Emerging uses of DNA mechanical devices

Strain-Modulated Flexible Bio-Organic/Graphene/PET Sensors Based on DNA-Curcumin Biopolymer

In recent years, there has been growing interest in the development of metal-free, environmentally friendly, and cost-effective biopolymer-based piezoelectric strain sensors (bio-PSSs) for flexible applications. In this study, we have developed a bio-PSS based on pure deoxyribonucleic acid (DNA) and curcumin materials in a thin-film form and studied its strain-induced current-voltage characteristics based on piezoelectric phenomena. The bio-PSS exhibited flexibility under varying compressive and tensile loads. Notably, the sensor achieved a strain gauge factor of 407 at an applied compressive strain of -0.027%, which is 8.67 times greater than that of traditional metal strain gauges. Furthermore, the flexible bio-PSS demonstrated a rapid response under a compressive strain of -0.08%. Our findings suggest that the proposed flexible bio-PSS holds significant promise as a motion sensor, addressing the demand for environmentally safe, wearable, and flexible strain sensor applications.

Decoding Biomechanical Cues Based on DNA Sensors

Biological systems perceive and respond to mechanical forces, generating mechanical cues to regulate life processes. Analyzing biomechanical forces has profound significance for understanding biological functions. Therefore, a series of molecular mechanical techniques have been developed, mainly including single-molecule force spectroscopy, traction force microscopy, and molecular tension sensor systems, which provide indispensable tools for advancing the field of mechanobiology. DNA molecules with a programmable structure and well-defined mechanical characteristics have attached much attention to molecular tension sensors as sensing elements, and are designed for the study of biomechanical forces to present biomechanical information with high sensitivity and resolution. In this work, a comprehensive overview of molecular mechanical technology is presented, with a particular focus on molecular tension sensor systems, specifically those based on DNA. Finally, the future development and challenges of DNA-based molecular tension sensor systems are looked upon.

The T-cell niche tunes immune function through modulation of the cytoskeleton and TCR-antigen forces

Obesity is a major public health crisis given its rampant growth and association with an increased risk for cancer. Interestingly, patients with obesity tend to have an increased tumor burden and decreased T-cell function. It remains unclear how obesity compromises T-cell mediated immunity. To address this question, we modeled the adipocyte niche using the secretome released from adipocytes as well as the niche of stromal cells and investigated how these factors modulated T-cell function. We found that the secretomes altered antigen-specific T-cell receptor (TCR) triggering and activation. RNA-sequencing analysis identified thousands of gene targets modulated by the secretome including those associated with cytoskeletal regulation and actin polymerization. We next used molecular force probes to show that T-cells exposed to the adipocyte niche display dampened force transmission to the TCR-antigen complex and conversely, stromal cell secreted factors lead to significantly enhanced TCR forces. These results were then validated in diet-induced obese mice. Importantly, secretome-mediated TCR force modulation mirrored the changes in T-cell functional responses in human T-cells using the FDA-approved immunotherapy, blinatumomab. Thus, this work shows that the adipocyte niche contributes to T-cell dysfunction through cytoskeletal modulation and reduces TCR triggering by dampening TCR forces consistent with the mechanosensor model of T-cell activation.

DNA mechanocapsules for programmable piconewton responsive drug delivery

The mechanical dysregulation of cells is associated with a number of disease states, that spans from fibrosis to tumorigenesis. Hence, it is highly desirable to develop strategies to deliver drugs based on the "mechanical phenotype" of a cell. To achieve this goal, we report the development of DNA mechanocapsules (DMC) comprised of DNA tetrahedrons that are force responsive. Modeling shows the trajectory of force-induced DMC rupture and predicts how applied force spatial position and orientation tunes the force-response threshold. DMCs functionalized with adhesion ligands mechanically denature in vitro as a result of cell receptor forces. DMCs are designed to encapsulate macromolecular cargos such as dextran and oligonucleotide drugs with minimal cargo leakage and high nuclease resistance. Force-induced release and uptake of DMC cargo is validated using flow cytometry. Finally, we demonstrate force-induced mRNA knockdown of HIF-1α in a manner that is dependent on the magnitude of cellular traction forces. These results show that DMCs can be effectively used to target biophysical phenotypes which may find useful applications in immunology and cancer biology.

DNA Origami-Based Single-Molecule Force Spectroscopy and Applications

Over the last years, single-molecule force spectroscopy provided insights into the intricate connection between mechanical stimuli and biochemical signaling. The underlying molecular mechanisms were uncovered and explored using techniques such as atomic force microscopy and force spectroscopy using optical or magnetic tweezers. These experimental approaches are limited by thermal noise resulting from a physical connection of the studied biological system to the macroscopic world. To overcome this limitation, we recently introduced the DNA origami force clamp (FC) which is a freely diffusing nanodevice that generates piconewton forces on a DNA sequence of interest. Binding of a protein to the DNA under tension can be detected employing fluorescence resonance energy transfer (FRET) as a sensitive readout.This protocol introduces the reader to the working principles of the FC and provides instructions to design and generate a DNA origami FC customized for a protein of interest. Molecular cloning techniques are employed to modify, produce, and purify a custom DNA scaffold. A fluorescently labeled DNA suitable to detect protein binding via FRET is generated via enzymatic ligation of commercial DNA oligonucleotides. After thermal annealing of all components, the DNA origami FC is purified using agarose gel electrophoresis. The final section covers the interrogation of the FC using confocal single-molecule FRET measurements and subsequent data analysis to quantify the binding of a DNA-binding protein to its cognate recognition site under a range of forces. Using this approach, force-dependent DNA-protein interactions can be studied on the single-molecule level on thousands of molecules in a parallelized fashion.

