Programming Cell Adhesion for On-Chip Sequential Boolean Logic Functions

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.

A Bivalent Aptamer-Based DNA Agonist for EGFR Signaling Effectively Alleviates Ulcerative Colitis In Vivo

While epidermal growth factor (EGF) shows promise in addressing the clinical manifestations of intestinal ulcerative diseases by activating the EGF receptor (EGFR)-mediated cell signaling, its clinical application is hampered by poor protein hydrolytic stability, low thermostability, and difficulty in modification. The development of a novel EGFR agonist for ulcerative colitis remains an urgent need, necessitating innovative solutions to overcome the limitations of current therapies via recombinant EGF protein. Herein, we introduce a novel DNA agonist for EGFR, Dimer-YL, which employs a bivalent aptamer to induce stable receptor dimerization, thereby activating the EGFR signaling and related cell behaviors. Dimer-YL has been demonstrated to recapitulate the EGF-promoted cellular behaviors, including proliferation and migration, as well as repair the damage of intercellular tight junctions. Furthermore, our findings demonstrate the potent therapeutic function of Dimer-YL in alleviating DSS-induced ulcerative colitis in vivo. Together, the present work has revealed Dimer-YL as an innovative DNA molecule for effective EGFR activation, offering promise for the development of EGFR-agonistic agents for therapeutic purposes.

DNA Logic Gates for Small Molecule Activation Circuits in Cells

DNA-based devices such as DNA logic gates self-assemble into supramolecular structures, as dictated by the sequences of the constituent oligonucleotides and their predictable Watson-Crick base pairing interactions. The programmable nature of DNA-based devices permits the design and implementation of DNA circuits that interact in a dynamic and sequential manner capable of spatially arranging disparate DNA species. Here, we report the application of an activatable fluorescence reporter based on a proximity-driven inverse electron demand Diels-Alder (IEDDA) reaction and its robust integration with DNA strand displacement circuits. In response to specific DNA input patterns, sequential strand displacement reactions are initiated and culminate in the hybridization of two modified DNA strands carrying probes capable of undergoing an IEDDA reaction between a vinyl-ether-caged fluorophore and its reactive partner tetrazine, leading to the activation of fluorescence. This approach provides a major advantage for DNA computing in mammalian cells since circuit degradation does not induce fluorescence, in contrast to traditional fluorophore-quencher designs. We demonstrate the robustness and sensitivity of the reporter by testing its ability to serve as a readout for DNA logic circuits of varying complexity inside cells.

DNA-Programmed Stem Cell Niches via Orthogonal Extracellular Vesicle-Cell Communications

Extracellular vesicles (EVs) are natural carriers for intercellular transfer of bioactive molecules, which are harnessed for wide biomedical applications. However, a facile yet general approach to engineering interspecies EV-cell communications is still lacking. Here, the use of DNA to encode the heterogeneous interfaces of EVs and cells in a manner free of covalent or genetic modifications is reported, which enables orthogonal EV-cell interkingdom interactions in complex environments. Cholesterol-modified DNA strands and tetrahedral DNA frameworks are employed with complementary sequences to serve as artificial ligands and receptors docking on EVs and living cells, respectively, which can mediate specific yet efficient cellular internalization of EVs via Watson-Crick base pairing. It is shown that based on this system, human cells can adopt EVs derived from the mouse, watermelon, and Escherichia coli. By implementing several EV-cell circuits, it shows that this DNA-programmed system allows orthogonal EV-cell communications in complex environments. This study further demonstrates efficient delivery of EVs with bioactive contents derived from feeder cells toward monkey female germline stem cells (FGSCs), which enables self-renewal and stemness maintenance of the FGSCs without feeder cells. This system may provide a universal platform to customize intercellular exchanges of materials and signals across species and kingdoms.

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.

Dynamic DNA Nanostructures for Cell Manipulation

Dynamic DNA nanostructures are DNA nanostructures with reconfigurable elements that can undergo structural transformations in response to specific stimuli. Thus, anchoring dynamic DNA nanostructures on cell membranes is an attractive and promising strategy for well-controlled cell manipulation. Here, we review the latest progress in dynamic DNA nanostructures for cell manipulation. Commonly used mechanisms for dynamic DNA nanostructures are first introduced. Subsequently, we summarize the anchoring strategies for dynamic DNA nanostructures on cell membranes and list possible applications (including programming cell membrane receptors, controlling ligand activity and drug delivery, capturing and releasing cells, and assembling cells into clusters). Finally, insights into the remaining challenges are presented.

