A proximity-based programmable DNA nanoscale assembly line

Dynamic Gold Nanostructures Based on DNA Self Assembly

The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties. Benefiting from the vast design possibilities, complete addressability, and sub-10 nm resolution, DNA duplexes, tiles, single-stranded tiles and origami structures serve as excellent platforms for constructing diverse 3D reconfigurable plasmonic nanostructures with tailored optical properties. Leveraging the responsive nature of DNA interactions, the fabrication of dynamic assemblies of NG becomes readily achievable, and environmental stimulation can be harnessed as a driving force for the nanomotors. It is envisioned that intelligent DNA-assembled NG nanodevices will assume increasingly important roles in the realms of biological, biomedical, and nanomechanical studies, opening a new avenue toward exploration and innovation.

Autonomous assembly and disassembly of gliding molecular robots regulated by a DNA-based molecular controller

In recent years, there has been a growing interest in engineering dynamic and autonomous systems with robotic functionalities using biomolecules. Specifically, the ability of molecular motors to convert chemical energy to mechanical forces and the programmability of DNA are regarded as promising components for these systems. However, current systems rely on the manual addition of external stimuli, limiting the potential for autonomous molecular systems. Here, we show that DNA-based cascade reactions can act as a molecular controller that drives the autonomous assembly and disassembly of DNA-functionalized microtubules propelled by kinesins. The DNA controller is designed to produce two different DNA strands that program the interaction between the microtubules. The gliding microtubules integrated with the controller autonomously assemble to bundle-like structures and disassemble into discrete filaments without external stimuli, which is observable by fluorescence microscopy. We believe this approach to be a starting point toward more autonomous behavior of motor protein-based multicomponent systems with robotic functionalities.

Label-free detection of biomolecules using inductively coupled plasma mass spectrometry (ICP-MS)

Bioassays using inductively coupled plasma mass spectrometry (ICP-MS) have gained increasing attention because of the high sensitivity of ICP-MS and the various strategies of labeling biomolecules with detectable metal tags. The classic strategy to tag the target biomolecules is through direct antibody-antigen interaction and DNA hybridization, and requires the separation of the bound from the unbound tags. Label-free ICP-MS techniques for biomolecular assays do not require direct labeling: they generate detectable metal ions indirectly from specific biomolecular reactions, such as enzymatic cleavage. Here, we highlight the development of three main strategies of label-free ICP-MS assays for biomolecules: (1) enzymatic cleavage of metal-labeled substrates, (2) release of immobilized metal ions from the DNA backbone, and (3) nucleic acid amplification-assisted aggregation and release of metal tags to achieve amplified detection. We briefly describe the fundamental basis of these label-free ICP-MS assays and discuss the benefits and drawbacks of various designs. Future research is needed to reduce non-specific adsorption and minimize background and interference. Analytical innovations are also required to confront challenges faced by in vivo applications.

Molecular robotic agents that survey molecular landscapes for information retrieval

DNA-based artificial motors have allowed the recapitulation of biological functions and the creation of new features. Here, we present a molecular robotic system that surveys molecular environments and reports spatial information in an autonomous and repeated manner. A group of molecular agents, termed 'crawlers', roam around and copy information from DNA-labeled targets, generating records that reflect their trajectories. Based on a mechanism that allows random crawling, we show that our system is capable of counting the number of subunits in example molecular complexes. Our system can also detect multivalent proximities by generating concatenated records from multiple local interactions. We demonstrate this capability by distinguishing colocalization patterns of three proteins inside fixed cells under different conditions. These mechanisms for examining molecular landscapes may serve as a basis towards creating large-scale detailed molecular interaction maps inside the cell with nanoscale resolution.

Tetrahedral DNA-Based Functional MicroRNA-21 Delivery System: Application to Corneal Epithelial Wound Healing

Corneal injury occurs frequently which may lead to serious visual impairment. Rapid and efficient re-epithelialization after corneal epithelial injury is the key issue for maintaining corneal homeostasis. Among various treatment strategies, microRNA (miR)-based therapy shows great potential. However, structural limitations of miRNAs hinder its biomedical functionality. Nucleic acid nanotechnology is an appealing candidate for gene delivery because of its flexible modification and excellent biocompatibility. Herein, modified 3D tetrahedral framework nucleic acids (tFNAs) utilized as gene carriers for miR-21 delivery are constructed. TFNAs-miR-21 (T-21) shows great enzymatic resistance in extracellular environment and payload delivery into human corneal epithelial cells (HCECs) via clathrin-mediated endocytosis. T-21 facilitates proliferation and migration in HCECs via activating PI3K/AKT and ERK1/2 signaling pathways in vitro. In vivo studies, T-21 can be internalized by corneal epithelium in mice. In the mice corneal scratch model, T-21 ophthalmic solutions used as eye drops show no apparent side effects on the ocular surface histologically and exert great potential in accelerating corneal wound healing. These findings demonstrate that modified tFNAs are promising candidates for miRNA delivery for corneal wound healing. The convenient administration and great biocompatibility of tetrahedral DNA nanoparticles highlight its potential as gene transporter in solving ocular problems.