An intelligent DNA nanomachine for amplified MicroRNA imaging and MicroRNA-Guided efficient gene silencing

The DNA nanomachines as excellent synthetic biological tools have been widely used for the sensitive detection of intracellular microRNA (miRNA) and DNAzyme-involved gene silencing. However, intelligent DNA nanomachines which have the ability to sense intracellular specific biomolecules and respond to external information in complex environments still remain challenging. Herein, we develop a miRNA-responsive DNAzyme cascaded catalytic (MDCC) nanomachine to perform multilayer cascade reactions, enabling the amplified intracellular miRNA imaging and miRNA-guided efficient gene silencing. The intelligent MDCC nanomachine is designed based on multiple DNAzyme subunit-encoded catalyzed hairpin assembly (CHA) reactants sustained by the pH-responsive Zeolitic imidazolate framework-8 (ZIF-8) nanoparticles. After cellular uptake, the MDCC nanomachine degrades in acidic endosome and releases three hairpin DNA reactants and Zn2+, and the latter can act as an effective cofactor for DNAzyme. In the presence of miRNA-21, a catalytic hairpin assembly (CHA) reaction is triggered, which produces a large number of Y-shaped fluorescent DNA constructs containing three DNAzyme modules for gene silencing. The construction of Y-shaped DNA modified with multisite fluorescence and the circular reaction realizes ultrasensitive miRNA-21 imaging of cancer cells. Moreover, miRNA-guided gene silencing inhibits the cancer cell proliferation through the DNAzyme-specific recognition and cleavage of target EGR-1 (Early Growth Response-1) mRNA, which is one key tumor-involved mRNA. The strategy may provide a promising platform for highly sensitive determination of biomolecules and accurate gene therapy of cancer cells.

Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips

Protein complex assembly facilitates the combination of individual protein subunits into functional entities, and thus plays a crucial role in biology and biotechnology. Recently, we developed quasi-twodimensional, silicon-based compartmental biochips that are designed to study and administer the synthesis and assembly of protein complexes. At these biochips, individual protein subunits are synthesized from locally confined high-density DNA brushes and are captured on the chip surface by molecular traps. Here, we investigate single-gene versions of our quasi-twodimensional synthesis systems and introduce the trap-binding efficiency to characterize their performance. We show by mathematical and computational modeling how a finite trap density determines the dynamics of protein-trap binding and identify three distinct regimes of the trap-binding efficiency. We systematically study how protein-trap binding is governed by the system's three key parameters, which are the synthesis rate, the diffusion constant and the trap-binding affinity of the expressed protein. In addition, we describe how spatially differential patterns of traps modulate the protein-trap binding dynamics. In this way, we extend the theoretical knowledge base for synthesis, diffusion, and binding in compartmental systems, which helps to achieve better control of directed molecular self-assembly required for the fabrication of nanomachines for synthetic biology applications or nanotechnological purposes.

Hydrogel-based molecular tension fluorescence microscopy for investigating receptor-mediated rigidity sensing

Extracellular matrix (ECM) rigidity serves as a crucial mechanical cue impacting diverse biological processes. However, understanding the molecular mechanisms of rigidity sensing has been limited by the spatial resolution and force sensitivity of current cellular force measurement techniques. Here we developed a method to functionalize DNA tension probes on soft hydrogel surfaces in a controllable and reliable manner, enabling molecular tension fluorescence microscopy for rigidity sensing studies. Our findings showed that fibroblasts respond to substrate rigidity by recruiting more force-bearing integrins and modulating integrin sampling frequency of the ECM, rather than simply overloading the existing integrin-ligand bonds, to promote focal adhesion maturation. We also demonstrated that ECM rigidity positively regulates the pN force of T cell receptor-ligand bond and T cell receptor mechanical sampling frequency, promoting T cell activation. Thus, hydrogel-based molecular tension fluorescence microscopy implemented on a standard confocal microscope provides a simple and effective means to explore detailed molecular force information for rigidity-dependent biological processes.

Fluctuotaxis: Nanoscale directional motion away from regions of fluctuation

Regulating the motion of nanoscale objects on a solid surface is vital for a broad range of technologies such as nanotechnology, biotechnology, and mechanotechnology. In spite of impressive advances achieved in the field, there is still a lack of a robust mechanism which can operate under a wide range of situations and in a controllable manner. Here, we report a mechanism capable of controllably driving directed motion of any nanoobjects (e.g., nanoparticles, biomolecules, etc.) in both solid and liquid forms. We show via molecular dynamics simulations that a nanoobject would move preferentially away from the fluctuating region of an underlying substrate, a phenomenon termed fluctuotaxis-for which the driving force originates from the difference in atomic fluctuations of the substrate behind and ahead of the object. In particular, we find that the driving force can depend quadratically on both the amplitude and frequency of the substrate and can thus be tuned flexibly. The proposed driving mechanism provides a robust and controllable way for nanoscale mass delivery and has potential in various applications including nanomotors, molecular machines, etc.

Dual DNA recycling amplifications coupled with Au NPs@ZIF-MOF accelerator for enhanced electrochemical ratiometric sensing of pathogenic bacteria

Sensitive and accurate quantification of pathogenic bacteria is vastly significant to the related food safety. Herein, a sensitive ratiometric electrochemical biosensor was developed for the detection of Staphylococcus aureus (S. aureus) based on dual DNA recycling amplifications and Au NPs@ZIF-MOF accelerator. Gold nanoparticles-loaded Zeolitic imidazolate metal-organic framework (Au NPs@ZIF-MOF) as electrode substrate possessed a large specific surface area for nucleic acid adsorption, and as an accelerator promoted the transfer of electrons. The strong recognition of aptamer to target S. aureus could initiate the padlock probe-based exponential rolling circle amplification (P-ERCA, as the first DNA recycling amplification), generating large numbers of trigger DNA strands. The released trigger DNA further activated the catalytic hairpin assembly (CHA, as the second DNA recycling amplification) on electrode surface. Consequently, P-ERCA and CHA continuously brought about one target to many signal transduction, leading to an exponential amplification. To achieve the accuracy of detection, the signal ratio of methylene blue (MB) and ferrocene (Fc) (I_MB/I_Fc) was applied for intrinsic self-calibrating. Taking advantages of dual DNA recycling amplifications and Au NPs@ZIF-MOF, the proposed sensing system displayed high sensitivity for S. aureus quantification with a linear range of 5-10⁸ CFU/mL, and the limit of detection was 1 CFU/mL. Moreover, this system represented excellent reproducibility, selectivity, and practicability for S. aureus analysis in foods.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications

DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.

