Regeneration of Burnt Bridges on a DNA Catenane Walker

Ingenious dual-circle DNA walker-mediated electrochemical biosensor for rapid and ultrasensitive detection of microRNA

In this work, an ingenious dual-circle DNA walker (DCDW) with pretty fast walking speed and high amplification efficiency was developed for rapid and ultrasensitive electrochemical detection of microRNA-221 (miRNA-221) related to liver cancer, combined with the toehold-mediated strand-displacement reactions (TSDRs). Impressively, compared with the traditional DNA walker, the DCDW with unique double-stranded interlocked DNA nanostructure not only possesses higher stability, flexibility, and anti-entanglement ability, but also enables more functional domain in a smaller area, thereby enhancing the local concentration, which can greatly improve the working efficiency. As a validation, the electrochemical biosensor realized rapid and ultrasensitive detection of miRNA-221 with a reaction time of 15 min and detection limit down to 1.9 aM, and had been applied in MHCC97L and HeLa cancer cell lysates, thus providing an innovative insight to design intelligent functional interlocked DNA walkers for ultimate application in the construction of biosensing platform and miRNA detection in biological sample.

Simulation-Guided Rational Design of DNA Walker-Based Theranostic Platform

Biomolecule-functionalized nanoparticles represent a type of promising biomaterials in biomedical applications owing to their excellent biocompatibility and versatility. DNA-based reactions on nanoparticles have enabled emerging applications including intelligent biosensors, drug delivery, and biomimetic devices. Among the reactions, strand hybridization is the critical step to control the sensitivity and specificity of biosensing, and the efficiency of drug delivery. However, a comprehensive understanding of DNA hybridization on nanoparticles is still lacking, which may differ from the process in homogeneous solutions. To address this limitation, coarse-grained model-based molecular dynamic simulation is harnessed to disclose the critical factors involved in intermolecular hybridization. Based on simulation guidance, DNA walker-based smart theranostic platform (DWTP) based on "on-particle" hybridization is developed, showing excellent consistency with simulation. DWTP is successfully applied for highly sensitive miRNA 21 detection and tumor-specific miRNA 21 imaging, driven by tumor-endogenous APE 1 enzyme. It enables the precise release of antisense oligonucleotide triggered by tumor-endogenous dual-switch miRNA 21 and APE 1, facilitating effective gene silencing therapy with high biosafety. The simulation of "on-particle" DNA hybridization has improved the corresponding biosensing performance and the release efficiency of therapeutic agents, representing a conceptually new approach for DNA-based device design.

Ultrahigh-Speed 3D DNA Walker with Dual Self-Protected DNAzymes for Ultrasensitive Fluorescence Detection and Intracellular Imaging of microRNA

Herein, a dual self-protected DNAzyme-based 3D DNA walker (dSPD walker), composed of activated dual self-protected walking particles (ac-dSPWPs) and track particles (TPs), was constructed for ultrasensitive and ultrahigh-speed fluorescence detection and imaging of microRNAs (miRNAs) in living cells. Impressively, compared with the defect that "one" target miRNA only initiates "one" walking arm of the conventional single self-protected DNAzyme walker, the dSPD walker benefits from the secondary amplification and spatial confinement effect and could guide "one" target miRNA to generate "n" secondary targets, thereby initiating "n" nearby walking strands immediately, realizing the initial rate over one-magnitude-order faster than that of the conventional one. Moreover, in the process of relative motion between ac-dSPWPs and TPs, the ac-dSPWPs could cleave multiple substrate strands simultaneously to speed up movement and reduce the derailment rate, as well as combine with successive TPs to facilitate a large amount of continuous signal accumulation, achieving an ultrafast detection of miRNA-221 within 10 min in vitro and high sensitivity with a low detection limit of 0.84 pM. In addition, the DNA nanospheres obtained by the rolling circle amplification reaction can capture the Cy5 fluorescence dispersed in liquids, which achieves the high-contrast imaging of miRNA-221, resulting in further ultrasensitive imaging of miRNA-221 in cancer cells. The proposed strategy has made a bold innovation in the rapid and sensitive detection as well as intracellular imaging of low-abundance biomarkers, offering promising application in early diagnosis and relevant research of cancer and tumors.