Molecular Visual Sensing, Boolean Logic Computing, and Data Security Using a Droplet-Based Superwetting Paradigm

Inspired by information processing and logic operations of life, many artificial biochemical systems have been designed for applications in molecular information processing. However, encoding the binary synergism between matter, energy, and information in a superwetting system remains challenging. Herein, a superwetting paradigm was proposed for multifunctional applications including molecular visual sensing and data security on a superhydrophobic surface. A Triton X-100-encapsulated gelatin (TeG) hydrogel was prepared and selectively decomposed by trypsin, releasing the surfactant to decrease the surface tension of a droplet. Integrating the droplet with the superhydrophobic surface, the superwetting behavior was utilized for visual detection and information encoding. Interestingly, the proposed TeG hydrogel can function as an artificial gelneuron for molecular-level logic computing, where the combination of matters (superhydrophobic surface, trypsin, and leupeptin) acts as inputs to interact with energy (liquid surface tension and solid surface energy) and information (binary character), resulting in superwettability transitions (droplet surface tension, contact angle, rolling angle, and bounce) as outputs. Impressively, the TeG gelneuron can be further developed as molecular-level double cryptographic steganography to encode, encrypt, and hide specific information (including the maze escape route and content of the classical literature) due to its programmability, stimuli responsive ability, and droplet concealment. This study will encourage the development of advanced molecular paradigms and their applications, such as superwetting visual sensing, molecular computing, interaction, and data security.

Hybrid Nanocomposites of Plasmonic Metal Nanostructures and 2D Nanomaterials for Improved Colorimetric Detection

Plasmonic phenomena and materials have been extensively investigated for a long time and gained popularity in the last few years, finding in the design of the biosensors platforms promising applications offering devices with excellent performances. Hybrid systems composed of graphene, or other 2D materials, and plasmonic metal nanostructures present extraordinary optical properties originated from the synergic connection between plasmonic optical effects and the unusual physicochemical properties of 2D materials, thus improving their application in a broad range of fields. In this work, firstly, an overview of the structures and properties of 2D nanomaterials will be provided along with the physics of surface plasmon resonance and localized surface plasmon resonance. In the second part of the work, some examples of colorimetric biosensors exploiting the outstanding properties of hybrids nanocomposites will be presented. Finally, concluding perspectives on the actual status, challenges, and future directions in plasmonic sensing biosensing will be provided. Special emphasis will be given to how this technology can be used to support digitalization and virtualization in pandemic handling.

Single-Molecule Resettable DNA Computing via Magnetic Tweezers

DNA-based Boolean logic computing has emerged as a leading technique in biosensing, diagnosis, and therapeutics. Due to the development of the biological and chemical methods, especially the toehold-mediated DNA strand displacement (TMSD) reaction, different logic gates as well as circuits can be performed. However, most of these methods have been conducted at the bulk level, which may lead to missing information and be less controllable. Herein, we engineered single-molecule DNA computing controlled by stretching forces using magnetic tweezers. By tracking the real-time signals of the DNA extension, the output can be determined at a single base-pair resolution. A kinetics-controllable TMSD reaction was realized in the range of a ∼19-fold change of the reaction rate by different stretching forces. OR, AND, and NOT gates were also achieved. In addition, resettable DNA computing using force stretching cycles has been further exemplified. Overall, such a real-time, label-free, and force-controlled single-molecule DNA computing system provided new insight into molecular computing.

Principles for the design of multicellular engineered living systems

Remarkable progress in bioengineering over the past two decades has enabled the formulation of fundamental design principles for a variety of medical and non-medical applications. These advancements have laid the foundation for building multicellular engineered living systems (M-CELS) from biological parts, forming functional modules integrated into living machines. These cognizant design principles for living systems encompass novel genetic circuit manipulation, self-assembly, cell-cell/matrix communication, and artificial tissues/organs enabled through systems biology, bioinformatics, computational biology, genetic engineering, and microfluidics. Here, we introduce design principles and a blueprint for forward production of robust and standardized M-CELS, which may undergo variable reiterations through the classic design-build-test-debug cycle. This Review provides practical and theoretical frameworks to forward-design, control, and optimize novel M-CELS. Potential applications include biopharmaceuticals, bioreactor factories, biofuels, environmental bioremediation, cellular computing, biohybrid digital technology, and experimental investigations into mechanisms of multicellular organisms normally hidden inside the "black box" of living cells.