Mechanical DNA Origami to Investigate Biological Systems

The ability to self-assemble DNA nanodevices with programmed structural dynamics that can sense and respond to the local environment can enable transformative applications in fields including mechanobiology and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. In this review, the current state-of-the-art in constructing complex DNA geometries with dynamic and mechanical properties to enable a molecular scale force measurement is first summarized. Next, an overview of engineering modular DNA devices that interact with cell surfaces is highlighted detailing examples of mechanosensitive proteins and the force-induced dynamic molecular interaction on the downstream biochemical signaling. Finally, the challenges and an outlook on this promising class of DNA devices acting as nanomachines to operate at a low piconewton range suitable for a majority of biological effects or as hybrid materials to achieve higher tension exertion required for other biological investigations, are discussed.

A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices

Toehold-mediated strand displacement and its regulatory tools are fundamental for DNA nanotechnology. However, current regulatory tools all need to change the original sequence of reactants, making the regulation inconvenient and cumbersome. More importantly, the booming development of DNA nanotechnology will soon promote the production of packaged and batched devices or circuits with specified functions. Regarding standardized, packaged DNA nanodevices, access to personalized post-modification will greatly help users, whereas none of the current regulatory tools can provide such access, which has greatly constrained DNA nanodevices from becoming more powerful and practical. Herein, we developed a novel regulation tool named Cap which has two basic functions of subtle regulation of the reaction rate and erasability. Based on these functions, we further developed three advanced functions. Through integration of all functions of Cap and its distinct advantage of working independently, we finally realized personalized tailor-made post-modification on pre-fabricated DNA circuits. A pre-fabricated dual-output DNA circuit was successfully transformed into an equal-output circuit, a signal-antagonist circuit and a covariant circuit according to our requirements. Taken together, Cap is easy to design and generalizable for all strand displacement-based DNA nanodevices. We believe the Cap tool will be widely used in regulating reaction networks and personalized tailor-made post-modification of DNA nanodevices.

High-throughput force measurement of individual kinesin-1 motors during multi-motor transport

Molecular motors often work in teams to move a cellular cargo. Yet measuring the forces exerted by each motor is challenging. Using a sensor made with denatured ssDNA and multi-color fluorescence, we measured picoNewtons of forces and nanometer distances exerted by individual constrained kinesin-1 motors acting together while driving a common microtubule in vitro. We find that kinesins primarily exerted less than 1 pN force, even while the microtubule is bypassing artificial obstacles of 20-100 nanometer size. Occasionally, individual forces increase upon encountering obstacles, although at other times they do not, with the cargo continuing in a directional manner. Our high-throughput technique, which can measure forces by many motors simultaneously, is expected to be useful for many different types of molecular motors.

Ultra-photostable DNA FluoroCubes: Mechanism of Photostability and Compatibility with FRET and Dark Quenching

DNA-based FluoroCubes were recently developed as a solution to photobleaching, a ubiquitous limitation of fluorescence microscopy (Niekamp; ; Stuurman; ; Vale Nature Methods, 2020). FluoroCubes, that is, compact ∼4 × 4 × 5.4 nm3 four-helix bundles coupled to ≤6 fluorescent dyes, remain fluorescent up to ∼50× longer than single dyes and emit up to ∼40× as many photons. The current work answers two important questions about the FluoroCubes. First, what is the mechanism by which photostability is enhanced? Second, are FluoroCubes compatible with Förster resonance energy transfer (FRET) and similar techniques? We use single particle photobleaching studies to show that photostability arises through interactions between the fluorophores and the four-helix DNA bundle. Supporting this, we discover that smaller ∼4 × 4 × 2.7 nm3 FluoroCubes also confer ultraphotostability. However, we find that certain dye-dye interactions negatively impact FluoroCube performance. Accordingly, 4-dye FluoroCubes lacking these interactions perform better than 6-dye FluoroCubes. We also demonstrate that FluoroCubes are compatible with FRET and dark quenching applications.

A modular spring-loaded actuator for mechanical activation of membrane proteins

How cells respond to mechanical forces by converting them into biological signals underlie crucial cellular processes. Our understanding of mechanotransduction has been hindered by technical barriers, including limitations in our ability to effectively apply low range piconewton forces to specific mechanoreceptors on cell membranes without laborious and repetitive trials. To overcome these challenges we introduce the Nano-winch, a robust, easily assembled, programmable DNA origami-based molecular actuator. The Nano-winch is designed to manipulate multiple mechanoreceptors in parallel by exerting fine-tuned, low- piconewton forces in autonomous and remotely activated modes via adjustable single- and double-stranded DNA linkages, respectively. Nano-winches in autonomous mode can land and operate on the cell surface. Targeting the device to integrin stimulated detectable downstream phosphorylation of focal adhesion kinase, an indication that Nano-winches can be applied to study cellular mechanical processes. Remote activation mode allowed finer extension control and greater force exertion. We united remotely activated Nano-winches with single-channel bilayer experiments to directly observe the opening of a channel by mechanical force in the force responsive gated channel protein, BtuB. This customizable origami provides an instrument-free approach that can be applied to control and explore a diversity of mechanotransduction circuits on living cells.