Collective Molecular Machines: Multidimensionality and Reconfigurability

Molecular machines are key to cellular activity where they are involved in converting chemical and light energy into efficient mechanical work. During the last 60 years, designing molecular structures capable of generating unidirectional mechanical motion at the nanoscale has been the topic of intense research. Effective progress has been made, attributed to advances in various fields such as supramolecular chemistry, biology and nanotechnology, and informatics. However, individual molecular machines are only capable of producing nanometer work and generally have only a single functionality. In order to address these problems, collective behaviors realized by integrating several or more of these individual mechanical units in space and time have become a new paradigm. In this review, we comprehensively discuss recent developments in the collective behaviors of molecular machines. In particular, collective behavior is divided into two paradigms. One is the appropriate integration of molecular machines to efficiently amplify molecular motions and deformations to construct novel functional materials. The other is the construction of swarming modes at the supramolecular level to perform nanoscale or microscale operations. We discuss design strategies for both modes and focus on the modulation of features and properties. Subsequently, in order to address existing challenges, the idea of transferring experience gained in the field of micro/nano robotics is presented, offering prospects for future developments in the collective behavior of molecular machines.

A DNA rotary nanodevice operated by enzyme-initiated strand resetting

DNA nanostructures that respond to external stimuli have found applications in several areas such as biosensing, drug delivery and molecular computation. The use of different types of stimuli in a single operation provides another layer of control for the reconfiguration of nucleic acid nanostructures. This work demonstrates the use of a ribonuclease to "unset" a nucleic acid nanodevice based on the paranemic crossover (PX) DNA and specific DNA inputs to "reset" the structure into a juxtaposed DNA (JX2) configuration, resulting in a 180° rotation of the helical domains. Such operations would be useful in translational applications where DNA nanostructures can be designed to reconfigure on the basis of more than one stimulus.

Toward three-dimensional DNA industrial nanorobots

Nanoscale industrial robots have potential as manufacturing platforms and are capable of automatically performing repetitive tasks to handle and produce nanomaterials with consistent precision and accuracy. We demonstrate a DNA industrial nanorobot that fabricates a three-dimensional (3D), optically active chiral structure from optically inactive parts. By making use of externally controlled temperature and ultraviolet (UV) light, our programmable robot, ~100 nanometers in size, grabs different parts, positions and aligns them so that they can be welded, releases the construct, and returns to its original configuration ready for its next operation. Our robot can also self-replicate its 3D structure and functions, surpassing single-step templating (restricted to two dimensions) by using folding to access the third dimension and more degrees of freedom. Our introduction of multiple-axis precise folding and positioning as a tool/technology for nanomanufacturing will open the door to more complex and useful nano- and microdevices.

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.

A geometric framework for reaction enumeration in computational nucleic acid devices

Cascades of DNA strand displacement reactions enable the design of potentially large circuits with complex behaviour. Computational modelling of such systems is desirable to enable rapid design and analysis. In previous work, the expressive power of graph theory was used to enumerate reactions implementing strand displacement across a wide range of complex structures. However, coping with the rich variety of possible graph-based structures required enumeration rules with complicated side-conditions. This paper presents an alternative approach to tackle the problem of enumerating reactions at domain level involving complex structures by integrating with a geometric constraint solving algorithm. The rule sets from previous work are simplified by replacing side-conditions with a general check on the geometric plausibility of structures generated by the enumeration algorithm. This produces a highly general geometric framework for reaction enumeration. Here, we instantiate this framework to solve geometric constraints by a structure sampling approach in which we randomly generate sets of coordinates and check whether they satisfy all the constraints. We demonstrate this system by applying it to examples from the literature where molecular geometry plays an important role, including DNA hairpin and remote toehold reactions. This work therefore enables integration of reaction enumeration and structural modelling.

Motility of Synthetic Cells from Engineered Lipids

Synthetic cells are artificial systems that resemble natural cells. Significant efforts have been made over the years to construct synthetic protocells that can mimic biological mechanisms and perform various complex processes. These include compartmentalization, metabolism, energy supply, communication, and gene reproduction. Cell motility is also of great importance, as nature uses elegant mechanisms for intracellular trafficking, immune response, and embryogenesis. In this review, we discuss the motility of synthetic cells made from lipid vesicles and relevant molecular mechanisms. Synthetic cell motion may be classified into surface-based or solution-based depending on whether it involves interactions with surfaces or movement in fluids. Collective migration behaviors have also been demonstrated. The swarm motion requires additional mechanisms for intercellular signaling and directional motility that enable communication and coordination among the synthetic vesicles. In addition, intracellular trafficking for molecular transport has been reconstituted in minimal cells with the help of DNA nanotechnology. These efforts demonstrate synthetic cells that can move, detect, respond, and interact. We envision that new developments in protocell motility will enhance our understanding of biological processes and be instrumental in bioengineering and therapeutic applications.

Engineering DNA-based cytoskeletons for synthetic cells

The development and bottom-up assembly of synthetic cells with a functional cytoskeleton sets a major milestone to understand cell mechanics and to develop man-made machines on the nano- and microscale. However, natural cytoskeletal components can be difficult to purify, deliberately engineer and reconstitute within synthetic cells which therefore limits the realization of multifaceted functions of modern cytoskeletons in synthetic cells. Here, we review recent progress in the development of synthetic cytoskeletons made from deoxyribonucleic acid (DNA) as a complementary strategy. In particular, we explore the capabilities and limitations of DNA cytoskeletons to mimic functions of natural cystoskeletons like reversible assembly, cargo transport, force generation, mechanical support and guided polymerization. With recent examples, we showcase the power of rationally designed DNA cytoskeletons for bottom-up assembled synthetic cells as fully engineerable entities. Nevertheless, the realization of dynamic instability, self-replication and genetic encoding as well as contractile force generating motors remains a fruitful challenge for the complete integration of multifunctional DNA-based cytoskeletons into synthetic cells.

