Antibody-powered nucleic acid release using a DNA-based nanomachine

Integration of DNA-Decorated Hapten in Emergency Immunoassays for Antibody and Small-Molecule Detection: A Review

DNA-decorated hapten (DDH)-based immunoassays have emerged, demonstrating supreme advantages in sensing applications because of their excellent sensitivity, specificity, and reliability. DDH combines both a recognition element (hapten) and a signal transduction element (DNA portion) with its highly programmable DNA structure enabling the trigger of signal transduction following a recognition event, thereby introducing a novel signal transduction mechanism to immunoassays. In this review, we provide a critical overview of recent research in the DDH-based immunoassays, which are designed to detect specific small molecules and antibodies. On the basis of the following events after binding of antibodies to DDH, the reported studies involved with DDH-based immunoassays can be categorized into three groups: (i) DDH-based immunoassay based on DNA conformational switches induced by antibody binding, (ii) DDH-based immunoassay based on co-localization of nucleic acids induced by antibody binding, and (iii) DDH-based immunoassay based on antibody steric hindrance. We also focus on several fundamental elements of DDH-based immunoassays, including the designed DNA structure, principles of signal transformation, and platform of DDH-based immunoassays. Then, the representative applications of DDH-based immunoassays in areas such as food safety, medical diagnostics, and environmental monitoring as well as the challenges and perspectives of DDH-based immunoassays are also explored.

Enhancing DNA-based nanodevices activation through cationic peptide acceleration of strand displacement

Dynamic DNA-based nanodevices offer versatile molecular-level operations, but the majority of them suffer from sluggish kinetics, impeding the advancement of device complexity. In this work, we present the self-assembly of a cationic peptide with DNA to expedite toehold-mediated DNA strand displacement (TMSD) reactions, a fundamental mechanism enabling the dynamic control and actuation of DNA nanostructures. The target DNA is modified with a fluorophore and a quencher, so that the TMSD process can be monitored by recording the time-dependent fluorescence changes. The boosting effect of the peptides is found to be dependent on the peptide/DNA N/P ratio, the toehold/invader binding affinity, and the ionic strength with stronger effects observed at lower ionic strengths, suggesting that electrostatic interactions play a key role. Furthermore, we demonstrate that the cationic peptide enhances the responsiveness and robustness of DNA machinery tweezers or logic circuits (AND and OR) involving multiple strand displacement reactions in parallel and cascade, highlighting its broad utility across DNA-based systems of varying complexity. This work offers a versatile approach to enhance the efficiency of toehold-mediated DNA nanodevices, facilitating flexible design and broader applications.

Nano revolution of DNA nanostructures redefining cancer therapeutics-A comprehensive review

DNA nanostructures are a promising tool in cancer treatment, offering an innovative way to improve the effectiveness of therapies. These nanostructures can be made solely from DNA or combined with other materials to overcome the limitations of traditional single-drug treatments. There is growing interest in developing nanosystems capable of delivering multiple drugs simultaneously, addressing challenges such as drug resistance. Engineered DNA nanostructures are designed to precisely deliver different drugs to specific locations, enhancing therapeutic effects. By attaching targeting molecules, these nanostructures can recognize and bind to cancer cells, increasing treatment precision. This approach offers tailored solutions for targeted drug delivery, enabling the delivery of multiple drugs in a coordinated manner. This review explores the advancements and applications of DNA nanostructures in cancer treatment, with a focus on targeted drug delivery and multi-drug therapy. It discusses the benefits and current limitations of nanoscale formulations in cancer therapy, categorizing DNA nanostructures into pure forms and hybrid versions optimized for drug delivery. Furthermore, the review examines ongoing research efforts and translational possibilities, along with challenges in clinical integration. By highlighting the advancements in DNA nanostructures, this review aims to underscore their potential in improving cancer treatment outcomes.

Enzyme-Linked DNA Displacement (ELIDIS) Assay for Ultrasensitive Electrochemical Detection of Antibodies

Here we report the development of a method for the electrochemical ultrasensitive detection of antibodies that couples the programmability and versatility of DNA-based systems with the sensitivity provided by enzymatic amplification. The platform, termed Enzyme-Linked DNA Displacement (ELIDIS), is based on the use of antigen-DNA conjugates that, upon the bivalent binding of a specific target antibody, induce the release of an enzyme-DNA hybrid strand from a preformed duplex. Such enzyme-DNA hybrid strand can then be electrochemically detected with a disposable electrode with high sensitivity. We applied ELIDIS to demonstrate the sensitive (limit of detection in the picomolar range), specific and multiplexed detection of five different antibodies including three clinically relevant ones. ELIDIS is also rapid (it only requires two reaction steps), works well in complex media (serum) and is cost-effective. A direct comparison with a commercial ELISA kit for the detection of Cetuximab demonstrates the promising features of ELIDIS as a point-of-care platform for antibodies detection.

Programing Chemical Communication: Allostery vs Multivalent Mechanism

The emergence of life has relied on chemical communication and the ability to integrate multiple chemical inputs into a specific output. Two mechanisms are typically employed by nature to do so: allostery and multivalent activation. Although a better understanding of allostery has recently provided a variety of strategies to optimize the binding affinity, sensitivity, and specificity of molecular switches, mechanisms relying on multivalent activation remain poorly understood. As a proof of concept to compare the thermodynamic basis and design principles of both mechanisms, we have engineered a highly programmable DNA-based switch that can be triggered by either a multivalent or an allosteric DNA activator. By precisely designing the binding interface of the multivalent activator, we show that the affinity, dynamic range, and activated half-life of the molecular switch can be programed with even more versatility than when using an allosteric activator. The simplicity by which the activation properties of molecular switches can be rationally tuned using multivalent assembly suggests that it may find many applications in biosensing, drug delivery, synthetic biology, and molecular computation fields, where precise control over the transduction of binding events into a specific output is key.

