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

Unidirectional molecular rotary motor with remotely switchable rotation direction

Light-driven rotary motors allow direct transformation of light energy into rotary motion at the nanoscale, giving rise to countless emerging applications in molecular engineering. The key feature enabling the unidirectional rotation and controlling its direction is the motor chirality, a factor hard to modify postsynthetically. Here, we propose a motor architecture, E-motor, whose operation direction can be switched remotely with an electric field pulse, without the need for chemical intervention. Our study relies on quantum chemical calculations and nonadiabatic molecular dynamics simulations performed for a specifically tailored system, PFCN, designed to provide illustration for the proposed motor type. We show that the PFCN chirality depends on the orientation of a covalently bound polar switching unit, which can be controlled with the electric field. At the same time, the proposed system manifests all characteristic photophysical properties of a molecular motor, and its set chirality is preserved during operation in the absence of the field.

Diverse applications of DNA origami as a cross-disciplinary tool

As knowledge from a single discipline is no longer sufficient to keep pace with the growing complexity of technological advancements, interdisciplinary collaboration has become a crucial driver of innovation. DNA nanotechnology exemplifies this integration, serving as a field where cross-disciplinary communication is particularly prominent. Since its introduction by Rothemund in 2006, DNA origami has proved to be a powerful tool for interdisciplinary research, offering exceptional structural stability, programmability, and addressability. This review provides an overview of the development of DNA origami technology, highlights its major advances, and explores its innovative applications across various disciplines in recent years, showcasing its vast potential and future prospects. We believe DNA origami is poised for even broader applications, driving progress across multiple fields.

Structural Influence of the Chemical Fueling System on a Catalysis-Driven Rotary Molecular Motor

Continuous directionally biased 360° rotation about a covalent single bond was recently realized in the form of a chemically fueled 1-phenylpyrrole 2,2'-dicarboxylic acid rotary molecular motor. However, the original fueling system and reaction conditions resulted in a motor directionality of only ∼3:1 (i.e., on average a backward rotation for every three forward rotations), along with a catalytic efficiency for the motor operation of 97% and a fuel efficiency of 14%. Here, we report on the efficacy of a series of chiral carbodiimide fuels and chiral hydrolysis promoters (pyridine and pyridine N-oxide derivatives) in driving improved directional rotation of this motor-molecule. We outline the complete reaction network for motor operation, composed of directional, futile, and slip cycles. Using derivatives of the motor where the final conformational step in the 360° rotation is either very slow or completely blocked, the phenylpyrrole diacid becomes enantiomerically enriched, allowing the kinetic gating of the individual steps in the catalytic cycle to be measured. The chiral carbodiimide fuel that produces the highest directionality gives 13% enantiomeric excess (e.e.) for the anhydride-forming kinetically gated step, while the most effective chiral hydrolysis promoter generates 90% e.e. for the kinetically gated hydrolysis step. Combining the best-performing fuel and hydrolysis promoter into a single fueling system results in a 92% e.e.. Under a dilute chemostated fueling regime (to avoid N-acyl urea formation at high carbodiimide concentrations with pyridine N-oxide hydrolysis promoters), the motor continuously rotates with a directionality of ∼24:1 (i.e., a backward rotation for every 24 forward rotations) with a catalytic efficiency of >99% and a fuel efficiency of 51%.

Spatially Preorganized Hybridization Chain Reaction for the Prompt Diagnosis of Inflammation

Biological systems utilize precise spatial organization to facilitate and regulate information transmission within signaling networks. Inspired by this, artificial scaffolds that enable delicate spatial arrangements are desirable to increase the local concentration of reactants, expedite specific interactions, and minimize undesired interference. In this study, we presented an integrated biosensing nanodevice, termed TRI-HCR, in which hybridization chain reaction (HCR) probes were precisely organized on a triangular DNA origami nanostructure (TRI) with finely-tuned distance, quantity, and pattern. Compared to traditional HCR in the free form, this nanodevice demonstrated increased reaction rate and signal level. We further employed the optimized TRI-HCR for in vivo imaging of a nucleic acid biomarker of inflammatory diseases. In both acute gouty arthritis (AGA) and sepsis-associated acute kidney injury (SA-AKI) model mice, TRI-HCR was capable of diagnosing inflammation in the early stages, significantly earlier than histological examination. We anticipate that this precise spatial preorganization strategy for HCR holds promise for broader applications in early disease detection and monitoring.

Multipedal DNA Walker: Engineering Strategy, Biosensing Application and Future Perspectives

With the continuous development of DNA nanotechnology, DNA walkers have attracted increased attention because of their autonomous and progressive walking along predesigned tracks. Compared with the traditional DNA walkers, the emerged multipedal DNA walkers showed their special charm with sustainable walking capability, higher reaction efficiency, expanded walking region, and improved amplification capability. Consequently, multipedal DNA walkers have developed rapidly and shown potential in biosensing applications. Hence, in this review, we make a comprehensive representation of the engineering strategy of multipedal DNA walkers, which focused on the design of multiple walking strands as well as the construction of tracks and driving forces. Meanwhile, the application of multipedal DNA walkers in biosensors has been thoroughly described according to the type of biosensing signal readout. By illustrating some representative works, we also summarized the merits and challenges of multipedal DNA walker-based biosensors and offered a deep discussion of the latest progress and future.

