A DNA-based system for selecting and displaying the combined result of two input variables

Understanding the relationship between sequences and kinetics of DNA strand displacements

Precisely modulating the kinetics of toehold-mediated DNA strand displacements (TMSD) is essential for its application in DNA nanotechnology. The sequence in the toehold region significantly influences the kinetics of TMSD. However, due to the large sample space resulting from various arrangements of base sequences and the resulted complex secondary structures, such a correlation is not intuitive. Herein, machine learning was employed to reveal the relationship between the kinetics of TMSD and the toehold sequence as well as the correlated secondary structure of invader strands. Key factors that influence the rate constant of TMSD were identified, such as the number of free hydrogen bonding sites in the invader, the number of free bases in the toehold, and the number of hydrogen bonds in intermediates. Moreover, a predictive model was constructed, which successfully achieved semi-quantitative prediction of rate constants of TMSD even with subtle distinctions in toehold sequence.

Tuning the stability of DNA tetrahedra with base-stacking interactions

DNA nanotechnology relies on programmable anchoring of regions of single-stranded DNA through base pair hybridization to create nanoscale objects such as polyhedra, tubes, sheets, and other desired shapes. Recent work from our lab measured energetics of base-stacking interactions and suggested that terminal stacking interactions between two adjacent strands could be an additional design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra held together with sticky ends which contain identical base pairing interactions but different terminal stacking interactions. Testing all 16 possible combinations, we found that the melting temperature of DNA tetrahedra varied by up to 10 °C from altering a single base stack in the design while retaining a common sequence in a 6-nt sticky end. This work clearly shows that stacking design influences DNA tetrahedra stability in a substantial and predictable way. The results likely apply to other types of DNA nanostructures and suggest that terminal stacking interactions play an integral role in formation and stability of DNA nanostructures.

Prediction and Control in DNA Nanotechnology

DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.

Emerging Approaches to DNA Data Storage: Challenges and Prospects

With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 10¹⁴ GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 10³ GB/mm³. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies.

Applications of Functional DNA Materials in Immunomodulatory Therapy

In recent years, nanoscale or microscale functional materials derived from DNA have shown great potential for immunotherapy as superior delivery carriers. DNA nanostructures with excellent programmability and addressability enable the precise assembly of molecules or nanoparticles. DNA hydrogels have predictable structures and adjustable mechanical strength, thus being advantageous in controllable release of cargos. In addition, utilizing systematic evolution of ligands by exponential enrichment technology, a variety of DNA aptamers have been screened for specific recognition of ions, molecules, and even cells. Moreover, a wide variety of chemical modifications can further enrich the function of DNA. The unique advantages of functional DNA materials make them extremely attractive in immunomodulation. Recently, functional DNA materials-based immunotherapy has shown great potential in fighting against many diseases like cancer, viral infection, and inflammation. Therefore, in this review, we focus on discussing the progress of the applications of functional DNA materials in immunotherapy; before that, we also summarize the characteristics of the functional DNA materials descried above. Finally, we discuss the challenges and future opportunities of functional DNA materials in immunomodulatory therapy.

Cell-Membrane-Anchored DNA Logic-Gated Nanoassemblies for In Situ Extracellular Bioimaging

Extracellular K⁺ and adenosine triphosphate (ATP) levels are significantly elevated in the tumor microenvironment (TME) and can be used as biomarkers for early cancer detection and tumor localization. Most reported TME sensors only respond to single abnormal factors, resulting in a lack of accuracy and specificity for the detection of complex environments. Thus, precisely locating the TME remains challenging. In this work, we aimed to develop an intelligent DNA nanoassembly controlled by a "YES-AND" logic circuit using a bimolecular G-quadruplex (G4) and ATP aptamer as logical control units. As a proof of concept, in the presence of K⁺ (input 1) and ATP (input 2), the YES-AND Boolean operator returned a true value and the output was the fluorescence resonance energy transfer (FRET) signal, indicating high sensitivity and selectivity. After being anchored to living cell surfaces, this logic nanosensor imaged extracellular K⁺ and ATP present at abnormal levels in situ. Owing to diverse disease markers in the TME, this novel logic sensor might hold great promise for the targeted delivery of intelligent anticancer drugs and Boolean logic-controlled treatment.