Programming conformational cooperativity to regulate allosteric protein-oligonucleotide signal transduction

Conformational cooperativity is a universal molecular effect mechanism and plays a critical role in signaling pathways. However, it remains a challenge to develop artificial molecular networks regulated by conformational cooperativity, due to the difficulties in programming and controlling multiple structural interactions. Herein, we develop a cooperative strategy by programming multiple conformational signals, rather than chemical signals, to regulate protein-oligonucleotide signal transduction, taking advantage of the programmability of allosteric DNA constructs. We generate a cooperative regulation mechanism, by which increasing the loop lengths at two different structural modules induced the opposite effects manifesting as down- and up-regulation. We implement allosteric logic operations by using two different proteins. Further, in cell culture we demonstrate the feasibility of this strategy to cooperatively regulate gene expression of PLK1 to inhibit tumor cell proliferation, responding to orthogonal protein-signal stimulation. This programmable conformational cooperativity paradigm has potential applications in the related fields.

Chemically programmable bacterial probes for the recognition of cell surface proteins

Common methods to label cell surface proteins (CSPs) involve the use of fluorescently modified antibodies (Abs) or small-molecule-based ligands. However, optimizing the labeling efficiency of such systems, for example, by modifying them with additional fluorophores or recognition elements, is challenging. Herein we show that effective labeling of CSPs overexpressed in cancer cells and tissues can be obtained with fluorescent probes based on chemically modified bacteria. The bacterial probes (B-probes) are generated by non-covalently linking a bacterial membrane protein to DNA duplexes appended with fluorophores and small-molecule binders of CSPs overexpressed in cancer cells. We show that B-probes are exceptionally simple to prepare and modify because they are generated from self-assembled and easily synthesized components, such as self-replicating bacterial scaffolds and DNA constructs that can be readily appended, at well-defined positions, with various types of dyes and CSP binders. This structural programmability enabled us to create B-probes that can label different types of cancer cells with distinct colors, as well as generate very bright B-probes in which the multiple dyes are spatially separated along the DNA scaffold to avoid self-quenching. This enhancement in the emission signal enabled us to label the cancer cells with greater sensitivity and follow the internalization of the B-probes into these cells. The potential to apply the design principles underlying B-probes in therapy or inhibitor screening is also discussed here.

Thermo-Programmed Synthetic DNA-Based Receptors

Herein, we present a generalizable and versatile strategy to engineer synthetic DNA ligand-binding devices that can be programmed to load and release a specific ligand at a defined temperature. We do so by re-engineering two model DNA-based receptors: a triplex-forming bivalent DNA-based receptor that recognizes a specific DNA sequence and an ATP-binding aptamer. The temperature at which these receptors load/release their ligands can be finely modulated by controlling the entropy associated with the linker connecting the two ligand-binding domains. The availability of a set of receptors with tunable and reversible temperature dependence allows achieving complex load/release behavior such as sustained ligand release over a wide temperature range. Similar programmable thermo-responsive synthetic ligand-binding devices can be of utility in applications such as drug delivery and production of smart materials.

A programmable catalytic molecular nanomachine for highly sensitive protein and small molecule detection

Herein, we report the construction of a programmable catalytic molecular nanomachine based on a cross-linked catalytic hairpin assembly (CCHA) reaction for the one-step highly sensitive detection of proteins and small molecules. In this system, when the recognition elements attached on split initiators bind to the target proteins, it can trigger the cascade of the CCHA reaction, resulting in the formation of many macromolecular fluorescent products for signaling. This platform couples the advantages of highly efficient DNA-based nanotechnology with specific protein-small molecule interactions. We demonstrated the sensitive detection of streptavidin and anti-digoxigenin antibody with detection limits as low as 48.8 pM and 0.85 nM, respectively. This nanomachine also demonstrated its flexibility in the nanomolar detection of corresponding small molecules, such as biotin and digoxigenin, using a competitive method. In addition, the nanomachine was robust enough to perform well with human serum samples. Overall, this programmable catalytic molecular nanomachine provides a versatile platform for the detection of proteins and small molecules by replacing the recognition elements, which can promote the development of DNA nanotechnology in disease diagnosis and therapeutic drug monitoring.

Engineering Homogeneous Photoactive Antibody Fragments

Genetically encoded site-specifically incorporated noncanonical amino acids (ncAAs) have been used to modulate properties of several proteins. Here, we describe a procedure for engineering photoactive antibody fragments that bind to their target antigen only after irradiation with 365 nm light. The procedure starts with identification of tyrosine residues in antibody fragments that are important for antibody-antigen binding and thus targets for replacement with photocaged tyrosine (pcY). This is followed by cloning of plasmids and expression of pcY-containing antibody fragments in E. coli. Finally, we describe a cost-effective and biologically-relevant method for measuring the binding affinity of photoactive antibody fragments to antigens expressed on the surface of live cancer cells.

Orthogonal Enzyme-Driven Timers for DNA Strand Displacement Reactions

Here, we demonstrate a strategy to rationally program a delayed onset of toehold-mediated DNA strand displacement reactions (SDRs). The approach is based on blocker strands that efficiently inhibit the strand displacement by binding to the toehold domain of the target DNA. Specific enzymatic degradation of the blocker strand subsequently enables SDR. The kinetics of the blocker enzymatic degradation thus controls the time at which the SDR starts. By varying the concentration of the blocker strand and the concentration of the enzyme, we show that we can finely tune and modulate the delayed onset of SDR. Additionally, we show that the strategy is versatile and can be orthogonally controlled by different enzymes each specifically targeting a different blocker strand. We designed and established three different delayed SDRs using RNase H and two DNA repair enzymes (formamidopyrimidine DNA glycosylase and uracil-DNA glycosylase) and corresponding blockers. The achieved temporal delay can be programed with high flexibility without undesired leak and can be conveniently predicted using kinetic modeling. Finally, we show three possible applications of the delayed SDRs to temporally control the ligand release from a DNA nanodevice, the inhibition of a target protein by a DNA aptamer, and the output signal generated by a DNA logic circuit.