Studies on mechanotransduction are limited by our ability to apply low range forces to specific mechanoreceptors on cell membranes. Here the authors report the Nano-winch, a programmable DNA origami-based molecular actuator, to manipulate multiple mechanoreceptors in parallel by exerting piconewton forces.

May the force be with your (immune) cells: an introduction to traction force microscopy in Immunology

For more than a couple of decades now, “force” has been recognized as an important physical parameter that cells employ to adapt to their microenvironment. Whether it is externally applied, or internally generated, cells use force to modulate their various actions, from adhesion and migration to differentiation and immune function. T lymphocytes use such mechano-sensitivity to decipher signals when recognizing cognate antigens presented on the surface of antigen presenting cells (APCs), a critical process in the adaptive immune response. As such, many techniques have been developed and used to measure the forces felt/exerted by these small, solitary and extremely reactive cells to decipher their influence on diverse T cell functions, primarily activation. Here, we focus on traction force microscopy (TFM), in which a deformable substrate, coated with the appropriate molecules, acts as a force sensor on the cellular scale. This technique has recently become a center of interest for many groups in the “ImmunoBiophysics” community and, as a consequence, has been subjected to refinements for its application to immune cells. Here, we present an overview of TFM, the precautions and pitfalls, and the most recent developments in the context of T cell immunology.

Force-Coded Strategy for the Simultaneous Detection of Multiple Tumor-Related Proteins

Multiplexed simultaneous detection of various cancer markers is required for accurate diagnosis and treatment of early cancer. In this work, we present a force-coded strategy for the simultaneous detection of tumor-related proteins with tunable dynamic range via magnetic sensing. The multiplexing capability of this method is achieved by designing DNA devices that can recognize different biomarkers and code them with different binding forces measured by the force-induced remnant magnetization spectroscopy, which is not influenced by the color of the light and the solution. Moreover, the force-coded assay with high sensitivity and adjustable detection range is robust, which could be used for practical biological applications such as magnetic sensing, handheld miniaturized systems, and potential in vivo diagnosis.

The Free-Energy Landscape of a Mechanically Bistable DNA Origami

Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed to exhibit two mechanically stable states and for which a bistable landscape has been inferred from ensembles of structures visualized by electron microscopy. Surprisingly, simulations using the oxDNA model predict that the defect-free origami has a single free-energy minimum. The expected second state is not stable because the hinge joints do not simply allow free angular motion but instead lead to increasing free-energetic penalties as the joint angles relevant to the second state are approached. This raises interesting questions about the cause of this difference between simulations and experiment, such as how assembly defects might affect the ensemble of structures observed experimentally.

Exploring Integrin-Mediated Force Transmission during Confined Cell Migration by DNA-Based Tension Probes

Mechanical forces have profound effects on the morphology and migration of cells in a two-dimensional environment. However, cells in vivo mostly migrate in three-dimensional space while physically constrained, and the mechanism by which cellular dynamic forces drive migration in this confined environment is unclear. Here, we present a method of fabricating microfluidic chips with integrated DNA-based tension probes to measure spatiotemporal variations in integrin-mediated force exerted during confined cell migration. Using this developed device, we measured the spatial locations, magnitudes, and temporal characteristics of integrin-ligand tension signals in motile cells in different microchannels and found that cells exerted less force and underwent increasingly transitory integrin-ligand interactions when migrating in confined spaces. This study demonstrates that the described method provides insights into understanding the migratory machinery of cells in geometrically confined environment that better mimics physiological conditions.

High-Throughput DNA Tensioner Platform for Interrogating Mechanical Heterogeneity of Single Living Cells

Cell mechanical forces play fundamental roles in regulating cellular responses to environmental stimulations. The shortcomings of conventional methods, including force resolution and cellular throughput, make them less accessible to mechanical heterogeneity at the single-cell level. Here, a DNA tensioner platform is introduced with high throughput (>10 000 cells per chip) and pN-level resolution. A microfluidic-based cell array is trapped on "hairpin-structured" DNA tensioners that enable transformation of the mechanical information of living cells into fluorescence signals. By using the platform, one can identify enhanced mechanical forces of drug-resistant cells as compared to their drug-sensitive counterparts, and mechanical differences between metastatic tumor cells in pleural effusion and nonmetastatic histiocytes. Further genetic analysis traces two genes, VEGFA and MINK1, that may play deterministic roles in regulating mechanical heterogeneities. In view of the ubiquity of cells' mechanical forces in the extracellular microenvironment (ECM), this platform shows wide potential to establish links of cellular mechanical heterogeneity to genetic heterogeneity.

Characterizing the free-energy landscapes of DNA origamis

We show how coarse-grained modelling combined with umbrella sampling using distance-based order parameters can be applied to compute the free-energy landscapes associated with mechanical deformations of large DNA nanostructures. We illustrate this approach for the strong bending of DNA nanotubes and the potentially bistable landscape of twisted DNA origami sheets. The homogeneous bending of the DNA nanotubes is well described by the worm-like chain model; for more extreme bending the nanotubes reversibly buckle with the bending deformations localized at one or two "kinks". For a twisted one-layer DNA origami, the twist is coupled to the bending of the sheet giving rise to a free-energy landscape that has two nearly-degenerate minima that have opposite curvatures. By contrast, for a two-layer origami, the increased stiffness with respect to bending leads to a landscape with a single free-energy minimum that has a saddle-like geometry. The ability to compute such landscapes is likely to be particularly useful for DNA mechanotechnology and for understanding stress accumulation during the self-assembly of origamis into higher-order structures.