Folding Double-Stranded DNA into Designed Shapes with Triplex-Forming Oligonucleotides

The compaction and organization of genomic DNA is a central mechanism in eukaryotic cells, but engineered architectural control over double-stranded DNA (dsDNA) is notably challenging. Here, long dsDNA templates are folded into designed shapes via triplex-mediated self-assembly. Triplex-forming oligonucleotides (TFOs) bind purines in dsDNA via normal or reverse Hoogsteen interactions. In the triplex origami methodology, these non-canonical interactions are programmed to compact dsDNA (linear or plasmid) into well-defined objects, which demonstrate a variety of structural features: hollow and raster-filled, single- and multi-layered, with custom curvatures and geometries, and featuring lattice-free, square-, or honeycomb-pleated internal arrangements. Surprisingly, the length of integrated and free-standing dsDNA loops can be modulated with near-perfect efficiency; from hundreds down to only six bp (2 nm). The inherent rigidity of dsDNA promotes structural robustness and non-periodic structures of almost 25.000 nt are therefore formed with fewer unique starting materials, compared to other DNA-based self-assembly methods. Densely triplexed structures also resist degradation by DNase I. Triplex-mediated dsDNA folding is methodologically straightforward and orthogonal to Watson-Crick-based methods. Moreover, it enables unprecedented spatial control over dsDNA templates.

Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics

Nanorobots powered by designed DNA molecular motors on DNA origami platforms are vigorously pursued but still short of fully autonomous and sustainable operation, as the reported systems rely on manually operated or autonomous but bridge-burning molecular motors. Expanding DNA nanorobotics requires origami-based autonomous non-bridge-burning motors, but such advanced artificial molecular motors are rare, and their integration with DNA origami remains a challenge. Here, we report an autonomous non-bridge-burning DNA motor tailor-designed for a triangle DNA origami substrate. This is a translational bipedal molecular motor but demonstrates effective translocation on both straight and curved segments of a self-closed circular track on the origami, including sharp ~90° turns by a single hand-over-hand step. The motor is highly directional and attains a record-high speed among the autonomous artificial molecular motors reported to date. The resultant DNA motor-origami system, with its complex translational-rotational motion and big nanorobotic capacity, potentially offers a self-contained "seed" nanorobotic platform to automate or scale up many applications.

Presketched DNA Origami Canvas for Polymerase-Driven DNA Kirigami

Reconfigurable DNA origami provides a versatile tool to manipulate the conformation of matter on the nanometer scale. Typically, the DNA kirigami method enables the transformation of an origami structure from an initial shape to another predesigned shape by reconfiguring the staple strands. In a regular origami structure, since the perfectly matched and densely packed DNA duplexes block the removal of staple strands, the construction of finely trimmed "sub-origami" structures by the DNA kirigami method has remained challenging. Herein, we proposed a strategy to construct the presketched DNA origami canvas, where the offcut area in the canvas was sketched by loosely fixed staple strands with single-base insertion, to enhance the fineness of polymerase-driven DNA kirigami. We successfully trimmed presketched two-dimensional rectangular canvas, three-dimensional Möbius strip, and genie bottle canvases into complex letter patterns, supercoiled rings, and nanorods, respectively. Finally, we demonstrated a size-controlled DNA kirigami system: a presketched 6HB origami was trimmed into a set of shorter nanowires with predefined lengths, which quantitatively characterized the fineness of the improved DNA kirigami. The presketched origami design was a general method that applied to both 2D and 3D DNA origami structures in square and honeycomb lattices. Loosening DNA origami structures by introducing single-base insertions provides a practical approach to constructing dynamic components when designing DNA nanomachines. Furthermore, the delicate trimming of the DNA origami canvas driven by polymerase may inspire strategies for graphical information encryption and storage.

Adsorbate motors for unidirectional translation and transport

Artificial molecular motors are designed to transform external energy into useful work in the form of unidirectional motion1. They have been studied mainly in solution2-4, but also on solid surfaces5,6, which provide fixed reference points, allowing for tracking of their movement. However, these molecules require sophisticated design and synthesis, because the motor function must be imprinted into the chemical structure, and show reduced functionality on surfaces compared with in solution5-8. DNA walkers9,10, on the other hand, impart high directionality as they include the surface as part of the motor function, but they require chemical surface patterning and sequential solvent modification for motor activation. Here we show how efficient motors can operate at much smaller length scales on a homogeneous metal surface without any liquid. This is realized by combining a surface with a simple molecule, which, by itself, does not contain any motor unit. The motion, which is tracked at the single-molecule level, is triggered by intramolecular proton transfer with a corresponding modulation of the potential energy surface. Each molecule moves with 100 percent unidirectionality along an atomically defined straight line. Proof of the motor performing meaningful work is shown by controlled transport of single carbon monoxide molecules. This simplistic concept could form the basis for the controlled bottom-up assembly of nanostructures at the atomic scale.