Homogeneous protein assays mediated by dynamic DNA nanotechnology

Driven by recent advances in DNA nanotechnology, analytical methods have been greatly improved for designing simple and homogeneous assays for proteins. The translation from target proteins to DNA outputs dramatically enhances the sensitivity of protein assays. More importantly, the protein-responsive DNA nanotechnology has offered diverse assay mechanisms, allowing flexible assay designs and high sensitivity without the need for sophisticated operational procedures. This review will focus on the design principles and mechanistic insight of analytical assays mediated by protein-responsive DNA nanotechnology, which will serve a general guide for assay design and applications.

Geometry of a DNA Nanostructure Influences Its Endocytosis: Cellular Study on 2D, 3D, and in Vivo Systems

Fabrication of nanoscale DNA devices to generate 3D nano-objects with precise control of shape, size, and presentation of ligands has shown tremendous potential for therapeutic applications. The interactions between the cell membrane and different topologies of 3D DNA nanostructures are crucial for designing efficient tools for interfacing DNA devices with biological systems. The practical applications of these DNA nanocages are still limited in cellular and biological systems owing to the limited understanding of their interaction with the cell membrane and endocytic pathway. The correlation between the geometry of DNA nanostructures and their internalization efficiency remains elusive. We investigated the influence of the shape and size of 3D DNA nanostructures on their cellular internalization efficiency. We found that one particular geometry, i.e., the tetrahedral shape, is more favored over other designed geometries for their cellular uptake in 2D and 3D cell models. This is also replicable for cellular processes like cell invasion assays in a 3D spheroid model, and passing the epithelial barriers in in vivo zebrafish model systems. Our work provides detailed information for the rational design of DNA nanodevices for their upcoming biological and biomedical applications.

Intelligent Programmable DNA Nanomachines for the Spatially Controllable Imaging of Intracellular MicroRNA

The high programmability of DNA molecules makes them particularly suitable for constructing artificial molecular machines to perform sophisticated functions by simulating complex living systems. However, intelligent DNA nanomachines which can perform precise tasks logically in complex environments still remain challenging. Herein, we develop a general strategy to design a pH-responsive programmable DNA (PRPD) nanomachine to perform multilayer DNA cascades, enabling precise sensing and calculation of intracellular biomolecules. The PRPD nanomachine is built on a four-stranded DNAzyme walker precursor with a DNA switch on the surface of an Au nanoparticle, which is capable of precisely responding to pH variations in living cells by sequence tuning. This multilayer DNA cascade networks have been applicated in spatially controlled imaging of intracellular microRNA, which efficiently avoided the DNA nanomachine activated by nonspecific extracellular molecules and achieved apparent signal amplification. Our strategy enables the sensing-computing-output functional integration of DNA nanomachines, facilitating the application of programmable and complex nanomachines in nanoengineering, chemistry, and biomedicine.

Simple and programmed three-dimensional DNA tweezer for simultaneous one-step detection of ochratoxin A and zearalenone

Three-dimensional (TD) deoxyribonucleic acid (DNA) tweezers were programmed for one-step identification and detection of ochratoxin A (OTA) and zearalenone (ZEN). The unfolding of the TD-DNA tweezers by aptamers specific to these two mycotoxins "turned" the fluorescent signals "on." The bonding of the aptamers to their corresponding targets in OTA and ZEN "turned" the fluorescent signals and the DNA tweezers "off." The detection limit of the TD-DNA tweezers for OTA and ZEN was 0.032 and 0.037 ng mL^-1, respectively. The feasibility of this method was tested using two samples. Detection via this method increased the recovery of OTA and ZEN from 95.8% to 110.2%. Spike recovery and certified food products were used to detect applicability in actual situations. Analyte detection in complex samples using TD-DNA tweezers is rapid, as the process involves a single operational step. This proposed design has considerable potential for application in mycotoxin detection.

Theranostic nanomachines for cancer treatment

Multifunctional programmed nanomachines with theranostic functions demonstrated great potential in the clinical practice of oncology, as well as the personalized nanomedicine. The reason is because such nanoagents with combined diagnostic and therapeutic functions were found to be highly effective for cancer treatment. The appropriate design of nanomachines allows them to overcome the biological barriers of proliferative tumors and to distinguish the cancer cells from their normal counterparts. Moreover, the use of biocompatible and biodegradable precursors for construction of nanomachines minimize significantly the caused adverse effects to the normal tissue cells, which is a main problem of the chemotherapy. In addition, the utilization of theranostic nanomachines also enables an improved selectivity to the cancer in respect to its intrinsic complexity, heterogeneity, and dynamic evolution. Here we present the programmable functions and performance of the microenvironment-responsive nanomachines at a molecular level for cancer imaging and therapy.

Controlling Dynamic DNA Reactions at the Surface of Single-Walled Carbon Nanotube Electrodes to Design Hybridization Platforms with a Specific Amperometric Readout

Carbon nanotube (CNT)-based electrodes are cheap, highly performing, and robust platforms for the fabrication of electrochemical sensors. Engineering programmable DNA nanotechnologies on the CNT surface can support the construction of new electrochemical DNA sensors providing an amperometric output in response to biomolecular recognition. This is a significant challenge, since it requires gaining control of specific hybridization processes and functional DNA systems at the interface, while limiting DNA physisorption on the electrode surface, which contributes to nonspecific signal. In this study, we provide design rules to program dynamic DNA structures at the surface of single-walled carbon nanotubes electrodes, showing that specific DNA interactions can be monitored through measurement of the current signal provided by redox-tagged DNA strands. We propose the use of pyrene as a backfilling agent to reduce nonspecific adsorption of reporter DNA strands and demonstrate the controlled formation of DNA duplexes on the electrode surface, which we then apply in the design and conduction of programmable DNA strand displacement reactions. Expanding on this aspect, we report the development of novel amperometric hybridization platforms based on artificial DNA structures templated by the small molecule melamine. These platforms enable dynamic strand exchange reactions orthogonal to conventional toehold-mediated strand displacement and may support new strategies in electrochemical sensing of biomolecular targets, combining the physicochemical properties of nanostructured carbon-based materials with programmable nucleic acid hybridization.