Nanopore Detection Assisted DNA Information Processing

The deoxyribonucleotide (DNA) molecule is a stable carrier for large amounts of genetic information and provides an ideal storage medium for next-generation information processing technologies. Technologies that process DNA information, representing a cross-disciplinary integration of biology and computer techniques, have become attractive substitutes for technologies that process electronic information alone. The detailed applications of DNA technologies can be divided into three components: storage, computing, and self-assembly. The quality of DNA information processing relies on the accuracy of DNA reading. Nanopore detection allows researchers to accurately sequence nucleotides and is thus widely used to read DNA. In this paper, we introduce the principles and development history of nanopore detection and conduct a systematic review of recent developments and specific applications in DNA information processing involving nanopore detection and nanopore-based storage. We also discuss the potential of artificial intelligence in nanopore detection and DNA information processing. This work not only provides new avenues for future nanopore detection development, but also offers a foundation for the construction of more advanced DNA information processing technologies.

Three-dimensional electron ptychography of organic-inorganic hybrid nanostructures

Three dimensional scaffolded DNA origami with inorganic nanoparticles has been used to create tailored multidimensional nanostructures. However, the image contrast of DNA is poorer than those of the heavy nanoparticles in conventional transmission electron microscopy at high defocus so that the biological and non-biological components in 3D scaffolds cannot be simultaneously resolved using tomography of samples in a native state. We demonstrate the use of electron ptychography to recover high contrast phase information from all components in a DNA origami scaffold without staining. We further quantitatively evaluate the enhancement of contrast in comparison with conventional transmission electron microscopy. In addition, We show that for ptychography post-reconstruction focusing simplifies the workflow and reduces electron dose and beam damage.

The authors demonstrate electron ptychographic computed tomography by simultaneously recording high contrast data from both the organic- and inorganic components in a 3D DNA-origami framework hybrid nanostructure.

A facile biosynthesis strategy of plasmid DNA-derived nanowires for readable microRNA logic operations

Multiple microRNAs (miRNAs) logical assays have attracted wide attention recently, which can be applied to mimic and reveal cellular events at the molecular level. However, it remains challenging to develop...

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.

DNA-based constitutional dynamic networks as functional modules for logic gates and computing circuit operations

A nucleic acid-based constitutional dynamic network (CDN) is introduced as a single computational module that, in the presence of different sets of inputs, operates a variety of logic gates including a half adder, 2 : 1 multiplexer and 1 : 2 demultiplexer, a ternary multiplication matrix and a cascaded logic circuit. The CDN-based computational module leads to four logically equivalent outputs for each of the logic operations. Beyond the significance of the four logically equivalent outputs in establishing reliable and robust readout signals of the computational module, each of the outputs may be fanned out, in the presence of different inputs, to a set of different logic circuits. In addition, the ability to intercommunicate constitutional dynamic networks (CDNs) and to construct DNA-based CDNs of higher complexity provides versatile means to design computing circuits of enhanced complexity.

Processing DNA-Based Molecular Signals into Graphical Displays

DNA is now well-established as a nanoscale building material with applications in fields such as biosensing and molecular computation. Molecular processes such as logic gates, nucleic acid circuits, and multiplexed detection have used different readout strategies to measure the output signal. In biosensing, this output can be the diagnosis of a disease biomarker, whereas in molecular computation, the output can be the result of a mathematical operation carried out using DNA. Recent developments have shown that the output of such processes can be displayed graphically as a macroscopic symbol or an alphanumeric character on multiwell plates, microarray chips, gels, lateral flow devices, and DNA origami surfaces. This review discusses the concepts behind such graphical readouts of molecular events, available display platforms, and the advantages and challenges in adapting such methods for practical use. Graphical display systems have the potential to be used in the creation of intelligent computing and sensing devices by which nanoscale binding events are translated into macroscopic visual readouts.