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.

Advances in Applications of Molecular Logic Gates

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

Biomimetic DNA Nanotechnology to Understand and Control Cellular Responses

At the cellular level, numerous nanocues guide the cells to adhere, interact, proliferate, differentiate, etc. Understanding and manipulating the cellular functions in vitro, necessitates the elucidation of these nanocues provided to the cells by the extracellular matrix (ECM), neighbouring cells or in the form of ligands. DNA nanotechnology is a biocompatible, flexible and a promising molecular level toolkit for mimicking cell-cell and cell-matrix interactions. In this review, we summarize various advances in cell-matrix, cell-cell and cell receptor-ligand interactions using DNA nanotechnology as a tool. We also provide a brief outlook on the current challenges and the future potentials of these DNA-based nanostructures so as to inspire novel innovations in the field.

Electrochemical-Based DNA Logic Devices Regulated by the Diffusion and Intercalation of Electroactive Dyes

Electrochemical-based logic gates are simple to operate, sensitive, controllable, and easy to integrate with silicon-based semiconductor logic devices, showing great application prospects and remaining largely unexplored. Herein, an immobilization-free dual-output electrochemical molecular logic system based on the different diffusivity of electroactive dyes ferrocene (Fc) and methylene blue (MB) toward an indium tin oxide (ITO) electrode under different DNA hybridization reactions was developed. In this system, the hybridization of the catalytic strand IN1 with Fc-modified hairpin DNA H1 triggered an exonuclease III (Exo III) cleavage cycle to obtain free Fc and produce a large number of long double-stranded DNAs via the hybridization chain reaction for intercalating MB, which was previously in the free state. Such a hybridization reaction caused a significant change in the diffusion capacity of MB and Fc toward the ITO electrode, resulting in two electrochemical signals with opposite changes. On this basis, a contrary logic pair library, a parity generator/checker system for differentiating the erroneous bits during data transmission, a parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits for meeting the needs of computational complexity were developed. The proposed electrochemical-based molecular logic system greatly expanded the application of the electrochemical method in the construction of logic circuits and provided a conceptual prototype for the development of more advanced and complicated logic devices.

Biocomputing Based on DNA Strand Displacement Reactions

The high sequence specificity and precise base complementary pairing principle of DNA provides a rich orthogonal molecular library for molecular programming, making it one of the most promising materials for developing bio-compatible intelligence. In recent years, DNA has been extensively studied and applied in the field of biological computing. Among them, the toehold-mediated strand displacement reaction (SDR) with properties including enzyme free, flexible design and precise control, have been extensively used to construct biological computing circuits. This review provides a systemic overview of SDR design principles and the applications. Strategies for designing DNA-only, enzymes-assisted, other molecules-involved and external stimuli-controlled SDRs are described. The recently realized computing functions and the application of DNA computing in other fields are introduced. Finally, the advantages and challenges of SDR-based computing are discussed.

Boolean logic gate based on DNA strand displacement for biosensing: current and emerging strategies

DNA computers are considered one of the most prominent next-generation molecular computers that perform Boolean logic using DNA elements. DNA-based Boolean logic gates, especially DNA strand displacement-based logic gates (SDLGs), have shown tremendous potential in biosensing since they can perform the logic analysis of multi-targets simultaneously. Moreover, SDLG biosensors generate a unique output in the form of YES/NO, which is contrary to the quantitative measurement used in common biosensors. In this review, the recent achievements of SDLG biosensing strategies are summarized. Initially, the development and mechanisms of Boolean logic gates, strand-displacement reaction, and SDLGs are introduced. Afterwards, the diversified input and output of SDLG biosensors are elaborated. Then, the state-of-the-art SDLG biosensors are reviewed in the classification of different signal-amplification methods, such as rolling circle amplification, catalytic hairpin assembly, strand-displacement amplification, DNA molecular machines, and DNAzymes. Most importantly, limitations and future trends are discussed. The technology reviewed here is a promising tool for multi-input analysis and lays a foundation for intelligent diagnostics.