Therapeutic Applications of Programmable DNA Nanostructures

Deoxyribonucleic acid (DNA) nanotechnology, a frontier in biomedical engineering, is an emerging field that has enabled the engineering of molecular-scale DNA materials with applications in biomedicine such as bioimaging, biodetection, and drug delivery over the past decades. The programmability of DNA nanostructures allows the precise engineering of DNA nanocarriers with controllable shapes, sizes, surface chemistries, and functions to deliver therapeutic and functional payloads to target cells with higher efficiency and enhanced specificity. Programmability and control over design also allow the creation of dynamic devices, such as DNA nanorobots, that can react to external stimuli and execute programmed tasks. This review focuses on the current findings and progress in the field, mainly on the employment of DNA nanostructures such as DNA origami nanorobots, DNA nanotubes, DNA tetrahedra, DNA boxes, and DNA nanoflowers in the biomedical field for therapeutic purposes. We will also discuss the fate of DNA nanostructures in living cells, the major obstacles to overcome, that is, the stability of DNA nanostructures in biomedical applications, and the opportunities for DNA nanostructure-based drug delivery in the future.

Programmable allosteric DNA regulations for molecular networks and nanomachines

Structure-based molecular regulations have been widely adopted to modulate protein networks in cells and recently developed to control allosteric DNA operations in vitro. However, current examples of programmable allosteric signal transmission through integrated DNA networks are stringently constrained by specific design requirements. Developing a new, more general, and programmable scheme for establishing allosteric DNA networks remains challenging. Here, we developed a general strategy for programmable allosteric DNA regulations that can be finely tuned by varying the dimensions, positions, and number of conformational signals. By programming the allosteric signals, we realized fan-out/fan-in DNA gates and multiple-layer DNA cascading networks, as well as expanding the approach to long-range allosteric signal transmission through tunable DNA origami nanomachines ~100 nm in size. This strategy will enable programmable and complex allosteric DNA networks and nanodevices for nanoengineering, chemical, and biomedical applications displaying sense-compute-actuate molecular functionalities.

Development of the DNA-based biosensors for high performance in detection of molecular biomarkers: More rapid, sensitive, and universal

The molecular biomarkers are molecules that are closely related to specific physiological states. Numerous molecular biomarkers have been identified as targets for disease diagnosis and biological research. To date, developing highly efficient probes for the precise detection of biomarkers has become an attractive research field which is very important for biological and biochemical studies. During the past decades, not only the small chemical probe molecules but also the biomacromolecules such as enzymes, antibodies, and nucleic acids have been introduced to construct of biosensor platform to achieve the detection of biomarkers in a highly specific and highly efficient way. Nevertheless, improving the performance of the biosensors, especially in clinical applications, is still in urgent demand in this field. A noteworthy example is the Corona Virus Disease 2019 (COVID-19) that breaks out globally in a short time in 2020. The COVID-19 was caused by the virus called SARS-CoV-2. Early diagnosis is very important to block the infection of the virus. Therefore, during these months scientists have developed dozens of methods to achieve rapid and sensitive detection of the virus. Nowadays some of these new methods have been applied for producing the commercial detection kit and help people against the disease worldwide. DNA-based biosensors are useful tools that have been widely applied in the detection of molecular biomarkers. The good stability, high specificity, and excellent biocompatibility make the DNA-based biosensors versatile in application both in vitro and in vivo. In this paper, we will review the major methods that emerged in recent years on the design of DNA-based biosensors and their applications. Moreover, we will also briefly discuss the possible future direction of DNA-based biosensors design. We believe this is helpful for people interested in not only the biosensor field but also in the field of analytical chemistry, DNA nanotechnology, biology, and disease diagnosis.

Using entropy-driven amplifier circuit response to build nonlinear model under the influence of Lévy jump

Background

Bioinformatics is a subject produced by the combination of life science and computer science. It mainly uses computer technology to study the laws of biological systems. The design and realization of DNA circuit reaction is one of the important contents of bioinformatics.

Results

In this paper, nonlinear dynamic system model with Lévy jump based on entropy-driven amplifier (EDA) circuit response is studied. Firstly, nonlinear biochemical reaction system model is established based on EDA circuit response. Considering the influence of disturbance factors on the system, nonlinear biochemical reaction system with Lévy jump is built. Secondly, in order to prove that the constructed system conforms to the actual meaning, the existence and uniqueness of the system solution is analyzed. Next, the sufficient conditions for the end and continuation of EDA circuit reaction are certified. Finally, the correctness of the theoretical results is proved by numerical simulation, and the reactivity of THTSignal in EDA circuit under different noise intensity is verified.

Conclusions

In EDA circuit reaction, the intensity of external noise has a significant impact on the system. The end of EDA circuit reaction is closely related to the intensity of Lévy noise, and Lévy jump has a significant impact on the nature of biochemical reaction system.

DNA tile self-assembly driven by antibody-mediated four-way branch migration

The antibody-mediated four-way branch migration mechanism provides a novel idea for realizing the assembly of nanostructures, simply by attaching structures such as tiles, proteins, quantum dots, etc. to the ends of the four-way branches.