Size-selective molecular recognition based on a confined DNA molecular sieve using cavity-tunable framework nucleic acids

Size selectivity is an important mechanism for molecular recognition based on the size difference between targets and non-targets. However, rational design of an artificial size-selective molecular recognition system for biological targets in living cells remains challenging. Herein, we construct a DNA molecular sieve for size-selective molecular recognition to improve the biosensing selectivity in living cells. The system consists of functional nucleic acid probes (e.g., DNAzymes, aptamers and molecular beacons) encapsulated into the inner cavity of framework nucleic acid. Thus, small target molecules are able to enter the cavity for efficient molecular recognition, while large molecules are prohibited. The system not only effectively protect probes from nuclease degradation and nonspecific proteins binding, but also successfully realize size-selective discrimination between mature microRNA and precursor microRNA in living cells. Therefore, the DNA molecular sieve provides a simple, general, efficient and controllable approach for size-selective molecular recognition in biomedical studies and clinical diagnoses.

Size-selective discrimination is an issue in biosensing. Here, the authors report on a size selective DNA nanocage which excludes agents based on size and protects the probes against degradation, and demonstrate the discrimination between mature and precursor miRNA.

Near-Atomic Fabrication with Nucleic Acids

Nucleic acids hold great promise for bottom-up construction of nanostructures via programmable self-assembly. Especially, the emerging of advanced sequence design principles and the maturation of chemical synthesis of nucleic acids together have led to the rapid development of structural DNA/RNA nanotechnology. Diverse nucleic acids-based nano objects and patterns have been constructed with near-atomic resolutions and with controllable sizes and geometries. The monodispersed distribution of objects, the up-to-submillimeter scalability of patterns, and the excellent feasibility of carrying other materials with spatial and temporal resolutions have made DNA/RNA assemblies extremely unique in molecular engineering. In this review, we summarize recent advances in nucleic acids-based (mainly DNA-based) near-atomic fabrication by focusing on state-of-the-art design techniques, toolkits for DNA/RNA nanoengineering, and related applications in a range of areas.

Encoding Carbon Nanotubes with Tubular Nucleic Acids for Information Storage

DNA has evolved to be a type of unparalleled material for storing and transmitting genetic information. Much recent attention has been drawn to translate the natural specificity of DNA hybridization reactions for information storage in vitro. In this work, we developed a new type of tubular nucleic acid (TNA) by condensing DNA chains on the surface of one-dimensional carbon nanotubes (CNTs). We find that DNA interacts with CNTs in a sequence-specific manner, resulting in different conformations including helix, i-motif, and G-quadruplex. Atomic force microscopic (AFM) imaging revealed that TNAs exhibit distinct patterns with characteristic height and distance that can be exploited for two-dimensional encoding on CNTs. We further demonstrate the use of TNA-CNT for information storage with visual output. This noncanonical, DNA hybridization-free strategy provides a new route to DNA-based data storage.

Valency-Controlled Molecular Spherical Nucleic Acids with Tunable Biosensing Performances

Spherical nucleic acids (SNAs) play critical roles in many fields, such as molecular diagnostics, disease therapeutics, and materials application. Due to the important role of DNA density on the properties of SNAs, the controlled synthesis of monodisperse SNAs with precise DNA density is an important approach for the structure-function relationship study and finite functions regulation of SNAs. In particular, the construction of monodisperse SNAs in a valency-tunable and site-specific manner is highly important; however, it is still challenging. Herein, on the basis of the high controllability, nanometer precision, and addressable modification ability of framework nucleic acid (FNA), we develop the concept of valency-controlled framework nucleic acid core-based molecular spherical nucleic acids (FNA-mSNAs) with tunable biosensing performances. The FNA-mSNAs consist of a valency-tunable FNA-based DNA nanocube as the core and a controlled, precise number of DNA strands per core. By simply alternating the binding site number for shell DNA strands on the DNA nanocube, homogeneous FNA-mSNAs with different valencies were easily designed, which enabled the molecular level study of the effect of valency on their properties, such as nuclease stability and cellular uptake. Furthermore, taking advantage of the addressable modification ability of FNA, the first heterogeneous molecular SNAs with tunable valency were demonstrated. Importantly, the valency of heterogeneous FNA-mSNAs was able to tune their biosensing performance, such as response dynamics, detection sensitivity, and response range. With these remarkable features, FNA-mSNAs provide new research methods for the development of functional SNAs at the molecular level for a wide range of biological applications.