Environmentally Controlled Oscillator with Triplex Guided Displacement of DNA Duplexes

The use of DNA triplex association is advantageous for the reconfiguration of dynamic DNA nanostructures through pH alteration and can provide environmental control for both structural changes and molecular signaling. The combination of pH-induced triplex-forming oligonucleotide (TFOs) binding with toehold-mediated strand displacement has recently garnered significant attention in the field of structural DNA nanotechnology. While most previous studies use single-stranded DNA to displace or replace TFOs within the triplex, here we demonstrate that pH alteration allows a DNA duplex, with a toehold assistance, to displace TFOs from the components of another DNA duplex. We examined the dependence of this process on toehold length and show that the pH changes allow for cyclic oscillations between two molecular formations. We implemented the duplex/triplex design onto the surface of 2D DNA origami in the form outlining binary digits 0 or 1 and verified the oscillatory conformational changes between the two formations with atomic force microscopy.

Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection

Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.

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.

A light-operated integrated DNA walker-origami system beyond bridge burning

Integrating rationally designed DNA molecular walkers and DNA origami platforms is a promising route towards advanced nano-robotics of diverse functions. Unleashing the full potential in this direction requires DNA walker-origami systems beyond the present simplistic bridge-burning designs for automated repeatable operation and scalable nano-robotic functions. Here we report such a DNA walker-origami system integrating an advanced light-powered DNA bipedal walker and a ∼170 nm-long rod-like DNA origami platform. This light-powered walker is fully qualified as a genuine translational molecular motor, and relies entirely on pure mechanical effects that are complicated by the origami surface but must be preserved for the walker's proper operation. This is made possible by tailor-designing the origami for optimal match with the walker to best preserve its core mechanics. A new fluorescence method is combined with site-controlled motility experiments to yield distinct and reliable signals for the walker's self-directed and processive motion despite origami-complicated fluorophore emission. The resultant integrated DNA walker-origami system provides a 'seed' system for future development of advanced light-powered DNA nano-robots (e.g., for scalable walker-automated chemical synthesis), and also truly bio-mimicking nano-muscles powered by genuine artificial translational molecular motors.

Multi-Reconfigurable DNA Origami Nanolattice Driven by the Combination of Orthogonal Signals

The progress of the scaffolded DNA origami technology has enabled the construction of various dynamic nanodevices imitating the shapes and motions of mechanical elements. To further expand the achievable configurational changes, the incorporation of multiple movable joints into a single DNA origami structure and their precise control are desired. Here, we propose a multi-reconfigurable 3 × 3 lattice structure consisting of nine frames with rigid four-helix struts connected with flexible 10-nucleotide joints. The configuration of each frame is determined by the arbitrarily selected orthogonal pair of signal DNAs, resulting in the transformation of the lattice into various shapes. We also demonstrated sequential reconfiguration of the nanolattice and its assemblies from one into another via an isothermal strand displacement reaction at physiological temperatures. Our modular and scalable design approach could serve as a versatile platform for a variety of applications that require reversible and continuous shape control with nanoscale precision.

Mobile Molecules: Reactivity Profiling Guides Faster Movement on a Cysteine Track

We previously reported a molecular hopper, which makes sub-nanometer steps by thiol-disulfide interchange along a track with cysteine footholds within a protein nanopore. Here we optimize the hopping rate (ca. 0.1 s-1 in the previous work) with a view towards rapid enzymeless biopolymer characterization during translocation within nanopores. We first took a single-molecule approach to obtain the reactivity profiles of individual footholds. The pK a values of cysteine thiols within a pore ranged from 9.17 to 9.85, and the pH-independent rate constants of the thiolates with a small-molecule disulfide varied by up to 20-fold. Through site-specific mutagenesis and a pH increase from 8.5 to 9.5, the overall hopping rate of a DNA cargo along a five-cysteine track was accelerated 4-fold, and the rate-limiting step 21-fold.

Mobile Molecules: Reactivity Profiling Guides Faster Movement on a Cysteine Track

We previously reported a molecular hopper, which makes sub-nanometer steps by thiol-disulfide interchange along a track with cysteine footholds within a protein nanopore. Here we optimize the hopping rate (ca. 0.1 s-1 in the previous work) with a view towards rapid enzymeless biopolymer characterization during translocation within nanopores. We first took a single-molecule approach to obtain the reactivity profiles of individual footholds. The pKa values of cysteine thiols within a pore ranged from 9.17 to 9.85, and the pH-independent rate constants of the thiolates with a small-molecule disulfide varied by up to 20-fold. Through site-specific mutagenesis and a pH increase from 8.5 to 9.5, the overall hopping rate of a DNA cargo along a five-cysteine track was accelerated 4-fold, and the rate-limiting step 21-fold.