Scalable Logic Circuits with Multiple Outputs and an Automatic Reset Function Based on DNAzyme-Mediated Branch Migration

A scalable logic platform made up of multilayer DNA circuits was constructed using Pb²⁺, Cu²⁺, and Zn²⁺ as the three inputs and three different fluorescent signals as the outputs. DNAzyme-guided cyclic cleavage reactions and DNA toehold-mediated strand branch migration were utilized to organize and connect nucleic acid probes for building the high-level logic architecture. The sequence communications between each circuit enable the logic network to work as a keypad lock, which is an information protection model at the molecular level. The multi-output mode was used to monitor the gradual unlocking process of the security system, from which one can determine which password is correct or not immediately. The autocatalytic cleavage of DNAzyme makes the biocomputing circuit feasible to realize the reset function automatically without external stimuli. Importantly, the logic platform is robust and can work effectively even in complex environmental samples.

Propelling DNA Computing with Materials' Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications

DNA computing is recognized as one of the most outstanding candidates of next-generation molecular computers that perform Boolean logic using DNAs as basic elements. Benefiting from DNAs' inherent merits of low-cost, easy-synthesis, excellent biocompatibility, and high programmability, DNA computing has evoked substantial interests and gained burgeoning advancements in recent decades, and also exhibited amazing magic in smart bio-applications. In this review, recent achievements of DNA logic computing systems using multifarious materials as building blocks are summarized. Initially, the operating principles and functions of different logic devices (common logic gates, advanced arithmetic and non-arithmetic logic devices, versatile logic library, etc.) are elaborated. Afterward, state-of-the-art DNA computing systems based on diverse "toolbox" materials, including typical functional DNA motifs (aptamer, metal-ion dependent DNAzyme, G-quadruplex, i-motif, triplex, etc.), DNA tool-enzymes, non-DNA biomaterials (natural enzyme, protein, antibody), nanomaterials (AuNPs, magnetic beads, graphene oxide, polydopamine nanoparticles, carbon nanotubes, DNA-templated nanoclusters, upconversion nanoparticles, quantum dots, etc.) or polymers, 2D/3D DNA nanostructures (circular/interlocked DNA, DNA tetrahedron/polyhedron, DNA origami, etc.) are reviewed. The smart bio-applications of DNA computing to the fields of intelligent analysis/diagnosis, cell imaging/therapy, amongst others, are further outlined. More importantly, current "Achilles' heels" and challenges are discussed, and future promising directions of this field are also recommended.

Programmable Live-Cell CRISPR Imaging with Toehold-Switch-Mediated Strand Displacement

The widespread application of CRISPR-Cas9 has transformed genome engineering. Nevertheless, the precision to control the targeting activity of Cas9 requires further improvement. We report a toehold-switch-based approach to engineer the conformation of single guide RNA (sgRNA) for programmable activation of Cas9. This activation circuit is responsive to multiple inputs and can regulate the conformation of the sgRNA through toehold-switch-mediated strand displacement. We demonstrate the orthogonal suppression and activation of Cas9 with orthogonal DNA inputs. Combination of toehold switches leads to a variety of intracellular Cas9 activation programs with simultaneous and orthogonal responses, through which multiple genome loci are displayed in different colors in a controllable manner. This approach provides a new route for programing CRISPR in living cells for genome imaging and engineering.

Highly Selective Detection of Metronidazole by Self-Assembly via 0D/2D N-C QDs/g-C3N4 Nanocomposites Through FRET Mechanism

A 0D/2D (0-dimensional/2-dimensional) nanostructure was designed by self-assembly of N-C QDs and carboxylated g-C3N4 nanosheets and used as a fluorescence resonance energy transfer (FRET) fluorescent sensor. The N-C QDs/g-C3N4 nanosheets were synthesized via the amino group on the N-C QD surface and the -COOH of the carboxylated g-C3N4 nanosheets. The mechanism of detection of metronidazole (MNZ) by N-C QDs/g-C3N4 nanocomposites is based on FRET between negatively charged N-QDs and positively charged carboxylated g-C3N4 nanoparticles. N-C QDs/g-C3N4 nanostructures displayed good responses for the detection of MNZ at normal temperature and pressure. The decrease in the fluorescence intensity showed a good linear relationship to MNZ concentration within 0-2.6 × 10-5 mol/L, and the detection limit was 0.66 μM. The novel FRET sensor will have a great potential in clinical analysis and biological studies.