Photoreactive Cytosine-Functionalized Self-Assembled Micelles with Enhanced Cellular Uptake Capability for Efficient Cancer Chemotherapy

Design, fabrication, and control of photoreactive supramolecular macromers─which are composed of a thermoresponsive polymer backbone and photoreactive nucleobase end-groups─to achieve the desired physical-chemical performance and provide the high efficiency required for chemotherapy drug delivery purposes still present challenges. Herein, a difunctional cytosine-terminated supramolecular macromer was successfully obtained at high yield. UV-irradiation induces the formation of cytosine photodimers within the structure. The irradiated macromer can self-assemble into nanosized spherical micelles in water that possess a number of interesting and unique features, such as desired micellar size and morphology, tunable drug-loading capacity, and excellent structural stability in serum-containing medium, in addition to well-controlled drug-release behaviors in response to changes in environmental temperature and pH; these extremely desirable, rare features are required to augment the functions of polymeric nanocarriers for drug delivery. Importantly, a series of in vitro studies demonstrated that photodimerized cytosine moieties within the drug-loaded micelles substantially enhance their internalization and accumulation inside cells via endocytosis and subsequently lead to induction of massive apoptotic cell death compared with the corresponding nonirradiated micelles. Thus, this newly developed "photomodified" nanocarrier system could provide a potentially fruitful route to enhance the drug delivery performance of nanocages without the need to introduce targeting moieties or additional components.

Applications of DNA-Functionalized Proteins

As an important component that constitutes all the cells and tissues of the human body, protein is involved in most of the biological processes. Inspired by natural protein systems, considerable efforts covering many discipline fields were made to design artificial protein assemblies and put them into application in recent decades. The rapid development of structural DNA nanotechnology offers significant means for protein assemblies and promotes their application. Owing to the programmability, addressability and accurate recognition ability of DNA, many protein assemblies with unprecedented structures and improved functions have been successfully fabricated, consequently creating many brand-new researching fields. In this review, we briefly introduced the DNA-based protein assemblies, and highlighted the limitations in application process and corresponding strategies in four aspects, including biological catalysis, protein detection, biomedicine treatment and other applications.

Complementary Nucleobase Interactions Drive Co-Assembly of Drugs and Nanocarriers for Selective Cancer Chemotherapy

A new concept in cooperative adenine-uracil (A-U) hydrogen bonding interactions between anticancer drugs and nanocarrier complexes was successfully demonstrated by invoking the co-assembly of water soluble, uracil end-capped polyethylene glycol polymer (BU-PEG) upon association with the hydrophobic drug adenine-modified rhodamine (A-R6G). This concept holds promise as a smart and versatile drug delivery system for the achievement of targeted, more efficient cancer chemotherapy. Due to A-U base pairing between BU-PEG and A-R6G, BU-PEG has high tendency to interact with A-R6G, which leads to the formation of self-assembled A-R6G/BU-PEG nanogels in aqueous solution. The resulting nanogels exhibit a number of unique physical properties, including extremely high A-R6G-loading capacity, well-controlled, pH-triggered A-R6G release behavior, and excellent structural stability in biological media. Importantly, a series of in vitro cellular experiments clearly demonstrated that A-R6G/BU-PEG nanogels improved the selective uptake of A-R6G by cancer cells via endocytosis and promoted the intracellular release of A-R6G to subsequently induce apoptotic cell death, while control rhodamine/BU-PEG nanogels did not exert selective toxicity in cancer or normal cell lines. Overall, these results indicate that cooperative A-U base pairing within nanogels is a critical factor that improves selective drug uptake and effectively promotes apoptotic programmed cell death in cancer cells.

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.

Turn-key mapping of cell receptor force orientation and magnitude using a commercial structured illumination microscope

Many cellular processes, including cell division, development, and cell migration require spatially and temporally coordinated forces transduced by cell-surface receptors. Nucleic acid-based molecular tension probes allow one to visualize the piconewton (pN) forces applied by these receptors. Building on this technology, we recently developed molecular force microscopy (MFM) which uses fluorescence polarization to map receptor force orientation with diffraction-limited resolution (~250 nm). Here, we show that structured illumination microscopy (SIM), a super-resolution technique, can be used to perform super-resolution MFM. Using SIM-MFM, we generate the highest resolution maps of both the magnitude and orientation of the pN traction forces applied by cells. We apply SIM-MFM to map platelet and fibroblast integrin forces, as well as T cell receptor forces. Using SIM-MFM, we show that platelet traction force alignment occurs on a longer timescale than adhesion. Importantly, SIM-MFM can be implemented on any standard SIM microscope without hardware modifications.

Multifunctional Clip Strand for the Regulation of DNA Strand Displacement and Construction of Complex DNA Nanodevices

Strand displacement reactions are important bricks for the construction of various DNA nanodevices, among which the toehold-mediated strand displacement reaction is the most prevalently adopted. However, only a limited number of tools could be used to finely regulate the toehold reaction, thus restricting DNA nanodevices from being more multifunctional and powerful. Herein, we developed a regulation tool, Clip, and achieved multiple regulatory functions, including subtle adjustment of the reaction rates, allosteric strand displacement, selective activation, and resetting of the reaction. Taking advantages of the multiple functions, we constructed Clip-toehold-based DNA walking machines. They showed behaviors of controllable walking, concatenation, and programmable pathways. Furthermore, we built Clip-toehold-based AND and OR logic gates and integrated those logic gates to construct multilayer circuits, which could be reset and reused to process different input signals. We believe that the proposed Clip tool has expanded the functionality of DNA strand displacement-based nanodevices to a much more complex and diverse level and anticipate that the tool will be widely adopted in DNA nanotechnology.