Steric Communication between Dynamic Components on DNA Nanodevices

Biomolecular nanotechnology has helped emulate basic robotic capabilities such as defined motion, sensing, and actuation in synthetic nanoscale systems. DNA origami is an attractive approach for nanorobotics, as it enables creation of devices with complex geometry, programmed motion, rapid actuation, force application, and various kinds of sensing modalities. Advanced robotic functions like feedback control, autonomy, or programmed routines also require the ability to transmit signals among subcomponents. Prior work in DNA nanotechnology has established approaches for signal transmission, for example through diffusing strands or structurally coupled motions. However, soluble communication is often slow and structural coupling of motions can limit the function of individual components, for example to respond to the environment. Here, we introduce an approach inspired by protein allostery to transmit signals between two distal dynamic components through steric interactions. These components undergo separate thermal fluctuations where certain conformations of one arm will sterically occlude conformations of the distal arm. We implement this approach in a DNA origami device consisting of two stiff arms each connected to a base platform via a flexible hinge joint. We demonstrate the ability for one arm to sterically regulate both the range of motion and the conformational state (latched or freely fluctuating) of the distal arm, results that are quantitatively captured by mesoscopic simulations using experimentally informed energy landscapes for hinge-angle fluctuations. We further demonstrate the ability to modulate signal transmission by mechanically tuning the range of thermal fluctuations and controlling the conformational states of the arms. Our results establish a communication mechanism well-suited to transmit signals between thermally fluctuating dynamic components and provide a path to transmitting signals where the input is a dynamic response to parameters like force or solution conditions.

Modular reconfiguration of DNA origami assemblies using tile displacement

The power of natural evolution lies in the adaptability of biological organisms but is constrained by the time scale of genetics and reproduction. Engineeringartificial molecular machines should not only include adaptability as a core feature but also apply it within a larger design space and at a faster time scale. A lesson from engineering electromechanical robots is that modular robots can perform diverse functions through self-reconfiguration, a large-scale form of adaptation. Molecular machines made of modular, reconfigurable components may form the basis for dynamic self-reprogramming in future synthetic cells. To achieve modular reconfiguration in DNA origami assemblies, we previously developed a tile displacement mechanism in which an invader tile replaces another tile in an array with controlled kinetics. Here, we establish design principles for simultaneous reconfigurations in tile assemblies using complex invaders with distinct shapes. We present toehold and branch migration domain configurations that expand the design space of tile displacement reactions by two orders of magnitude. We demonstrate the construction of multitile invaders with fixed and variable sizes and controlled size distributions. We investigate the growth of three-dimensional (3D) barrel structures with variable cross sections and introduce a mechanism for reconfiguring them into 2D structures. Last, we show an example of a sword-shaped assembly transforming into a snake-shaped assembly, illustrating two independent tile displacement reactions occurring concurrently with minimum cross-talk. This work serves as a proof of concept that tile displacement could be a fundamental mechanism for modular reconfiguration robust to temperature and tile concentration.

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.

Immunomodulation with Nucleic Acid Nanodevices

The precise regulation of interactions of specific immunological components is crucial for controllable immunomodulation, yet it remains a great challenge. With the assistance of advanced computer design, programmable nucleic acid nanotechnology enables the customization of synthetic nucleic acid nanodevices with unprecedented geometrical and functional precision, which have shown promising potential for precise immunoengineering. Notably, the inherently immunologic functions of nucleic acids endow these nucleic acid-based assemblies with innate advantages in immunomodulatory engagement. In this review, the roles of nucleic acids in innate immunity are discussed, focusing on the definition, immunologic modularity, and enhanced bioavailability of structural nucleic acid nanodevices. In light of this, molecular programming and precise organization of functional modules with nucleic acid nanodevices for immunomodulation are emphatically reviewed. At last, the present challenges and future perspectives of nucleic acid nanodevices for immunomodulation are discussed.

Research Progress in Construction and Application of Enzyme-Based DNA Logic Gates

As a research hotspot in the field of information processing, DNA computing exhibits several important underlying characteristics-from parallel computing and low energy consumption to high-performance storage capabilities-thereby enabling its wide application in nanomachines, molecular encryption, biological detection, medical diagnosis, etc. Based on DNA computing, the most rapidly developed field focuses on DNA molecular logic-gates computing. In particular, the recent advances in enzyme-based DNA logic gates has emerged as ideal materials for constructing DNA logic gates. In this review, we explore protein enzymes that can manipulate DNA, especially, nicking enzymes and polymerases with high efficiency and specificity, which are widely used in constructing DNA logic gates, as well as ribozyme that can construct DNA logic gates following various mechanism with distinct biomaterials. Accordingly, the review highlights the characteristics and applications of various types of DNAzyme-based logic gates models, considering their future developments in information, biomedicine, chemistry, and computers.

Prime factorization via localized tile assembly in a DNA origami framework

Modern cybersecurity built on public-key cryptosystems like Rivest-Shamir-Adleman is compromised upon finding solutions to the prime factorization. Nevertheless, solving the prime factorization problem, given a large N, remains computationally challenging. Here, we design DNA origami frameworks (DOFs) to direct localized assembly of double-crossover (DX) tiles for solving prime factorization with a model consisting of the computing, decision-making, and reporting motifs. The model implementation is based on the sequential assembly of different DX tiles in the DOF cavity that carries overhangs encoding the prime and composite integers. The primes are multiplied and then verified with the composite, and the result is visualized under atomic force microscopy via the presence (success) or absence (failure) of biotin-streptavidin labels on the reporting DX tile. The factorization of semiprimes 6 and 15 is realized with this DOF-based demonstration. Given the potential of massively parallel processing ability of DNA, this strategy opens an avenue to solve complex mathematical puzzles like prime factoring with molecular computing.