Biomimetic preparation of core-shell structured surface-enhanced Raman scattering substrate with antifouling ability, good stability, and reliable quantitative capability

The fouling and stability are two most critical limiting factors for practical applications of surface-enhanced Raman scattering (SERS)-based microfluidic electrophoresis device. Herein, we present a novel biomimetic nanoengineering strategy to achieve a SERS substrate featuring antifouling ability, good stability, and reliable quantitative capability. Typically, by employing tea polyphenol as the reducing agent, the substrate made of silver core-gold shell nanostructures in situ grown on silicon wafer surface is fabricated. The core-shell nanostructures are further embedded with internal standard molecules. Remarkably, the fabricated substrate preserves distinct SERS effects, adaptable reproducibility, and reliable quantitative ability even if the substrate is incubated with 15% H₂ O₂ , 13% HNO₃ , or 10⁸  CFU/mL bacteria, or suffered from 12-day continuous vibration at 250 rpm/min in PBS buffer. As a proof-of-concept application, the DNA-functionalized substrate is capable of precise quantification of Hg²⁺ with a limit of detection down to ca. 1 pM even in sewage water.

Dipole-Modulated Downconversion Nanoparticles as Label-Free Biological Sensors

Ultrasensitive detection of proteins and biomolecules has been previously achieved by optical nanoparticles (NPs) using the principles of Förster resonance energy transfer (FRET). However, the inherent need for labeling the target analyte in these assays hinders their applicability in point-of-use (POU) diagnostics. In this work, a label-free NP-based sensor has been developed that utilizes downconversion luminescence and surface electric dipoles as a novel approach for the detection of avidin. The long-lived luminescence of Eu³⁺-doped biotinylated NPs was effectively quenched in the presence of avidin in a concentration-dependent manner. The NPs exhibited high avidin selectivity and sensitivity with a limit of detection (LOD) of 7.8 nM and a wide dynamic range spanning 1 nM to 10 μM in deionized (DI) water. The application of the assay in a complex biological matrix consisting of cell growth medium supplemented with 10% v/v serum was verified with minor effects on avidin sensitivity exhibited by an LOD of 34.7 nM. The performance of the system was evaluated by comparing the photoluminescence (PL) intensities of known avidin concentration and the values predicted by the generated calibration curve. The new biosensing strategy has the potential to be extended to the detection of other disease biomarkers or pathogens with LOD and limited matrix effects in POU settings.

Implementing digital computing with DNA-based switching circuits

DNA strand displacement reactions (SDRs) provide a set of intelligent toolboxes for developing molecular computation. Whereas SDR-based logic gate circuits have achieved a high level of complexity, the scale-up for practical achievable computational tasks remains a hurdle. Switching circuits that were originally proposed by Shannon in 1938 and nowadays widely used in telecommunication represent an alternative and efficient means to realize fast-speed and high-bandwidth communication. Here we develop SDR-based DNA switching circuits (DSCs) for implementing digital computing. Using a routing strategy on a programmable DNA switch canvas, we show that arbitrary Boolean functions can be represented by DSCs and implemented with molecular switches with high computing speed. We further demonstrate the implementation of full-adder and square-rooting functions using DSCs, which only uses down to 1/4 DNA strands as compared with a dual-rail logic expression-based design. We expect that DSCs provide a design paradigm for digital computation with biomolecules.

DNA strand displacement reactions can be difficult to scale up for computational tasks. Here the authors develop DNA switching circuits that achieve high-speed computing with fewer molecules.

