detection performance. Exploring a novel ratiometric fluorescent UA sensor with high sensitivity, reliability and portable sensing ability based on facile, low-cost nanozymes is still challenging. Herein, we report the first metal-organic-framework (MOF) nanozyme-originated ratiometric fluorescent UA sensor based on Fe3Ni-MOF-NH2 propelled UA/uricase/o-phenylenediamine tandem catalytic reaction. Different from previous reports, the peroxidase-like property and fluorescence of Fe3Ni-MOF-NH2 were simultaneously employed. In the absence of UA, only the MOF's fluorescence at 430 nm (FI430) can be observed, while the addition of UA will initiate UA/uricase catalytic reaction, and the generated H2O2 could oxidize o-phenylenediamine into highly fluorescent 2,3-diaminophenazine (DAP) (emission at 565 nm, FI565) under the catalysis of the MOF nanozyme. Coincidently, MOF's fluorescence can be quenched by DAP via the inner filter effect, resulting in a low FI430 value and high FI565 value, respectively. Therefore, H2O2 and UA can be alternatively detected through monitoring the above contrary fluorescence changes. The limit of detection for UA is 24 nM, which is much lower than those in most previous works, and the lowest among nanozyme-based ratiometric fluorescent UA sensors reported to date. Moreover, the portable sensing of UA via smartphone-based RGB analysis was facilely achieved by virtue of the above nanozyme-propelled tandem catalytic system, and MOF nanozyme-based molecular contrary logic pairs were further implemented accordingly.

A cost-effective, "mix & act" G-quadruplex/Cu (II) metal-nanozyme-based ratiometric fluorescent platform for highly sensitive and selective cysteine/bleomycin detection and multilevel contrary logic computing

Versatile nanozymes with fascinating catalytic properties provide inspiring and effective options for biosensing and pharmaceutical analysis. Herein, we report the first nanozyme-based ratiometric fluorescent platform for cysteine (Cys) and bleomycin (BLM) detection by harnessing the cost-effective and "mix & act" G-quadruplex/Cu(II) (G4/Cu) metal-nanozyme with satisfactory peroxidase-like activity, which was fully proven by circular dichroism (CD), electron paramagnetic resonance (EPR) spectra and reactive oxygen species (ROS) scavenging experiments. Based on the catalytic oxidation of G4/Cu metal-nanozyme toward two fluorescent substrates (Amplex Ultrared, AU; Scopoletin, Sc) with opposite responses in the presence of H2O2, and the specific interaction between Cu2+ and targets, we achieved the highly sensitive detection of Cys and BLM. Through recording the fluorescence changes of AU (emission at 590 nm, F590) and Sc (emission at 465 nm, F465), we obtained good linear relationships between ratiometric fluorescence values (F590/F465) and variable contents of targets, resulting in the competitive LODs of Cys (6.7 nM) and BLM (10 nM), respectively. Moreover, this platform presented high selectivity (without the need for masking agent) and acceptable performance in human serum samples. Furthermore, a library of DNA contrary logic pairs (CLPs) and multilevel concatenated circuits were fabricated based on the reverse dual-output of the above platform, enriching the building blocks of biocomputing. This work not only enlightened the design of affordable, "mix & act" type nanozyme-based ratiometric biosensors with high reliability, but also facilitated the pluralistic application of nucleic acid-templated nanozymes to innovative biocomputing.

Combination of Ternary Electrochemiluminescence System of BNQDs/AgMOG-K2S2O8 and Electrochemiluminescence Resonance Energy Transfer Strategy for Ultrasensitive Immunoassay of Amyloid-β Protein

In this work, based on boron nitride quantum dots (BNQDs) as energy donors and MnO2@MWCNTs-COOH as energy receptors, we designed an efficient electrochemiluminescence resonance energy transfer (ECL-RET) immunosensor for the detection of amyloid-β (Aβ42) protein, a biomarker of Alzheimer's disease (AD). First, the signal amplification of a ternary ECL system composed of BNQDs (as the ECL emitter), K2S2O8 (as the coreactant), and silver metal-organic gels (AgMOG, as the coreaction accelerator) was realized, and PDDA as stabilizer was added, a strong and stable initial ECL signal was obtained. AgMOG could not only support a large amount of BNQDs and Aβ42 capture antibody (Ab1) through Ag-N bond but also exhibit excellent ECL catalytic performance and enhance the luminescent intensity of BNQDs@PDDA-K2S2O8 system. In addition, due to the broad absorption spectrum of MnO2@MWCNTs-COOH and the extensive overlap with the ECL emission spectrum of BNQDs, the quenching probe Ab2-MnO2@MWCNTs-COOH could be introduced into the ternary system through a sandwich immune response. On this basis, the signal on-off ECL immunosensor was constructed to achieve the ultrasensitive detection of Aβ42 through signal transformation. Under the optimal conditions, the prepared ECL biosensor manifested a wide linear range (10 fg/mL-100 ng/mL) with a detection limit of 2.89 fg/mL and showed excellent stability, selectivity, and repeatability, which provided an effective strategy for the ultrasensitive detection of biomarkers in clinical analysis.