Controllable dynamics of complex DNA nanostructures

In the past four decades, a variety of self-assembly design frameworks have led to the construction of versatile DNA nanostructures with increasing complexity and controllability. The controllable dynamics of DNA nanostructures has garnered much interest and emerged as a powerful tool for conducting sophisticated tasks at the molecular level. In this minireview, we summarized the controllable reconfigurations of complex DNA nanostructures induced by nucleic acid strands, environmental stimuli and enzymatic treatments. We also envisioned that with the optimization of response time, sensitivity and specificity, dynamic DNA nanostructures have great promise in applications ranging from nanorobotics to life sciences.

An RNA Paranemic Crossover Triangle as A 3D Module for Cotranscriptional Nanoassembly

RNA nanotechnology takes advantage of structural modularity to build self-assembling nano-architectures with applications in medicine and synthetic biology. The use of paranemic motifs, that form without unfolding existing secondary structure, allows for the creation of RNA nanostructures that are compatible with cotranscriptional folding in vitro and in vivo. In previous work, kissing-loop (KL) motifs have been widely used to design RNA nanostructures that fold cotranscriptionally. However, the paranemic crossover (PX) motif has not yet been explored for cotranscriptional RNA origami architectures and information about the structural geometry of the motif is unknown. Here, a six base pair-wide paranemic RNA interaction that arranges double helices in a perpendicular manner is introduced, allowing for the generation of a new and versatile building block: the paranemic-crossover triangle (PXT). The PXT is self-assembled by cotranscriptional folding and characterized by cryogenic electron microscopy, revealing for the first time an RNA PX interaction in high structural detail. The PXT is used as a building block for the construction of multimers that form filaments and rings and a duplicated PXT motif is used as a building block to self-assemble cubic structures, demonstrating the PXT as a rigid self-folding domain for the development of wireframe RNA origami architectures.

DNA double helix, a tiny electromotor

Flowing fluid past chiral objects has been used for centuries to power rotary motion in man-made machines. By contrast, rotary motion in nanoscale biological or chemical systems is produced by biasing Brownian motion through cyclic chemical reactions. Here we show that a chiral biological molecule, a DNA or RNA duplex rotates unidirectionally at billions of revolutions per minute when an electric field is applied along the duplex, with the rotation direction being determined by the chirality of the duplex. The rotation is found to be powered by the drag force of the electro-osmotic flow, realizing the operating principle of a macroscopic turbine at the nanoscale. The resulting torques are sufficient to power rotation of nanoscale beads and rods, offering an engineering principle for constructing nanoscale systems powered by electric field.

Multiscale Biofabrication: Integrating Additive Manufacturing with DNA-Programmable Self-Assembly

Structure and hierarchical organization are crucial elements of biological systems and are likely required when engineering synthetic biomaterials with life-like behavior. In this context, additive manufacturing techniques like bioprinting have become increasingly popular. However, 3D bioprinting, as well as other additive manufacturing techniques, show limited resolution, making it difficult to yield structures on the sub-cellular level. To be able to form macroscopic synthetic biological objects with structuring on this level, manufacturing techniques have to be used in conjunction with biomolecular nanotechnology. Here, a short overview of both topics and a survey of recent advances to combine additive manufacturing with microfabrication techniques and bottom-up self-assembly involving DNA, are given.

Transformable Plasmonic Helix with Swinging Gold Nanoparticles

Control over multiple optical elements that can be dynamically rearranged to yield substantial three-dimensional structural transformations is of great importance to realize reconfigurable plasmonic nanoarchitectures with sensitive and distinct optical feedback. In this work, we demonstrate a transformable plasmonic helix system, in which multiple gold nanoparticles (AuNPs) can be directly transported by DNA swingarms to target positions without undergoing consecutive stepwise movements. The swingarms allow for programmable AuNP translocations in large leaps within plasmonic nanoarchitectures, giving rise to tailored circular dichroism spectra. Our work provides an instructive bottom-up solution to building complex dynamic plasmonic systems, which can exhibit prominent optical responses through cooperative rearrangements of the constituent optical elements with high fidelity and programmability.

Endogenous Enzyme-Operated Spherical Nucleic Acids for Cell-Selective Protein Capture and Localization Regulation

Precise regulation of protein activity and localization in cancer cells is crucial to dissect the function of the protein-involved cellular network in tumorigenesis, but there is a lack of suitable methodology. Here we report the design of enzyme-operated spherical nucleic acids (E-SNAs) for manipulation of the nucleocytoplasmic translocation of proteins with cancer-cell selectivity. The E-SNAs are constructed by programmable engineering of aptamer-based modules bearing enzyme-responsive units in predesigned sites and further combination with SNA nanotechnology. We demonstrate that E-SNAs are able to regulate cytoplasmic-to-nuclear shuttling of RelA protein efficiently and specifically in tumor cells, while they remain inactive in normal cells due to insufficient enzyme expression. We further confirmed the generality of this strategy by investigating the enzyme-modulated inhibition/activation of thrombin activity by varying the aptamer-based design.