A Molecular Hero Suit for In Vitro and In Vivo DNA Nanostructures

Precise control of DNA base pairing has rapidly developed into a field full of diverse nanoscale structures and devices that are capable of automation, performing molecular analyses, mimicking enzymatic cascades, biosensing, and delivering drugs. This DNA-based platform has shown the potential of offering novel therapeutics and biomolecular analysis but will ultimately require clever modification to enrich or achieve the needed "properties" and make it whole. These modifications total what are categorized as the molecular hero suit of DNA nanotechnology. Like a hero, DNA nanostructures have the ability to put on a suit equipped with honing mechanisms, molecular flares, encapsulated cargoes, a protective body armor, and an evasive stealth mode.

Solving mazes with single-molecule DNA navigators

Molecular devices with information-processing capabilities hold great promise for developing intelligent nanorobotics. Here we demonstrate a DNA navigator system that can perform single-molecule parallel depth-first search on a ten-vertex rooted tree defined on a two-dimensional DNA origami platform. Pathfinding by the DNA navigators exploits a localized strand exchange cascade, which is initiated at a unique trigger site on the origami with subsequent automatic progression along paths defined by DNA hairpins containing a universal traversal sequence. Each single-molecule navigator autonomously explores one of the possible paths through the tree. A specific solution path connecting a given pair of start and end vertices can then be easily extracted from the set of all paths taken by the navigators collectively. The solution path laid out on origami is illustrated with single-molecule imaging. Our approach points towards the realization of molecular materials with embedded computational functions operating at the single-molecule level.

A resettable supramolecular platform for constructing scalable encoders

A supramolecular platform prototype for implementing resettable encoding functions was designed, which could be configured into a series of encoders, from 4-to-2 to 7-to-3, and even 14-to-4 ECs.

Dual-Emitting Eu(III)-Cu(II) Heterometallic-Organic Framework: Simultaneous, Selective, and Sensitive Detection of Hydrogen Sulfide and Ascorbic Acid in a Wide Range

As important biomolecules, the deficiency or maladjustment of hydrogen sulfide (H₂S) or ascorbic acid (AA) is associated with the symptoms of the same disease (e.g., cardiovascular disease or cancer). There is an urgent need to develop a fluorescent probe capable of distinguishing between H₂S and AA simultaneously. Here, we report the syntheses, structure, and property of the first dual-detection fluorescent probe which can differentiate H₂S or/and AA in aqueous media. Accordingly, a novel [EuCu(pydc)₂(ox)_0.5(H₂O)₃·1.5H₂O]_{2 n} (1, H₂pydc = 2,3-pyridinedicarboxylic acid and ox = oxalic acid) for selective and sensitive detection of H₂S and AA in a wide range has been constructed (H₂S: [130 nM, +∞); AA: [55 nM, +∞)), exhibiting excellent catalytic activity comparable to horseradish peroxidase. In addition, the highly efficient detection in human serum sample also proves the potential application in medical diagnosis. Meanwhile, a combinatorial logic gate (AND(INH)-OR) based on activated 1 has also been constructed. Furthermore, this approach for simultaneous H₂S and AA detection suggests that the current work will expand the potential application of metal-organic frameworks for dual or multiple detections in biomedical fields.