Antigen-Triggered Logic-Gating of DNA Nanodevices

Synthetic nanoscale devices that reconfigure dynamically in response to physiological stimuli could offer new avenues for diagnostics and therapy. Here, we report a strategy for controlling the state of DNA nanodevices based on sensing antigens with IgG antibodies. To this end, we use IgG antibodies as structural elements to kinetically trap reconfigurable DNA origami structures in metastable states. Addition of soluble antigens displace the IgGs from the objects and triggers reconfiguration. We demonstrate this mechanism by antigen-triggered disassembly of DNA origami shells for two different IgGs and their cognate antigens, and we determined the corresponding dose response curves. We also describe the logic-gated actuation of DNA objects with combinations of antigens, as demonstrated with AND-type shells that disassemble only when two different antigens are detected simultaneously. We apply our system for the antigen-triggered release of molecular payload as exemplified by the release of virus particles that we loaded into the DNA origami shells. We expect our approach to be applicable in many types of DNA nanostructures and with many other IgG-antigen combinations.

Amphiphilic DNA nanostructures for bottom-up synthetic biology

DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.

Stimuli-Responsive Three-Dimensional DNA Nanomachines Engineered by Controlling Dynamic Interactions at Biomolecule-Nanoparticle Interfaces

Stimuli-responsive nanomachines are attractive tools for biosensing, imaging, and drug delivery. Herein, we demonstrate that the orientation of macromolecules and subsequent dynamic interactions at the biomolecule-nanoparticle (bio-nano) interfaces can be rationally controlled to engineer stimuli-responsive DNA nanomachines. The success of this design principle was demonstrated by engineering a series of antibody-responsive DNA walkers capable of moving persistently on a three-dimensional track made of DNA functionalized gold nanoparticles. We show that drastically different responses to antibodies could be achieved using DNA walkers of identical sequences but with varying number or sites of modifications. We also show that multiple interfacial factors could be combined to engineer stimuli-responsive DNA nanomachines with high sensitivity and modularity. The potential of our strategy for practical uses was finally demonstrated for the amplified detection of antibodies and small molecules in both buffer and human serum samples. Unlike many DNA-based nanomachines, the performance of which could be significantly hindered by the matrix of serum, our system shows a matrix-enhanced sensitivity as a result of the engineering approach at the bio-nano interface.

Antibody-Responsive Ratiometric Fluorescence Biosensing of Biemissive Silver Nanoclusters Wrapped in Switchable DNA Tweezers

Exploring the ratiometric fluorescence biosensing of DNA-templated biemissive silver nanoclusters (AgNCs) is significant in bioanalysis, yet the design of a stimuli-responsive DNA device is a challenge. Herein, using the anti-digoxin antibody (anti-Dig) with two identical binding sites as a model, a tweezer-like DNA architecture is assembled to populate fluorescent green- and red-AgNCs (g-AgNCs and r-AgNCs), aiming to produce a ratio signal via specific recognition of anti-Dig with two haptens (DigH). To this end, four DNA probes are programmed, including a reporter strand (RS) dually ended with a g-/r-AgNC template sequence, an enhancer strand (ES) tethering two same G-rich tails (G18), a capture strand (CS) labeled with DigH at two ends, and a help strand (HS). Initially, both g-AgNCs and r-AgNCs wrapped in the intact RS are nonfluorescent, whereas the base pairing between RS, ES, CS, and HS resulted in the construction of DNA mechanical tweezers with two symmetric arms hinged by a rigid "fulcrum", in which g-AgNCs are lighted up due to G18 proximity ("green-on"), and r-AgNCs away from G18 are still dark ("red-off"). When two DigHs in proximity recognize and bind anti-Dig, the conformation switch of these tweezers resultantly occurs, taking g-AgNCs away from G18 for "green-off" and bringing r-AgNCs close to G18 for "red-on". As such, the ratiometric fluorescence of r-AgNCs versus g-AgNCs is generated in response to anti-Dig, achieving reliable quantization with a limit of detection at the picomolar level. Based on the fast stimulated switch of unique DNA tweezers, our ratiometric strategy of dual-emitting AgNCs would provide a new avenue for a variety of bioassays.

Antibody-powered DNA switches to initiate the hybridization chain reaction for the amplified fluorescence immunoassay

Designing antibody-powered DNA nanodevice switches is crucial and fascinating to perform a variety of functions in response to specific antibodies as regulatory inputs, achieving highly sensitive detection by integration with simple amplified methods. In this work, we report a unique DNA-based conformational switch, powered by a targeted anti-digoxin mouse monoclonal antibody (anti-Dig) as a model, to rationally initiate the hybridization chain reaction (HCR) for enzyme-free signal amplification. As a proof-of-concept, both a fluorophore Cy3-labeled reporter hairpin (RH) in the 3' terminus and a single-stranded helper DNA (HS) were individually hybridized with a recognition single-stranded DNA (RS) modified with Dig hapten, while the unpaired loop of RH was hybridized with the exposed 3'-toehold of HS, isothermally self-assembling an intermediate metastable DNA structure. The introduction of target anti-Dig drove the concurrent conjugation with two tethered Dig haptens, powering the directional switch of this DNA structure into a stable conformation. In this case, the unlocked 3'-stem of RH was implemented to unfold the 5'-stem of the BHQ-2-labeled quench hairpin (QH), rationally initiating the HCR between them by the overlapping complementary hybridization. As a result, numerous pairs of Cy3 and BHQ-2 in the formed long double helix were located in spatial proximity. In response to this, the significant quenching of the fluorescence intensity of Cy3 by BHQ-2 was dependent on the variable concentration of anti-Dig, achieving a highly sensitive quantification down to the picomolar level based on a simplified protocol integrated with enzyme-free amplification.

DNA Assembly-Based Stimuli-Responsive Systems

Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.