Controlled Assembly of Fluorophores inside a Nanoliposome

Cellular compartmentalization plays an essential role in organizing the complex and multiple biochemical reactions in the cell. An artificial compartment would provide powerful strategies to develop new biochemical tools for material production and diagnosis, but it is still a great challenge to synthesize the compartments that encapsulate materials of interest while controlling their accurate locations, numbers, and stoichiometry. In this study, we evaluated chemical characteristics of a liposome-encapsulated compartment, which has great potential to locate various materials of interest with precise control of their locations and numbers in the compartment. A nanoliposome was constructed inside a ring-shaped DNA origami skeleton according to the method of Yang et al., and further equipped with a double-stranded DNA platform to assemble molecules of interest in the nanoliposome. Upon formation of the nanoliposome, a pH-sensitive fluorophore on the bridged platform showed little or no response to the pH change of the outer buffer, ensuring that the molecules assembled on the platform are effectively shielded from the outer environment. The ring-shaped DNA skeleton equipped with a double-stranded DNA platform allows spatial assembly of several functional molecules inside the nanoliposome to isolate them from the outer environment.

Nucleic acid-based artificial nanocarriers for gene therapy

Nucleic acid nanotechnology is a powerful tool in the fields of biosensing and nanomedicine owing to their high editability and easy synthesis and modification. Artificial nucleic acid nanostructures have become an emerging research hotspot as gene carriers with low cytotoxicity and immunogenicity for therapeutic approaches. In this review, recent progress in the design and functional mechanisms of nucleic acid-based artificial nano-vectors especially for exogenous siRNA and antisense oligonucleotide delivery is summarized. Different types of DNA nanocarriers, including DNA junctions, tetrahedrons, origami, hydrogels and scaffolds, are introduced. The enhanced targeting strategies to improve the delivery efficacy are demonstrated. Furthermore, RNA based gene nanocarrier systems by self-assembly of short strands, rolling circle transcription, chemical crosslinking and using RNA motifs and DNA-RNA hybrids are demonstrated. Finally, the outlook and potential challenges are highlighted. The nucleic acid-based artificial nanocarriers offer a promising and precise tool for gene delivery and therapy.

Electrical Actuation of DNA-Based Nanomechanical Systems

DNA nanotechnology provides efficient methods for the sequence-programmable construction of mechanical devices with nanoscale dimensions. The resulting nanomachines could serve as tools for the manipulation of macromolecules with similar functionalities as mechanical tools and machinery in the macroscopic world. In order to drive and control these machines and to perform specific tasks, a fast, reliable, and repeatable actuation mechanism is required that can work against external loads. Here we describe a highly effective method for actuating DNA structures using externally applied electric fields. To this end, electric fields are generated with controllable direction and amplitude inside a miniature electrophoresis device integrated with an epifluorescence microscope. With this setup, DNA-based nanoelectromechanical devices can be precisely controlled. As an example, we demonstrate how a DNA-based nanorobotic system can be used to dynamically position molecules on a molecular platform with high speeds and accuracy. The microscopy setup also described here allows simultaneous monitoring of a large number of nanorobotic arms in real time and at the single nanomachine level.

Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking

Biomolecular nanomechanical devices are of great interest as tools for the processing and manipulation of molecules, thereby mimicking the function of nature's enzymes. DNA nanotechnology provides the capability to build molecular analogs of mechanical machine elements such as joints and hinges via sequence-programmable self-assembly, which are otherwise known from traditional mechanical engineering. Relative to their size, these molecular machine elements typically do not reach the same relative precision and reproducibility that we know from their macroscopic counterparts; however, as they are scaled down to molecular sizes, physical effects typically not considered by mechanical engineers such as Brownian motion, intramolecular forces, and the molecular roughness of the devices begin to dominate their behavior. In order to investigate the effect of different design choices on the roughness of the mechanical energy landscapes of DNA nanodevices in greater detail, we here study an exemplary DNA origami-based structure, a modularly designed rotor-stator arrangement, which resembles a rotatable nanorobotic arm. Using fluorescence tracking microscopy, we follow the motion of individual rotors and record their corresponding energy landscapes. We then utilize the modular construction of the device to exchange its constituent parts individually and systematically test the effect of different design variants on the movement patterns. This allows us to identify the design parameters that most strongly affect the shape of the energy landscapes of the systems. Taking into account these insights, we are able to create devices with significantly flatter energy landscapes, which translates to mechanical nanodevices with improved performance and behaviors more closely resembling those of their macroscopic counterparts.

Tomography of DNA tiles influences the kinetics of surface-mediated DNA self-assembly

This manuscript studies the impact of extruding hairpins on two-dimensional self-assembly of DNA tiles on solid surface. Hairpins are commonly used as tomographic markers in DNA nanostructures for atomic force microscopy imaging. In this study, we have discovered that hairpins play a more active role. They modulate the adsorption of the DNA tiles onto the solid surface, thus changing the tile assembly kinetics on the solid surface. Based on this discovery, we were able to promote or slow down DNA self-assembly on the surface by changing the hairpin locations on the DNA tiles. This knowledge gained will be helpful for the future design of DNA self-assembly on surface.

DNA-Based Molecular Machines

Artificial molecular machines have found widespread applications ranging from fundamental studies to biomedicine. More recent advances in exploiting unique physical and chemical properties of DNA have led to the development of DNA-based artificial molecular machines. The unprecedented programmability of DNA provides a powerful means to design complex and sophisticated DNA-based molecular machines that can exert mechanical force or motion to realize complex tasks in a controllable, modular fashion. This Perspective highlights the potential and strategies to construct artificial molecular machines using double-stranded DNA, functional nucleic acids, and DNA frameworks, which enable improved control over reaction pathways and motion behaviors. We also outline the challenges and opportunities of using DNA-based molecular machines for biophysics, biosensing, and biocomputing.