DNA quadruplexes as molecular scaffolds for controlled assembly of fluorogens with aggregation-induced emission

Aggregation-induced emission (AIE) can be generated due to the restriction of intramolecular motions. The controllable assembly of fluorogens with AIE properties (AIEgens) is able to provide a new opportunity for precise manipulation of fluorescent signal transduction. Here, a tetrapod DNA quadruplex (TP-G4) was designed as a molecular scaffold for assembly and precise modulation of light emission of an oligonucleotide-grafted fluorogen with aggregation-induced emission (Oligo-AIEgen). The Oligo-AIEgen was synthesized by attaching the AIEgen to the 3'-terminus of the oligonucleotide through a dibenzylcyclooctyne mediated coupling reaction. The AIEgen emitted no detectable fluorescence in the context of a double-stranded structure. When hybridized to the parallel-stranded TP-G4, several AIEgens were located in close proximity to generate fluorescence. The fluorescence intensity has been precisely regulated by manipulation of the spacer length between the core structure of the scaffold and AIEgen, as well as by altering the quartet number of the G-quadruplex. Similar control of fluorescence was also demonstrated using tetramolecular and bimolecular i-motif quadruplex structures as the scaffolds. These scaffolds provide a proof of concept on the manipulation of molecular interactions, which forms a universal molecular tool for the design of new biosensing strategies.

DNA Nanotechnology-Enabled Drug Delivery Systems

Over the past decade, we have seen rapid advances in applying nanotechnology in biomedical areas including bioimaging, biodetection, and drug delivery. As an emerging field, DNA nanotechnology offers simple yet powerful design techniques for self-assembly of nanostructures with unique advantages and high potential in enhancing drug targeting and reducing drug toxicity. Various sequence programming and optimization approaches have been developed to design DNA nanostructures with precisely engineered, controllable size, shape, surface chemistry, and function. Potent anticancer drug molecules, including Doxorubicin and CpG oligonucleotides, have been successfully loaded on DNA nanostructures to increase their cell uptake efficiency. These advances have implicated the bright future of DNA nanotechnology-enabled nanomedicine. In this review, we begin with the origin of DNA nanotechnology, followed by summarizing state-of-the-art strategies for the construction of DNA nanostructures and drug payloads delivered by DNA nanovehicles. Further, we discuss the cellular fates of DNA nanostructures as well as challenges and opportunities for DNA nanostructure-based drug delivery.

Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing

Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.

Addressable configurations of DNA nanostructures for rewritable memory

DNA serves as nature's information storage molecule, and has been the primary focus of engineered systems for biological computing and data storage. Here we combine recent efforts in DNA self-assembly and toehold-mediated strand displacement to develop a rewritable multi-bit DNA memory system. The system operates by encoding information in distinct and reversible conformations of a DNA nanoswitch and decoding by gel electrophoresis. We demonstrate a 5-bit system capable of writing, erasing, and rewriting binary representations of alphanumeric symbols, as well as compatibility with 'OR' and 'AND' logic operations. Our strategy is simple to implement, requiring only a single mixing step at room temperature for each operation and standard gel electrophoresis to read the data. We envision such systems could find use in covert product labeling and barcoding, as well as secure messaging and authentication when combined with previously developed encryption strategies. Ultimately, this type of memory has exciting potential in biomedical sciences as data storage can be coupled to sensing of biological molecules.

A detailed experimental study of a DNA computer with two endonucleases

Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro's group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effect of the number of states, the length of input data, and the nondeterminism on the computing process. We also tested different automata (with three, four, and six states) running on various accepted input words of different lengths such as ab, aab, aaab, ababa, and of an unaccepted word ba. Moreover, this article presents the reaction optimization and the methods of eliminating certain biochemical problems occurring in the implementation of a biomolecular DNA automaton based on two endonucleases.

Cavity-Type DNA Origami-Based Plasmonic Nanostructures for Raman Enhancement

DNA origami has been established as addressable templates for site-specific anchoring of gold nanoparticles (AuNPs). Given that AuNPs are assembled by charged DNA oligonucleotides, it is important to reduce the charge repulsion between AuNPs-DNA and the template to realize high yields. Herein, we developed a cavity-type DNA origami as templates to organize 30 nm AuNPs, which formed dimer and tetramer plasmonic nanostructures. Transmission electron microscopy images showed that high yields of dimer and tetramer plasmonic nanostructures were obtained by using the cavity-type DNA origami as the template. More importantly, we observed significant Raman signal enhancement from molecules covalently attached to the plasmonic nanostructures, which provides a new way to high-sensitivity Raman sensing.