Active liquid crystals powered by force-sensing DNA-motor clusters

Cytoskeletal active nematics exhibit striking nonequilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which kinesin motors are linked by a double-stranded DNA linker. The efficiency by which DNA-based clusters power active nematics depends on both the stepping dynamics of the kinesin motors and the chemical structure of the polymeric linker. Fluorescence anisotropy measurements reveal that the motor clusters, like filamentous microtubules, exhibit local nematic order. The properties of the DNA linker enable the design of force-sensing clusters. When the load across the linker exceeds a critical threshold, the clusters fall apart, ceasing to generate active stresses and slowing the system dynamics. Fluorescence readout reveals the fraction of bound clusters that generate interfilament sliding. In turn, this yields the average load experienced by the kinesin motors as they step along the microtubules. DNA-motor clusters provide a foundation for understanding the molecular mechanism by which nanoscale molecular motors collectively generate mesoscopic active stresses, which in turn power macroscale nonequilibrium dynamics of active nematics.

Programmable DNA-augmented hydrogels for controlled activation of human lymphocytes

Contractile forces within the planar interface between T cell and antigen-presenting surface mechanically stimulate T cell receptors (TCR) in the mature immune synapses. However, the origin of mechanical stimulation during the initial, i.e., presynaptic, microvilli-based TCR activation in the course of immune surveillance remains unknown and new tools to help address this problem are needed. In this work, we develop nucleic acid nanoassembly (NAN)-based technology for functionalization of hydrogels using isothermal toehold-mediated reassociation of RNA/DNA heteroduplexes. Resulting platform allows for regulation with NAN linkers of 3D force momentum along the TCR mechanical axis, whereas hydrogels contribute to modulation of 2D shear modulus. By utilizing different lengths of NAN linkers conjugated to polyacrylamide gels of different shear moduli, we demonstrate an efficient capture of human T lymphocytes and tunable activation of TCR, as confirmed by T-cell spreading and pY foci.

Burnt bridge ratchet motor force scales linearly with polyvalency: a computational study

Nano- and micro-scale burnt bridge ratchet motors, which translocate via "guide" molecules that bind to and degrade a field of "fuel" molecules, have recently emerged in several biological and engineering contexts. The capacity of these motors to generate mechanical forces remains an open question. Here, chemomechanical modeling suggests that BBR force scales linearly with the steady-state number of guide-fuel bonds.

DNA origami-based protein networks: from basic construction to emerging applications

Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.

Progress in the mechanical modulation of cell functions in tissue engineering

In mammals, mechanics at multiple stages-nucleus to cell to ECM-underlie multiple physiological and pathological functions from its development to reproduction to death. Under this inspiration, substantial research has established the role of multiple aspects of mechanics in regulating fundamental cellular processes, including spreading, migration, growth, proliferation, and differentiation. However, our understanding of how these mechanical mechanisms are orchestrated or tuned at different stages to maintain or restore the healthy environment at the tissue or organ level remains largely a mystery. Over the past few decades, research in the mechanical manipulation of the surrounding environment-known as substrate or matrix or scaffold on which, or within which, cells are seeded-has been exceptionally enriched in the field of tissue engineering and regenerative medicine. To do so, traditional tissue engineering aims at recapitulating key mechanical milestones of native ECM into a substrate for guiding the cell fate and functions towards specific tissue regeneration. Despite tremendous progress, a big puzzle that remains is how the cells compute a host of mechanical cues, such as stiffness (elasticity), viscoelasticity, plasticity, non-linear elasticity, anisotropy, mechanical forces, and mechanical memory, into many biological functions in a cooperative, controlled, and safe manner. High throughput understanding of key cellular decisions as well as associated mechanosensitive downstream signaling pathway(s) for executing these decisions in response to mechanical cues, solo or combined, is essential to address this issue. While many reports have been made towards the progress and understanding of mechanical cues-particularly, substrate bulk stiffness and viscoelasticity-in regulating the cellular responses, a complete picture of mechanical cues is lacking. This review highlights a comprehensive view on the mechanical cues that are linked to modulate many cellular functions and consequent tissue functionality. For a very basic understanding, a brief discussion of the key mechanical players of ECM and the principle of mechanotransduction process is outlined. In addition, this review gathers together the most important data on the stiffness of various cells and ECM components as well as various tissues/organs and proposes an associated link from the mechanical perspective that is not yet reported. Finally, beyond addressing the challenges involved in tuning the interplaying mechanical cues in an independent manner, emerging advances in designing biomaterials for tissue engineering are also explored.

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.

Astigmatic traction force microscopy (aTFM)

Quantifying small, rapidly progressing three-dimensional forces generated by cells remains a major challenge towards a more complete understanding of mechanobiology. Traction force microscopy is one of the most broadly applied force probing technologies but ascertaining three-dimensional information typically necessitates slow, multi-frame z-stack acquisition with limited sensitivity. Here, by performing traction force microscopy using fast single-frame astigmatic imaging coupled with total internal reflection fluorescence microscopy we improve the temporal resolution of three-dimensional mechanical force quantification up to 10-fold compared to its related super-resolution modalities. 2.5D astigmatic traction force microscopy (aTFM) thus enables live-cell force measurements approaching physiological sensitivity.

Quantitative Methodologies to Dissect Immune Cell Mechanobiology

Mechanobiology seeks to understand how cells integrate their biomechanics into their function and behavior. Unravelling the mechanisms underlying these mechanobiological processes is particularly important for immune cells in the context of the dynamic and complex tissue microenvironment. However, it remains largely unknown how cellular mechanical force generation and mechanical properties are regulated and integrated by immune cells, primarily due to a profound lack of technologies with sufficient sensitivity to quantify immune cell mechanics. In this review, we discuss the biological significance of mechanics for immune cells across length and time scales, and highlight several experimental methodologies for quantifying the mechanics of immune cells. Finally, we discuss the importance of quantifying the appropriate mechanical readout to accelerate insights into the mechanobiology of the immune response.