Development of the Right- and Left-Handed Gamma Peptide Nucleic Acid Building Blocks for On-Resin Chemical Functionalization

Gamma peptide nucleic acids (PNAs) are a promising class of nucleic acid mimics that adopt either a right- or left-handed helical motif as individual strands and hybridize to DNA or RNA with high affinity and sequence specificity, or not at all, depending on the helical sense. They are attractive as antisense and antigene reagents, as well as building blocks for molecular self-assembly; however, they have not been widely adopted due to their relatively poor biophysical attributes and the challenge in chemical modifications. Here, we report the development of a set of universal monomers, four each for both the right- and left-handed conformers, that permit rapid and selective on-resin chemical functionalization and diversification. The system is modular, permitting incorporation of different chemical groups in the backbone without causing adverse effects on hybridization. The approach overcomes the need to prepare a new set of monomers each time a different chemical group is introduced in the backbone. The newly added synthetic flexibility, along with superior hybridization property, recognition orthogonality, and helical sense translational capability, significantly expands the scope of gamma PNA in biology, biotechnology, and molecular engineering.

Engineering DNA-based synthetic condensates with programmable material properties, compositions, and functionalities

Biomolecular condensates participate in diverse cellular processes, ranging from gene regulation to stress survival. Bottom-up engineering of synthetic condensates advances our understanding of the organizing principle of condensates. It also enables the synthesis of artificial systems with novel functions. However, building synthetic condensates with a predictable organization and function remains challenging. Here, we use DNA as a building block to create synthetic condensates that are assembled through phase separation. The programmability of intermolecular interactions between DNA molecules enables the control over various condensate properties including assembly, composition, and function. Similar to the way intracellular condensates are organized, DNA clients are selectively partitioned into cognate condensates. We demonstrate that the synthetic condensates can accelerate DNA strand displacement reactions and logic gate operation by concentrating specific reaction components. We envision that the DNA-based condensates could help the realization of the high-order functions required to build more life-like artificial systems.

Applications of Functional DNA Materials in Immunomodulatory Therapy

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

DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications

Recent advances in DNA technology have made it possible to combine with the plasmonics to fabricate reconfigurable dynamic nanodevices with extraordinary property and function. These DNA-mediated plasmonic nanostructures have been investigated for a variety of unique and beneficial physicochemical properties and their dynamic behavior has been controlled by endogenous or exogenous stimuli for a variety of interesting biological applications. In this perspective, the recent efforts to use the DNA nanostructures as molecular linkers for fabricating dynamic plasmonic nanostructures are reviewed. Next, the actuation media for triggering the dynamic behavior of plasmonic nanostructures and the dynamic response in optical features are summarized. Finally, the applications, remaining challenges and perspectives of the DNA-mediated dynamic plasmonic nanostructures are discussed.

Adhesive Dynamics Simulations of Highly Polyvalent DNA Motors

Molecular motors, such as myosin and kinesin, perform diverse tasks ranging from vesical transport to bulk muscle contraction. Synthetic molecular motors may eventually be harnessed to perform similar tasks in versatile synthetic systems. The most promising type of synthetic molecular motor, the DNA walker, can undergo processive motion but generally exhibits low speeds and virtually no capacity for force generation. However, we recently showed that highly polyvalent DNA motors (HPDMs) can rival biological motors by translocating at micrometer per minute speeds and generating 100+ pN of force. Accordingly, DNA nanotechnology-based designs may hold promise for the creation of synthetic, force-generating nanomotors. However, the dependencies of HPDM speed and force on tunable design parameters are poorly understood and difficult to characterize experimentally. To overcome this challenge, we present RoloSim, an adhesive dynamics software package for fine-grained simulations of HPDM translocation. RoloSim uses biophysical models for DNA duplex formation and dissociation kinetics to explicitly model tens of thousands of molecular scale interactions. These molecular interactions are then used to calculate the nano- and microscale motions of the motor. We use RoloSim to uncover how motor force and speed scale with several tunable motor properties such as motor size and DNA duplex length. Our results support our previously defined hypothesis that force scales linearly with polyvalency. We also demonstrate that HPDMs can be steered with external force, and we provide design parameters for novel HPDM-based molecular sensor and nanomachine designs.

Nucleic acid paranemic structures: a promising building block for functional nanomaterials in biomedical and bionanotechnological applications

Over the past few decades, DNA has been recognized as a powerful self-assembling material capable of crafting supramolecular nanoarchitectures with quasi-angstrom precision, which promises various applications in the fields of materials science, nanoengineering, and biomedical science. Notable structural features include biocompatibility, biodegradability, high digital encodability by Watson-Crick base pairing, nanoscale dimension, and surface addressability. Bottom-up fabrication of complex DNA nanostructures relies on the design of fundamental DNA motifs, including parallel (PX) and antiparallel (AX) crossovers. However, paranemic or PX motifs have not been thoroughly explored for the construction of DNA-based nanostructures compared to AX motifs. In this review, we summarize the developments of PX-based DNA nanostructures, highlight the advantages as well as challenges of PX-based assemblies, and give an overview of the structural and chemical features that lend their utilization in a variety of applications. The works presented cover PX-based DNA nanostructures in biological systems, dynamic systems, and biomedical contexts. The possible future advances of PX structures and applications are also summarized, discussed, and postulated.