Multi-Mode Reconfigurable DNA-Based Chemical Reaction Circuits for Soft Matter Computing and Control

Developing smart material systems for performing different tasks in diverse environments remains challenging. Here, we show that by integrating stimuli-responsive soft materials with multi-mode reconfigurable DNA-based chemical reaction circuits (D-CRCs), it can control size change of microgels with multiple reaction pathways and adapt expansion behaviors to meet diverse environments. We first use pH-responsive intramolecular conformational switches for regulating DNA strand displacement reactions (SDRs). The ability to regulate SDRs with tunable pH-dependence allows to build dynamic chemical reaction networks with diverse reaction pathways. We confirm that the designed DNA switching circuits are reconfigurable at different pH and perform different logic operations, and the swelling of DNA switching circuit-integrated microgel systems can be programmably directed by D-CRCs. Our approach provides insight into building smart responsive materials and fabricating autonomous soft robots.

Smart Nucleic Acids as Future Therapeutics

Nucleic acid therapeutics (NATs) hold promise in treating undruggable diseases and are recognized as the third major category of therapeutics in addition to small molecules and antibodies. Despite the milestones that NATs have made in clinical translation over the past decade, one important challenge pertains to increasing the specificity of this class of drugs. Activating NATs exclusively in disease-causing cells is highly desirable because it will safely broaden the application of NATs to a wider range of clinical indications. Smart NATs are triggered through a photo-uncaging reaction or a specific molecular input such as a transcript, protein, or small molecule, thus complementing the current strategy of targeting cells and tissues with receptor-specific ligands to enhance specificity. This review summarizes the programmable modalities that have been incorporated into NATs to build in responsive behaviors. We discuss the various inputs, transduction mechanisms, and output response functions that have been demonstrated to date.

Synthetic chemical ligands and cognate antibodies for biorthogonal drug targeting and cell engineering

A vast range of biomedical applications relies on the specificity of interactions between an antigen and its cognate receptor or antibody. This specificity can be highest when said antigen is a non-natural (synthetic) molecule introduced into a biological setting as a bio-orthogonal ligand. This review aims to present the development of this methodology from the early discovery of haptens a century ago to the recent clinical trials. We discuss such methodologies as antibody recruitment, artificial internalizing receptors and chemically induced dimerization, present the use of chimeric receptors and/or bispecific antibodies to achieve drug targeting and transcytosis, and illustrate how these platforms most impressively found use in the engineering of therapeutic cells such as the chimeric antigen receptor cells. This review aims to be of interest to a broad scientific audience and to spur the development of synthetic artificial ligands for biomedical applications.

Triggered Dimerization and Trimerization of DNA Tetrahedra for Multiplexed miRNA Detection and Imaging of Cancer Cells

The reversible and switchable triggered reconfiguration of tetrahedra nanostructures from monomer tetrahedra structures into dimer or trimer structures is introduced. The triggered bridging of monomer tetrahedra by K⁺ -ion-stabilized G-quadruplexes or T-A•T triplexes leads to dimer or trimer tetrahedra structures that are separated by crown ether or basic pH conditions, respectively. The signal-triggered dimerization/trimerization of DNA tetrahedra structures is used to develop multiplexed miRNA-sensing platforms, and the tetrahedra mixture is used for intracellular sensing and imaging of miRNAs.

Multifunctional biomolecule nanostructures for cancer therapy

Biomolecule-based nanostructures are inherently multifunctional and harbour diverse biological activities, which can be explored for cancer nanomedicine. The supramolecular properties of biomolecules can be precisely programmed for the design of smart drug delivery vehicles, enabling efficient transport in vivo, targeted drug delivery and combinatorial therapy within a single design. In this Review, we discuss biomolecule-based nanostructures, including polysaccharides, nucleic acids, peptides and proteins, and highlight their enormous design space for multifunctional nanomedicines. We identify key challenges in cancer nanomedicine that can be addressed by biomolecule-based nanostructures and survey the distinct biological activities, programmability and in vivo behaviour of biomolecule-based nanostructures. Finally, we discuss challenges in the rational design, characterization and fabrication of biomolecule-based nanostructures, and identify obstacles that need to be overcome to enable clinical translation.

Nanomedicines: Redefining traditional medicine

Nanomedicines offer nanoscale drug delivery system. They offer ways of promising drug transportation, and address the issues of lack of targeting and permeability of traditional drugs. The physical and chemical properties in the domain of nanomedicine applications in vivo have not been sufficiently delivered. What's more, the metabolic of nanomedicines is not clear enough. Those factors which mentioned above determine that many nanomedicines have not yet realized clinical application due to their safety problems and in vivo efficacy. For example, they may cause immune response and cytotoxicity, as well as the ability to clear organs in vivo, the penetration ability of them and the lack of targeting ability may also cause poor efficacy of drugs in vivo. In this review, the new progresses of different kinds of nanomedicines (including gold nanoparticles, nanorobots, black phosphorus nanoparticles, brain diseases, gene editing and immunotherapy etc.) in anti-tumor, antibacterial, ocular diseases and arteriosclerosis in recent years were summarized. Their shortcomings were pointed out, and the new methods to improve the biosafety and efficacy were summarized.

Cross-Inhibitor: a time-sensitive molecular circuit based on DNA strand displacement

Designing biochemical systems that can be effectively used in diverse fields, including diagnostics, molecular computing and nanomachines, has long been recognized as an important goal of molecular programming and DNA nanotechnology. A key issue in the development of such practical devices on the nanoscale lies in the development of biochemical components with information-processing capacity. In this article, we propose a molecular device that utilizes DNA strand displacement networks and allows interactive inhibition between two input signals; thus, it is termed a cross-inhibitor. More specifically, the device supplies each input signal with a processor such that the processing of one input signal will interdict the signal of the other. Biochemical experiments are conducted to analyze the interdiction performance with regard to effectiveness, stability and controllability. To illustrate its feasibility, a biochemical framework grounded in this mechanism is presented to determine the winner of a tic-tac-toe game. Our results highlight the potential for DNA strand displacement cascades to act as signal controllers and event triggers to endow molecular systems with the capability of controlling and detecting events and signals.