Toward Minute-Level DNA Computing: An Ultrafast, Cost-Effective, and Universal System for Lighting Up Various Concurrent DNA Logic Nanodevices (CDLNs) and Concatenated Circuits

DNA logic nanodevices are powerful tools for both molecular computing tasks and smart bioanalytical applications. Nevertheless, the hour-level operation time and high cost caused by the frequent redesign/reconstruction of gates, tedious strand-displacement reaction, and expensive labeled probes (or tool enzymes) in previous works are ineluctable drawbacks. Herein, we report an ultrafast and cost-effective system for engineering concurrent DNA logic nanodevices (CDLNs) by combining polythymine CuNCs with SYBR Green I (SG I) as universal dual-output producers. Particularly, benefiting from the concomitant minute-level quick response of both unlabeled illuminators and the exquisite strand-displacement-free design, all CDLNs including contrary logic pairs (YES∧NOT, OR∧NOR, and Even∧Odd number classifier), noncontrary ones (IDE∧IMP, OR∧NAND), and concatenated circuits are implemented in just 10 min via a "one-stone-two-birds" method, resulting in only 1/12 the operation time and 1/4 the cost needed in previous works, respectively. Moreover, all of them share the same threshold value, and the dual output can be easily visualized by the naked eye under a portable UV lamp, indicating the universality and practicality of this system. Furthermore, by exploiting the "positive/negative cross-verification" advantages of concurrent contrary logic, the smart in vitro analysis of the polyadenine strand and its polymerase is realized, providing novel molecular tools for the early diagnosis of cancer-related diseases.

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

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

Leveraging DNA-Based Nanostructures for Advanced Error Detection and Correction in Data Communication

This study demonstrates the implementation of the Hamming code using DNA-based nanostructures for error detection and correction in communication systems. The designed DNA nanostructures conduct logical operations to compute check codes and identify and correct erroneous data based on fluorescence signals. The execution of intricate DNA logic operations requires individuals with specialized training. By interpretation of the fluorescence signals generated by the DNA nanostructures, binary language can be extracted, effectively protecting data security. The findings highlight the potential of DNA as a versatile platform for reliable data transmission.

Implementing Logic Gates by DNA Crystal Engineering

DNA self-assembly computation is attractive for its potential to perform massively parallel information processing at the molecular level while at the same time maintaining its natural biocompatibility. It has been extensively studied at the individual molecule level, but not as much as ensembles in 3D. Here, the feasibility of implementing logic gates, the basic computation operations, in large ensembles: macroscopic, engineered 3D DNA crystals is demonstrated. The building blocks are the recently developed DNA double crossover-like (DXL) motifs. They can associate with each other via sticky-end cohesion. Common logic gates are realized by encoding the inputs within the sticky ends of the motifs. The outputs are demonstrated through the formation of macroscopic crystals that can be easily observed. This study points to a new direction of construction of complex 3D crystal architectures and DNA-based biosensors with easy readouts.

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.

Size-Independent Reconfigurable Logic Gate with Bismuth Oxide Based Photoelectrochemical Device

XOR gate, an important building block in computational circuits, is often constructed by combining other basic logic gates, and the hybridity inevitably leads to its complexity. A photoelectrochemical device could realize XOR function based on the current change of the photoelectrode; however, such signal is highly sensitive to photoelectrode size and therefore requires precise manufacturing at a high cost. Herein we developed a novel XOR gate based on the light-induced open-circuit potential (OCP) of the Bi₂O₃ photoelectrode. Surprisingly, the OCP of Bi₂O₃ does not increase with light intensity according to the traditional logarithmic relationship. Instead, an unusual decrease in OCP is observed at high light intensity, which is attributed to the dramatic light-induced increase in surface states that can be easily regulated by varying the oxygen partial pressure during reactive magnetron sputtering. Based on such a nonmonotonic variation of OCP, a facile Bi₂O₃-based gate is designed to realize the XOR function. Unlike the commonly used current signal, OCP is size independent, and therefore, the Bi₂O₃-based gate does not require high manufacturing accuracy. Moreover, in addition to XOR, the Bi₂O₃-based PEC gate also demonstrates great versatility in realizing other logic functions including AND, OR, NOT, NIH, NAND, and NOR. The strategy of modulating and applying nonmonotonic OCP signal opens a new avenue for designing size-independent reconfigurable logic gates at low manufacturing cost.