Engineering chemical reaction modules via programming the assembly of DNA hairpins

The architect of enzyme-free chemical reaction modules, working as building blocks in implementing complex computing tasks, was achieved by modulating the assembly of DNA hairpins, including non-catalytic and catalytic systems. The performance of heterogeneous outputted sequences, which were programmed on different hairpins for triggering the downstream reaction, was asymmetric in the non-catalytic system, whereas symmetric in the catalytic system. Furthermore, complicated DNA-only chemical modules possessing controllable species of inputs or outputs were constructed based on our strategy. The kinetic studies revealed that the performance of the chemical modules was toehold length correlated; on the basis of which, a DNA concentration monitor was constructed.

A DNA-based parity generator/checker for error detection through data transmission with visual readout and an output-correction function

During any type of binary data transmission, the occurrence of bit errors is an inevitable and frequent problem suffered. These errors, which have fatal effects on the correct logic computation, especially in sophisticated logic circuits, can be checked through insertion of a parity generator (pG) at the transmitting end and a parity checker (pC) at the receiving end. Herein, taking even pG/pC as a model device, we constructed the first DNA-based molecular parity generator/checker (pG/pC) for error detection through data transmission, on a universal single-strand platform according to solely DNA hybridization. Compared with previous pG/pC systems, the distinct advantage of this one is that it can present not only fluorescence signals but also visual outputs, which can be directly recognized by the naked eye, using DNA inputs modulated split-G-quadruplex and its DNAzyme as signal reporters, thus greatly extending its potential practical applications. More importantly, an "Output-Correction" function was introduced into the pC for the first time, in which all of the erroneous outputs can be adequately corrected to their normal states, guaranteeing the regular operation of subsequent logic devices. Furthermore, through negative logic conversion towards the constructed even pG/pC, the odd pG/pC with equal functions was obtained. Furthermore, this system can also execute multi-input triggered concatenated logic computations with dual output-modes, which largely fulfilled the requirements of complicated computing.

Exploiting Polydopamine Nanospheres to DNA Computing: A Simple, Enzyme-Free and G-Quadruplex-Free DNA Parity Generator/Checker for Error Detection during Data Transmission

Molecular logic devices with various functions play an indispensable role in molecular data transmission/processing. However, during any kinds of data transmission, a constant and unavoidable circumstance is the appearance of bit errors, which have serious effects on the regular logic computation. Fortunately, these errors can be detected via plugging a parity generator (pG) at the transmitting terminal and a parity checker (pC) at the receiving terminal. Herein, taking advantage of the efficient adsorption/quenching ability of polydopamine nanospheres toward fluorophore-labeled single-stranded DNA, we explored this biocompatible nanomaterial to DNA logic computation and constructed the first simple, enzyme-free, and G-quadruplex-free DNA pG/pC for error detection through data transmission. Besides, graphene oxide (GO) was innovatively introduced as the "corrective element" to perform the output-correction function of pC. All the erroneous outputs were corrected to normal conditions completely, ensuring the regular operation of later logic computing. The total operation of this non-G4 pG/pC system (error checking/output-correction) could be completed within 1 h (about ¹/₃ of previous G4 platform) in a simpler and more efficient way. Notably, the odd pG/pC with analogous functions was also achieved through negative logic conversion to the fabricated even one. Furthermore, the same system could also perform three-input concatenated logic computation (XOR-INHIBIT), enriching the complexity of PDs-based logic computation.

Cellular processing and destinies of artificial DNA nanostructures

This review gives a panoramic view of the many DNA nanotechnology applications in cells, mechanistic understanding of how and where their interactions occur and their subsequent outcomes.