DNA Walking and Rolling Nanomachine for Electrochemical Detection of miRNA

miRNAs, a class of endogenous noncoding RNAs, are involved in many crucial biological processes, which have emerged as a new set of biomarkers for disease theranostics. Exploring efficient signal amplification strategy is highly desired to pursue a highly sensitive miRNA biosensing platform. DNA nanotechnology shows great promise in the fabrication of amplified miRNA biosensors. In this work, a novel DNA walking and rolling nanomachine is developed for highly sensitive and selective detection of miRNA. Particularly, this approach programs two forms of dynamic DNA nanomachines powered by corresponding enzymes, which are well integrated. It is able to achieve a limit of detection as low as 39 × 10^-18 m, along with excellent anti-interfering performance and clinical applications. In addition, by designing pH-controlled detachable intermolecular DNA triplex, the main sensing elements can be conveniently reset, which fulfills the requirements of point-of-care profiling of miRNA. The high consistency between the proposed approach and quantitative real-time polymerase chain reaction validates the robustness and reliability. Therefore, it is anticipated that the DNA walking and rolling nanomachine has attractive application prospects in miRNA assay for biological researches and clinical diagnosis.

Switching the activity of Taq polymerase using clamp-like triplex aptamer structure

In nature, allostery is the principal approach for regulating cellular processes and pathways. Inspired by nature, structure-switching aptamer-based nanodevices are widely used in artificial biotechnologies. However, the canonical aptamer structures in the nanodevices usually adopt a duplex form, which limits the flexibility and controllability. Here, a new regulating strategy based on a clamp-like triplex aptamer structure (CLTAS) was proposed for switching DNA polymerase activity via conformational changes. It was demonstrated that the polymerase activity could be regulated by either adjusting structure parameters or dynamic reactions including strand displacement or enzymatic digestion. Compared with the duplex aptamer structure, the CLTAS possesses programmability, excellent affinity and high discrimination efficiency. The CLTAS was successfully applied to distinguish single-base mismatches. The strategy expands the application scope of triplex structures and shows potential in biosensing and programmable nanomachines.

Guanine-Lighting-Up Fluorescence Biosensing of Silver Nanoclusters Populated in Functional DNA Constructs by a pH-Triggered Switch

Dark or weak-emissive DNA-harbored silver nanoclusters (AgNCs) can be remarkably lighted up when approaching to guanine bases. The resultant bright AgNCs acting as a fluorescent reporter are fascinating in biosensing. To explore the applicable guanine-enhanced emission of AgNCs for biosensing microRNA-155 (miR-155) as a model, here we designed a unique stem-loop hairpin beacon (HB) encoding with an miR-155-recognizable sequence and a AgNCs-nucleable template, as well as a hairpin helper tethering a partially locked guanine-rich (15-nt) tail (G₁₅H), while two identical cytosine-rich segments were inserted in HB and G₁₅H to merge for folding/unfolding of i-motif at changed pHs. Initially, the intact clusters populated in HB (HB/AgNCs) were almost nonfluorescent in a buffer (pH 7.0). Then, miR-155 was introduced to trigger a repeated hairpin assembly of HB and G₁₅H by competitive strand displacement reactions at decreased pH 5.0 within 10 min, consequently generating numerous duplex DNA constructs (DDCs). With the resultant template of pH-responsive i-motifs incorporated in DDCs, their folding at pH 5.0 brought the proximity of unlocked G₁₅ overhang to the clusters in a crowded environment, remarkably lighting up the red-emitting fluorescence of HB/AgNCs (λ_em = 628 ± 5 nm) for amplified signal readout. About 3.5-fold enhancement of quantum yield was achievable using different variants of i-motif length and G₁₅ position. Simply by adding OH^-, the configuration fluctuation of i-motifs was implemented for switchable fluorescence biosensing to variable miR-155. Based on a one-step amplification and signaling scheme, this subtle strategy was rapid, low-cost, and specific for miR-155 with high sensitivity down to 67 pM.

Programming Impulsive Deformation with Mechanical Metamaterials

Impulsive deformation is widely observed in biological systems to generate movement with high acceleration and velocity. By storing elastic energy in a quasistatic loading and releasing it through an impulsive elastic recoil, organisms circumvent the intrinsic trade-off between force and velocity and achieve power amplified motion. However, such asymmetry in strain rate in loading and unloading often results in reduced efficiency in converting elastic energy to kinetic energy for homogeneous materials. Here, we demonstrate that specific internal structural designs can offer the ability to tune quasistatic and high-speed recoil independently to control energy storage and conversion processes. Experimental demonstrations with mechanical metamaterials reveal that certain internal structures optimize energy conversion far beyond unstructured materials under the same conditions. Our results provide the first quantitative model and experimental demonstration for tuning energy conversion processes through internal structures of metamaterials.

Glycoform Differentiation by a Targeted, Self-Assembled, Pattern-Generating Protein Surface Sensor

A method for generating targeted, pattern-generating, protein surface sensors via the self-assembly of modified oligodeoxynucleotides (ODNs) is described. The simplicity by which these systems can be created enabled the development of a sensor that can straightforwardly discriminate between distinct glycoform populations. By using this sensor to identify glycosylation states of a therapeutic protein, we demonstrate the diagnostic potential of this approach as well as the feasibility of integrating a wealth of supramolecular receptors and sensors into higher-order molecular analytical devices with advanced properties. For example, the facile device integration was used to attach the well-known anthracene-boronic acid (An-BA) probe to a biomimetic DNA scaffold and consequently, to use the unique photophysical properties of An-BA to improve glycoform differentiation. In addition, the noncovalent assembly enabled us to modify the sensor with a trinitrilotriacetic acid (tri-NTA)-Ni²⁺ complex, which endows it with selectivity toward a hexa-histidine tag (His-tag). The selective responses of the system to diverse His-tag-labeled proteins further demonstrate the potential applicability of such sensors and validate the mechanism underlying their function.