Sequential Pull-Down Purification of DNA Origami Superstructures

Higher-order superstructures of individual DNA origami building blocks are frequently used in DNA nanotechnology in order to increase the structure dimensions and complexity. Here, a purification method is presented to specifically enrich a fully assembled superstructure out of an excess of substructures. The approach is based on pull-down reactions with magnetic beads, where superstructures are captured via an anchor strand on a specific terminus and then become separated from terminus-free structures. By carrying out several pull-down reactions sequentially on different termini, the full superstructures that possess all termini become finally enriched. The approach is demonstrated by purifying linear origami superstructures with up to nine monomers by two-sided pull-down reactions and a T-shaped superstructure in a three-sided pull-down reaction. In all cases, high recovery yields and purities are obtained. A crucial prerequisite for the sequential pull-down scheme is the establishment of highly specific, orthogonal sequence sets for capture, and anchor strands. It is expected that the introduced approach provides a useful and universal method to purify complex DNA origami superstructures with high specificity and yield and this way allows the massive parallel fabrication of nanostructures at high homogeneity.

Imaging methods in mechanosensing: a historical perspective and visions for the future

Over the past three decades, as mechanobiology has become a distinct area of study, researchers have developed novel imaging tools to discover the pathways of biomechanical signaling. Early work with substrate engineering and particle tracking demonstrated the importance of cell–extracellular matrix interactions on the cell cycle as well as the mechanical flux of the intracellular environment. Most recently, tension sensor approaches allowed directly measuring tension in cell–cell and cell–substrate interactions. We retrospectively analyze how these various optical techniques progressed the field and suggest our vision forward for a unified theory of cell mechanics, mapping cellular mechanosensing, and novel biomedical applications for mechanobiology.

Multivalent molecular tension probes as anisotropic mechanosensors: concept and simulation

Cells use protein-based mechanosensors to measure the physical properties of their surroundings. Synthetic tension sensors made of proteins, DNA, and other molecular building blocks have recently emerged as tools to visualize and perturb the mechanics of these mechanosensors. While almost all synthetic tension sensors are designed to exhibit orientation-independent force responses, recent work has shown that biological mechanosensors often function in a manner that is highly dependent on force orientation. Accordingly, the design of synthetic mechanosensors with orientation-dependent force responses can provide a means to study the role of orientation in mechanosensation. Furthermore, the process of designing anisotropic force responses may yield insight into the physical basis for orientation-dependence in biological mechanosensors. Here, we propose a DNA-based molecular tension sensor design wherein multivalency is used to create an orientation-dependent force response. We apply chemomechanical modeling to show that multivalency can be used to create synthetic mechanosensors with force response thresholds that vary by tens of pN with respect to force orientation.

Spectroscopic Analysis of a Library of DNA Tension Probes for Mapping Cellular Forces at Fluid Interfaces

Oligonucleotide-based probes offer the highest spatial resolution, force sensitivity, and molecular specificity for cellular tension sensing and have been developed to measure a variety of molecular forces mediated by individual receptors in T cells, platelets, fibroblasts, B-cells, and immortalized cancer cell lines. These fluorophore-oligonucleotide conjugate probes are designed with a stem-loop structure that engages cell receptors and reversibly unfolds due to mechanical strain. With the growth of recent work bridging molecular mechanobiology and biomaterials, there is a need for a detailed spectroscopic analysis of DNA tension probes that are used for cellular imaging. In this manuscript, we conducted an analysis of 19 DNA hairpin-based tension probe variants using molecular dynamics simulations, absorption spectroscopy, and fluorescence imaging (epifluorescence and fluorescence lifetime imaging microscopy). We find that tension probes are highly sensitive to their molecular design, including donor and acceptor proximity and pairing, DNA stem-loop structure, and conjugation chemistry. We demonstrate the impact of these design features using a supported lipid bilayer model of podosome-like adhesions. Finally, we discuss the requirements for tension imaging in various biophysical contexts and offer a series of experimental recommendations, thus providing a guide for the design and application of DNA hairpin-based molecular tension probes.

Shear Stress-Responsive Polymersome Nanoreactors Inspired by the Marine Bioluminescence of Dinoflagellates

Some marine plankton called dinoflagellates emit light in response to the movement of surrounding water, resulting in a phenomenon called milky seas or sea sparkle. The underlying concept, a shear-stress induced permeabilisation of biocatalytic reaction compartments, is transferred to polymer-based nanoreactors. Amphiphilic block copolymers that carry nucleobases in their hydrophobic block are self-assembled into polymersomes. The membrane of the vesicles can be transiently switched between an impermeable and a semipermeable state by shear forces occurring in flow or during turbulent mixing of polymersome dispersions. Nucleobase pairs in the hydrophobic leaflet separate when mechanical force is applied, exposing their hydrogen bonding motifs and therefore making the membrane less hydrophobic and more permeable for water soluble compounds. This polarity switch is used to release payload of the polymersomes on demand, and to activate biocatalytic reactions in the interior of the polymersomes.

Progress in Nanorobotics for Advancing Biomedicine

Nanorobotics, which has long been a fantasy in the realm of science fiction, is now a reality due to the considerable developments in diverse fields including chemistry, materials, physics, information and nanotechnology in the past decades. Not only different prototypes of nanorobots whose sizes are nanoscale are invented for various biomedical applications, but also robotic nanomanipulators which are able to handle nano-objects obtain substantial achievements for applications in biomedicine. The outstanding achievements in nanorobotics have significantly expanded the field of medical robotics and yielded novel insights into the underlying mechanisms guiding life activities, remarkably showing an emerging and promising way for advancing the diagnosis & treatment level in the coming era of personalized precision medicine. In this review, the recent advances in nanorobotics (nanorobots, nanorobotic manipulations) for biomedical applications are summarized from several facets (including molecular machines, nanomotors, DNA nanorobotics, and robotic nanomanipulators), and the future perspectives are also presented.