A Light-Powered Single-Stranded DNA Molecular Motor with Colour-Selective Single-Step Control

Top-down control of small motion is possible through top-down controlled molecular motors in replacement of larger actuators like MEMS or NEMS (micro- or nano-electromechanical systems) in the current precision technology. Improving top-down control of molecular motors to every single step is desirable for this purpose, and also for synchronization of motor actions for amplified effects. Here we report a designed single-stranded DNA molecular motor powered by alternated ultraviolet and visible light for processive track-walking, with the two light colours each locking the motor in a full directional step to allow saturated driving but no overstepping. This novel nano-optomechanical driving mechanism pushes the top-down control of molecular motors down to every single step, thus providing a key technical capability to advance the molecular motor-based precision technology and also motor synchronization for amplified effects.

Programmably engineered stochastic RNA nanowalker for ultrasensitive miRNA detection

A programmably engineered stochastic RNA nanowalker powered by duplex-specific nuclease (DSN) is developed. By utilizing poly-adenine-based spherical nucleic acids (polyA-SNA) to accurately regulate the densities of DNA tracks, the nanowalker showcases its capability to identify miRNA-21, miRNA-486, and miRNA-155 with quick kinetics and attomolar sensitivity, positioning it as a promising option for cancer clinical surveillance.

Mechanomaterials and Nanomechanics: Toward Proactive Design of Material Properties and Functionalities

While conventional mechanics of materials offers a passive understanding of the mechanical properties of materials in existing forms, a paradigm shift, referred to as mechanomaterials, is emerging to enable the proactive programming of materials' properties and functionalities by leveraging force-geometry-property relationships. One of the foundations of this new paradigm is nanomechanics, which permits functional and structural materials to be designed based on principles from the nanoscale and beyond. Although the field of mechanomaterials is still in its infancy at the present time, we discuss the current progress in three specific directions closely linked to nanomechanics and provide perspectives on these research foci by considering the potential research directions, chances for success, and existing research capabilities. We believe this new research paradigm will provide future materials solutions for infrastructure, healthcare, energy, and environment.

AI-enhanced biomedical micro/nanorobots in microfluidics

Human beings encompass sophisticated microcirculation and microenvironments, incorporating a broad spectrum of microfluidic systems that adopt fundamental roles in orchestrating physiological mechanisms. In vitro recapitulation of human microenvironments based on lab-on-a-chip technology represents a critical paradigm to better understand the intricate mechanisms. Moreover, the advent of micro/nanorobotics provides brand new perspectives and dynamic tools for elucidating the complex process in microfluidics. Currently, artificial intelligence (AI) has endowed micro/nanorobots (MNRs) with unprecedented benefits, such as material synthesis, optimal design, fabrication, and swarm behavior. Using advanced AI algorithms, the motion control, environment perception, and swarm intelligence of MNRs in microfluidics are significantly enhanced. This emerging interdisciplinary research trend holds great potential to propel biomedical research to the forefront and make valuable contributions to human health. Herein, we initially introduce the AI algorithms integral to the development of MNRs. We briefly revisit the components, designs, and fabrication techniques adopted by robots in microfluidics with an emphasis on the application of AI. Then, we review the latest research pertinent to AI-enhanced MNRs, focusing on their motion control, sensing abilities, and intricate collective behavior in microfluidics. Furthermore, we spotlight biomedical domains that are already witnessing or will undergo game-changing evolution based on AI-enhanced MNRs. Finally, we identify the current challenges that hinder the practical use of the pioneering interdisciplinary technology.

Programmable Primer Switching for Regulating Enzymatic DNA Circuits

Developing DNA strand displacement reactions (SDRs) offers crucial technical support for regulating artificial nucleic acid circuits and networks. More recently, enzymatic SDR-based DNA circuits have gained significant attention because of their modular design, high orthogonality signaling, and extremely fast reaction rates. Typical enzymatic SDRs are regulated by relatively long primers (20-30 nucleotides) that hybridize to form stable double-stranded structures, facilitating enzyme-initiated events. Implementing more flexible primer-based enzymatic SDR regulations remains challenging due to the lack of convenient and simple primer control mechanism, which consequently limits the development of enzymatic DNA circuits. In this study, we propose an approach, termed primer switching regulation, that implements programmable and flexible regulations of enzymatic circuits by introducing switchable wires into the enzymatic circuits. We applied this method to generate diverse enzymatic DNA circuits, including cascading, fan-in/fan-out, dual-rail, feed-forward, and feedback functions. Through this method, complex circuit functions can be implemented by just introducing additional switching wires without reconstructing the basic circuit frameworks. The method is experimentally demonstrated to provide flexible and programmable regulations to control enzymatic DNA circuits and has future applications in DNA computing, biosensing, and DNA storage.

Programming and monitoring surface-confined DNA computing

DNA-based molecular computing has evolved to encompass a diverse range of functions, demonstrating substantial promise for both highly parallel computing and various biomedical applications. Recent advances in DNA computing systems based on surface reactions have demonstrated improved levels of specificity and computational speed compared to their solution-based counterparts that depend on three-dimensional molecular collisions. Herein, computational biomolecular interactions confined by various surfaces such as DNA origamis, nanoparticles, lipid membranes and chips are systematically reviewed, along with their manipulation methodologies. Monitoring techniques and applications for these surface-based computing systems are also described. The advantages and challenges of surface-confined DNA computing are discussed.