Robotic DNA Nanostructures

Over the past decade, DNA nanotechnology has spawned a broad variety of functional nanostructures tailored toward the enabled state at which applications are coming increasingly in view. One of the branches of these applications is in synthetic biology, where the intrinsic programmability of the DNA nanostructures may pave the way for smart task-specific molecular robotics. In brief, the synthesis of the user-defined artificial DNA nano-objects is based on employing DNA molecules with custom lengths and sequences as building materials that predictably assemble together by obeying Watson-Crick base pairing rules. The general workflow of creating DNA nanoshapes is getting more and more straightforward, and some objects can be designed automatically from the top down. The versatile DNA nano-objects can serve as synthetic tools at the interface with biology, for example, in therapeutics and diagnostics as dynamic logic-gated nanopills, light-, pH-, and thermally driven devices. Such diverse apparatuses can also serve as optical polarizers, sensors and capsules, autonomous cargo-sorting robots, rotary machines, precision measurement tools, as well as electric and magnetic-field directed robotic arms. In this review, we summarize the recent progress in robotic DNA nanostructures, mechanics, and their various implementations.

A molecular device: A DNA molecular lock driven by the nicking enzymes

As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molecular lock is still a serious challenge. Therefore, taking advantage of the DNA strand displacement and enzyme control technology, we constructed a molecular lock with a self-destructive mechanism. This molecular lock is mainly composed of logic circuits and takes nicking enzymes as inputs. To build this molecular lock, we first constructed a series of cascade circuits, including a YES–YES cascade circuit and a YES–AND cascade circuit. Then, an Inhibit logic gate was constructed to explore the inhibitory properties between different combinations of two nicking enzymes. Finally, using the characteristics of mutual inhibition between several enzymes, a DNA molecular lock driven by three nicking enzymes was constructed. In this molecular device, only the correct sequence of nicking enzymes can be input to ensure the normal operation of the molecular lock. Once the wrong password is entered, the device will be destroyed and cannot be recovered, which effectively prevents intruders from cracking the lock through exhaustive methods. The molecular lock has the function of simulating an electronic keyboard, which can realize the protection of information at the molecular level, and provides a new implementation method for building more advanced and complex molecular devices.

Nucleic acid-based drug delivery strategies

Nucleic acids have not been widely considered as an optimal material for drug delivery. Indeed, unmodified nucleic acids are enzymatically unstable, too hydrophilic for cell uptake and payload encapsulation, and may cause unintended biological responses such as immune system activation and prolongation of the blood coagulation pathway. Recently, however, three major areas of development surrounding nucleic acids have made it worthwhile to reconsider their role for drug delivery. These areas include DNA/RNA nanotechnology, multivalent nucleic acid nanostructures, and nucleic acid aptamers, which, respectively, provide the ability to engineer nanostructures with unparalleled levels of structural control, completely reverse certain biological properties of linear/cyclic nucleic acids, and enable antibody-level targeting using an all-nucleic acid construct. These advances, together with nucleic acids' ability to respond to various stimuli (engineered or natural), have led to a rapidly increasing number of drug delivery systems with potential for spatiotemporally controlled drug release. In this review, we discuss recent progress in nucleic acid-based drug delivery strategies, their potential, unique use cases, and risks that must be overcome or avoided.

A photo zipper locked DNA nanomachine with an internal standard for precise miRNA imaging in living cells

DNA nanomachines are capable of converting tiny triggers into autonomous accelerated cascade hybridization reactions and they have been used as a signal amplification strategy for intracellular imaging. However, the "always active" property of most DNA nanomachines with an "absolute intensity-dependent" signal acquisition mode results in "false positive signal amplification" by extracellular analytes and impairs detection accuracy. Here we design a photo zipper locked miRNA responsive DNA nanomachine (PZ-DNA nanomachine) based on upconversion nanoparticles (UCNPs) with a photo-cleavable DNA strand to block the miRNA recognition region, which provided sufficient protection to the DNA nanomachine against nonspecific extracellular activation and allowed satisfactory signal amplification for sensitive miRNA imaging after intracellular photoactivation. Multiple emissions from the UCNPs were also utilized as an internal standard to self-calibrate the intracellular miRNA responsive fluorescence signal. The presented PZ-DNA nanomachine demonstrated the sensitive imaging of intracellular miRNA from different cell lines, which resulted in good accordance with qRT-PCR measurements, providing a universal platform for precise imaging in living cells with high spatial-temporal specificity.

An orthogonally regulatable DNA nanodevice for spatiotemporally controlled biorecognition and tumor treatment

Despite the potential of nanodevices for intelligent drug delivery, it remains challenging to develop controllable therapeutic devices with high spatial-temporal selectivity. Here, we report a DNA nanodevice that can achieve tumor recognition and treatment with improved spatiotemporal precision under the regulation of orthogonal near-infrared (NIR) light. The nanodevice is built by combining an ultraviolet (UV) light-activatable aptamer module and a photosensitizer (PS) with up-conversion nanoparticle (UCNP) that enables the operation of the nanodevice with deep tissue-penetrable NIR light. The UCNPs can convert two distinct NIR excitations into orthogonal UV and green emissions for programmable photoactivation of the aptamer modules and PSs, respectively, allowing spatiotemporally controlled target recognition and photodynamic antitumor effect. Furthermore, when combined with immune checkpoint blockade therapy, the nanodevice results in regression of untreated distant tumors. This work provides a new approach for regulation of diagnostic and therapeutic activity at the right time and place.