Stretching DNA origami: effect of nicks and Holliday junctions on the axial stiffness

The axial stiffness of DNA origami is determined as a function of key nanostructural characteristics. Different constructs of two-helix nanobeams with specified densities of nicks and Holliday junctions are synthesized and stretched by fluid flow. Implementing single particle tracking to extract force–displacement curves enables the measurement of DNA origami stiffness values at the enthalpic elasticity regime, i.e. for forces larger than 15 pN. Comparisons between ligated and nicked helices show that the latter exhibit nearly a two-fold decrease in axial stiffness. Numerical models that treat the DNA helices as elastic rods are used to evaluate the local loss of stiffness at the locations of nicks and Holliday junctions. It is shown that the models reproduce the experimental data accurately, indicating that both of these design characteristics yield a local stiffness two orders of magnitude smaller than the corresponding value of the intact double-helix. This local degradation in turn leads to a macroscopic loss of stiffness that is evaluated numerically for multi-helix DNA bundles.

Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures

To study the elastic properties of rodlike DNA nanostructures, we perform long simulations of these structures using the oxDNA coarse-grained model. By analyzing the fluctuations in these trajectories, we obtain estimates of the bend and twist persistence lengths and the underlying bend and twist elastic moduli and couplings between them. Only on length scales beyond those associated with the spacings between the interhelix crossovers do the bending fluctuations behave like those of a wormlike chain. The obtained bending persistence lengths are much larger than that for double-stranded DNA and increase nonlinearly with the number of helices, whereas the twist moduli increase approximately linearly. To within the numerical error in our data, the twist-bend coupling constants are of order zero. That the bending persistence lengths that we obtain are generally somewhat higher than in experiment probably reflects both that the simulated origamis have no assembly defects and that the oxDNA extensional modulus for double-stranded DNA is too large.

Measuring Internal Forces in Single-Stranded DNA: Application to a DNA Force Clamp

We present a new method for calculating internal forces in DNA structures using coarse-grained models and demonstrate its utility with the oxDNA model. The instantaneous forces on individual nucleotides are explored and related to model potentials, and using our framework, internal forces are calculated for two simple DNA systems and for a recently published nanoscopic force clamp. Our results highlight some pitfalls associated with conventional methods for estimating internal forces, which are based on elastic polymer models, and emphasize the importance of carefully considering secondary structure and ionic conditions when modeling the elastic behavior of single-stranded DNA. Beyond its relevance to the DNA nanotechnological community, we expect our approach to be broadly applicable to calculations of internal force in a variety of structures-from DNA to protein-and across other coarse-grained simulation models.

Live-cell super-resolved PAINT imaging of piconewton cellular traction forces

Despite the vital role of mechanical forces in biology, it still remains a challenge to image cellular force with sub-100-nm resolution. Here, we present tension points accumulation for imaging in nanoscale topography (tPAINT), integrating molecular tension probes with the DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) technique to map piconewton mechanical events with ~25-nm resolution. To perform live-cell dynamic tension imaging, we engineered reversible probes with a cryptic docking site revealed only when the probe experiences forces exceeding a defined mechanical threshold (~7-21 pN). Additionally, we report a second type of irreversible tPAINT probe that exposes its cryptic docking site permanently and thus integrates force history over time, offering improved spatial resolution in exchange for temporal dynamics. We applied both types of tPAINT probes to map integrin receptor forces in live human platelets and mouse embryonic fibroblasts. Importantly, tPAINT revealed a link between platelet forces at the leading edge of cells and the dynamic actin-rich ring nucleated by the Arp2/3 complex.

Nonlinear Elastic and Inelastic Properties of Cells

Mechanical forces play an important role in various physiological processes, such as morphogenesis, cytokinesis, and migration. Thus, in order to illuminate mechanisms underlying these physiological processes, it is crucial to understand how cells deform and respond to external mechanical stimuli. During recent decades, the mechanical properties of cells have been studied extensively using diverse measurement techniques. A number of experimental studies have shown that cells are far from linear elastic materials. Cells exhibit a wide variety of nonlinear elastic and inelastic properties. Such complicated properties of cells are known to emerge from unique mechanical characteristics of cellular components. In this review, we introduce major cellular components that largely govern cell mechanical properties and provide brief explanations of several experimental techniques used for rheological measurements of cell mechanics. Then, we discuss the representative nonlinear elastic and inelastic properties of cells. Finally, continuum and discrete computational models of cell mechanics, which model both nonlinear elastic and inelastic properties of cells, will be described.

Periodically Ordered, Nuclease-Resistant DNA Nanowires Decorated with Cell-Specific Aptamers as Selective Theranostic Agents

DNA nanostructures have shown potential in cancer therapy. However, their clinical application is hampered by the difficulty to deliver them into cancer cells and susceptibility to nuclease degradation. To overcome these limitations, we report herein a periodically ordered nick-hidden DNA nanowire (NW) with high serum stability and active targeting functionality. The inner core is made of multiple connected DNA double helices, and the outer shell is composed of regularly arranged standing-up hairpin aptamers. All termini of the components are hidden from nuclease attack, whereas the target-binding sites are exposed to allow delivery to the cancer target. The DNA NW remained intact during incubation for 24 h in serum solution. Animal imaging and cell apoptosis showed that NWs loaded with an anticancer drug displayed long blood-circulation time and high specificity in inducing cancer-cell apoptosis, thus validating this approach for the targeted imaging and therapy of cancers.