A quantitative assessment of the dynamic modification of lipid-DNA probes on live cell membranes

Synthetic lipid-DNA probes have recently attracted much attention for cell membrane analysis, transmembrane signal transduction, and regulating intercellular networks. These lipid-DNA probes can spontaneously insert onto plasma membranes simply after incubation. The highly precise and controllable DNA interactions have further allowed the programmable manipulation of these membrane-anchored functional probes. However, we still have quite limited understanding of how these lipid-DNA probes interact with cell membranes and also what parameters determine this process. In this study, we have systematically studied the dynamic process of cell membrane modification with a group of lipid-DNA probes. Our results indicated that the hydrophobicity of the lipid-DNA probes is strongly correlated with their membrane insertion and departure rates. Most cell membrane insertion stems from the monomeric form of probes, rather than the aggregates. Lipid-DNA probes can be removed from cell membranes through either endocytosis or direct outflow into the solution. As a result, long-term probe modifications on cell membranes can be realized in the presence of excess probes in the solution and/or endocytosis inhibitors. For the first time, we have successfully improved the membrane persistence of lipid-DNA probes to more than 24 h. Our quantitative data have dramatically improved our understanding of how lipid-DNA probes dynamically interact with cell membranes. These results can be further used to allow a broad range of applications of lipid-DNA probes for cell membrane analysis and regulation.

An enzyme-free DNA circuit for the amplified detection of Cd2+ based on hairpin probe-mediated toehold binding and branch migration

An enzyme-free DNA circuit was designed for the amplified detection of Cd2+ based on hairpin probe-mediated toehold binding and branch migration. A Cd2+-specific aptamer was used to recognize Cd2+ and a G-quadruplex was used to report the detection signal. The assay is sensitive, with a detection limit of 5 pM.

Logic-Gate-Actuated DNA-Controlled Receptor Assembly for the Programmable Modulation of Cellular Signal Transduction

Programming cells to sense multiple inputs and activate cellular signal transduction cascades is of great interest. Although this goal has been achieved through the engineering of genetic circuits using synthetic biology tools, a nongenetic and generic approach remains highly demanded. Herein, we present an aptamer-controlled logic receptor assembly for modulating cellular signal transduction. Aptamers were engineered as "robotic arms" to capture target receptors (c-Met and CD71) and a DNA logic assembly functioned as a computer processor to handle multiple inputs. As a result, the DNA assembly brings c-Met and CD71 into close proximity, thus interfering with the ligand-receptor interactions of c-Met and inhibiting its functions. Using this principle, a set of logic gates was created that respond to DNA strands or light irradiation, modulating the c-Met/HGF signal pathways. This simple modular design provides a robust chemical tool for modulating cellular signal transduction.

Nonlinear Regulation of Enzyme-Free DNA Circuitry with Ultrasensitive Switches

DNA is used to construct synthetic chemical reaction networks (CRNs), such as inorganic oscillators and gene regulatory networks. Nonlinear regulation with a simpler molecular mechanism is particularly important in large-scale CRNs with complex dynamics, such as bistability, adaptation, and oscillation of cellular functions. Here we introduce a new approach based on ultrasensitive switches as modular regulatory elements to nonlinearly regulate DNA-based CRNs. The nonlinear behavior of the systems can be finely tuned by programmable regulation of the linker length and the ligand binding sites, of which the Hill coefficients (n_H) are in the range of 1.00-2.32. By integrating two different strand displacement reactions with low-order nonlinearities (n_H ≈ 1.44 and 1.54), we could construct CRNs exhibiting high-order nonlinearities with Hill coefficients of up to ∼2.70. In addition, this could provide an efficient approach for designing CRNs at will with complex chemical dynamics by incorporating our design with previously developed enzyme-free DNA circuits.

Fluorescence decay rate of selected compounds from Eysenhardtia polystachya extracts and their viability as biosensors