Functionalized Graphitic Carbon Nitride Nanomaterials for Electrochemiluminescent Detection of Cancer Cells

Biosensors capable of detecting cancer cell quantity is significant for cancer pathological investigation and prognosis. Herein, a facile electrochemiluminescent (ECL) biosensor is developed for cancer cell detection by comprehensively utilizing the features of functionalized graphitic carbon nitride (g-CN) nanomaterials like well film-forming capability and functionalization level tunability. The solid-state ECL biosensor is fabricated via a simple dropping-drying method by subsequent deposition of g-CN nanosheets/graphene oxide nanocomposites (CNNS/GO) as ECL emitter, folate functionalized g-CN quantum dots (FA-CNQDs) as cancer cell capture agent, and bull serum albumin (BSA) as blocker to prevent nonspecific binding on glassy carbon electrodes (GCEs). The strong and stable ECL emission of CNNS/GO along with the tunability of FA content in FA-CNQDs endow the ECL biosensor with competitive sensitivity, which is able to detect folate receptor-positive cancer cells (HepG2) in the concentration range of 102 − 104 cells ml−1 under optimal condition. Additionally, the proposed ECL biosensor shows high specificity, reproducibility and long-term stability as well as good reliability towards serum sample detection.

Enhanced Electrochemiluminescence of Graphitic Carbon Nitride by Adjustment of Carbon Vacancy for Supersensitive Detection of MicroRNA

Herein, a supersensitive biosensor was constructed by using graphitic carbon nitride with a carbon vacancy (V_C-g-C₃N₄) as an efficient electrochemiluminescence (ECL) emitter for detection of microRNA-21 (miRNA-21). Impressively, V_C-g-C₃N₄ could be prepared by formaldehyde (HCHO)-assisted urea ploycondensation, and the concentration of the carbon vacancy could be controlled by adjusting the dosage of HCHO to improve the ECL performance, in which the carbon vacancy could improve the charge carrier transfer to enhance the conductivity and it also could be used as an electron trap to prevent electrode passivation and facilitate the adsorption of coreactant S₂O₈^2- to accelerate its reduction. Compared with original g-C₃N₄, the introduction of carbon vacancies resulted in a significant enhancement of the ECL efficiency of V_C-g-C₃N₄. With the aid of improved cascade strand displacement amplification (IC-SDA), the ECL biosensor realized sensitive detection of miRNA-21 with a low detection limit of 3.34 aM. This successful strategy promoted the development of g-C₃N₄ in the ECL field to construct the sensitive biosensor for molecular and disease diagnoses.

Mercury mediated DNA-Au/Ag nanocluster ensembles to generate a gray code encoder for biocomputing

Boolean operations utilizing DNA as a platform for biocomputing have become a promising tool for next-generation bio-molecular computers. In the whole process of any binary data transmission, bit errors are unavoidable and commonly occur. Cascades of exclusive-OR (XOR) operations show the great potential to evaluate these errors by introducing a parity generator (pG) and a parity checker (pC). Herein, we constructed a DNA hybrid architecture platform employing a chemosensing ensemble of mercury-mediated DNA-Au/Ag nanoclusters (M-Au/Ag NCs) to operate unconventional pG/pC for "error detection". Taking advantage of pG/pC, the transmitted and received data is converted to secure information using a binary to gray code encoder. To the best of our knowledge, this is the first molecular gray code encoder for biocomputing, which discovers an exciting avenue to protect information security through sophisticated logic circuits.

Nucleic acid isothermal amplification-based soft nanoarchitectonics as an emerging electrochemical biosensing platform

The emergence of nucleic acid isothermal amplification strategies based on soft nanoarchitectonics offers a new dimension to the traditional electrochemical technique, particularly because of its flexibility, high efficiency, and increased sensitivity for analytical applications. Various DNA/RNA isothermal amplification strategies have been developed for the design and fabrication of new electrochemical biosensors for efficient and important biomolecular detection. Herein, we provide an overview of recent efforts in this research field and the strategies for signal-amplified sensing systems, with their biological applications, current challenges and prospects in this promising new area.