Eysenhardtia polystachya (EP) is an endemic Mexican plant that has been widely studied for its antidiabetic, antibacterial, and antioxidant properties. Several studies had reported the main components of EP, but their fluorescence properties had not been broadly studied. In a previous study we obtained extracts with different composition from this plant and they presented florescence. In this work we study fluorescent compounds from EP and evaluate their fluorescence properties. EP extracts were obtained by Soxhlet extraction with ethanol, samples were dried, and compounds were separated by column chromatography. Fluorescent fractions were classified apart from other fractions and characterized by Scanning electron microscopy (SEM), UV-Vis, Raman, FTIR and ¹H NMR spectra. Additionally, we obtained functional nanomaterials (using silica nanoparticles). TD-DFT molecular calculations of the fluorescent components were carried out to compare their theoretical UV-Vis spectra to experimental results. Nine fractions were obtained by chromatography and five of them showed fluorescence. Fluorescence of extracts from Eysenhardtia polystachya is due to more than one component and we suggest that could be other hydrochalcones for which we present possible structures. This finding would help to dissipate questions about which component is responsible for fluorescence in extracts from the plant and in this way determinate the appropriate use for these fluorophores. Finally, the application and viability as a biosensor using pulmonary epithelium fibroblast cell culture IMR-90 was proved, and in the concentration used are non-toxic materials.

Engineering Cell-Surface Receptors with DNA Nanotechnology for Cell Manipulation

Cell-surface receptors play pivotal roles in the regulation of cell fate. Molecular engineering of cell-surface receptors enables control of cell signaling and manipulation of cell behavior in a user-defined way. Currently, the development of chemical-biological approaches for non-genetic engineering and regulation of membrane receptors is attracting significant interest. Recent research advances in functional nucleic acids and DNA nanotechnology have made it possible to use DNA as a new and promising molecular toolkit for controlling receptor-mediated signaling and cell fates. In this minireview we summarize the advances in the use of DNA nanotechnology for the spatiotemporal regulation of cell receptors and highlight practical applications in manipulating cell functions including cell adhesion, cell-cell contact, cell migration, and cellular immunity. We also provide a perspective on the potential of and challenges facing DNA-based receptor engineering in future applications of cell manipulation and cell-based therapy.

A Janus-inspired amphichromatic system that kills two birds with one stone for operating a "DNA Janus Logic Pair" (DJLP) library

Although DNA computing has exhibited a magical power across diverse areas, current DNA logic gates with different functions are always separately operated and can only produce hard-to-visualize output. The fussy/obligatory gates' redesign/reconstruction and the non-intuitive output cause the wastage of time and costs, low efficiency and practicality. Herein, inspired by the ancient Roman mythical God Janus, for the first time, we propose the concept of "DNA Janus Logic Pair" (DJLP) to classify the DNA logic gates with contrary functions into "Positive + Negative" gates (DJLP = Pos + Neg). Based on the biocatalytic property of G-quadruplex DNAzyme (G4zyme) and the luminescence quenching ability of oxidized 3,3',5,5'-tetramethylbenzidine (OxTMB) towards the upconversion (UC) particles, we fabricated a universal amphichromatic platform that kills two birds with one stone for operating a versatile DJLP library. Different from the previous DNA logic systems, the "Pos + Neg" gates of each DJLP in this study were concomitantly achieved via the same one-time DNA reaction, which avoided the gates' redesign/reoperation and reduced the operating costs/time of the DNA gates by at least half. Besides, both the amphichromatic outputs (Visual-blue and UC luminescent-green) can be visualized under harmless-NIR, thus bringing greatly enhanced practicality to the method. Moreover, we constructed various concatenated logic circuits via logically modulating the G4zyme's biocatalytic property with glutathione, thus enabling the largely improved computing complexity. Furthermore, taking the circuit "YES-INH-1-2 decoder" as the "computing core", we designed an "antioxidant indicator" with ratiometric logical responses that could recognize the presence of antioxidants smartly (output changed from "10" to "01"), which provided a typical prototype for potential intelligent bio-applications.

Design and fabrication of flexible DNA polymer cocoons to encapsulate live cells

The capability to encapsulate designated live cells into a biologically and mechanically tunable polymer layer is in high demand. Here, an approach to weave functional DNA polymer cocoons has been proposed as an encapsulation method. By developing in situ DNA-oriented polymerization (isDOP), we demonstrate a localized, programmable, and biocompatible encapsulation approach to graft DNA polymers onto live cells. Further guided by two mutually aided enzymatic reactions, the grafted DNA polymers are assembled into DNA polymer cocoons at the cell surface. Therefore, the coating of bacteria, yeast, and mammalian cells has been achieved. The capabilities of this approach may offer significant opportunities to engineer cell surfaces and enable the precise manipulation of the encapsulated cells, such as encoding, handling, and sorting, for many biomedical applications.