Ratiometric fluorescence platform for the ultrasensitive detection of kanamycin based on split aptamer co-recognition triggers Mg2+-DNAzyme-driven DNA walker systems

In this work, a novel 3D-DNA walker signal amplification strategy was designed to construct a fluorescent aptasensor for the detection of kanamycin (KAN). The aptasensor utilizes split aptamers for the synergistic recognition of KAN. The presence of KAN induces the split aptamers recombination to form the Mg2+-DNAzyme structure, which is activated by Mg2+ to drive the 3D-DNA walker process for cascading signal amplification. Employing gold nanoflowers (AuNFs) as walking substrate material increases the local DNA concentration to enhance the walker efficiency. The prepared fluorescent aptasensor achieved efficient and sensitive detection of KAN with satisfactory results in the concentration range of 1 × 10-8 - 1 × 10-3 μg/kg and the detection limit of 5.63 fg/kg. Meanwhile, the designed fluorescent aptasensor exhibited favorable specificity, anti-interference, storage stability and reproducibility, and verified the feasibility of its application in milk samples. The present work provides an effective tool for the regulation of KAN contamination in animal-derived foods with promising prospects.

DNA-Based Molecular Machines: Controlling Mechanisms and Biosensing Applications

The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed.

Bubble DNA tweezer: A triple-conformation sensor responsive to concentration-ratios

DNA tweezers, with their elegant simplicity and flexibility, have been pivotal in biosensing and DNA computing. However, conventional tweezers are confined to a binary transformation pre/post target signal recognition, limiting them to presence/absence judgments. This study introduces bubble DNA tweezers (BDT), capable of three distinct conformations based on variable target signal ratios. In contrast to traditional compact tweezers, BDT features a looser structure centered around a non-complementary bubble domain located between the tweezer arms' connecting axis and target signal recognition jaws. This bubble triggers toehold-free DNA strand displacement, leading to three conformational changes at different target signal concentrations. BDT detects presence/absence and true concentration with remarkable specificity and sensitivity. This adaptability is not confined to ideal scenarios, proving valuable in complex, noisy environments. Our method facilitates target DNA/miRNA signal quantification within a specific length range, promising applications in clinical research and environmental detection, while inspiring future biological assay innovations.

Ratiometric electrochemical biosensor based on lateral movement of multi-pedal DNA tetrahedron machine on biomimetic interface

In this work, a lateral moving multi-pedal DNA tetrahedron machine (MTM) is designed and coupled with dual-signal output system to construct a biomimetic electrochemical ratiometric strategy for ultrasensitive target DNA analysis. The tetrahedral structure provided rigid support for the pedal, ensuring efficient replacement of the rail chain modified with ferrocene. By conjugating cholesterol molecules to one vertex of MTM, it is decorated on a lipid bilayer. This molecular architecture confers lateral movement of MTM on an electrode surface while prevents its detachment from the system. The methylene blue tagged hairpin probe provides constant power to support MTM swim on lipid bilayer. Compared with the conventional motion mode, the lateral moving mechanism has the fastest reaction rate and the highest signal-to-noise ratio. Additionally, the dual-signal reporting system further improves the accuracy of target detection on the basis of ensuring motion efficiency. The work improved movement efficiency and shortened time fragment. A linear relationship between the ratio value of two reporters and target DNA concentration was observed from 0.5 fM to 50 pM with a detection limit of 28 aM. The lateral motion mode of DNA machine coalescing with ratiometric system made this sensing platform ultrasensitive and accurate, which holds new avenue of early diagnosis.

Motility of an autonomous protein-based artificial motor that operates via a burnt-bridge principle

Inspired by biology, great progress has been made in creating artificial molecular motors. However, the dream of harnessing proteins - the building blocks selected by nature - to design autonomous motors has so far remained elusive. Here we report the synthesis and characterization of the Lawnmower, an autonomous, protein-based artificial molecular motor comprised of a spherical hub decorated with proteases. Its "burnt-bridge" motion is directed by cleavage of a peptide lawn, promoting motion towards unvisited substrate. We find that Lawnmowers exhibit directional motion with average speeds of up to 80 nm/s, comparable to biological motors. By selectively patterning the peptide lawn on microfabricated tracks, we furthermore show that the Lawnmower is capable of track-guided motion. Our work opens an avenue towards nanotechnology applications of artificial protein motors.

A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower

Molecular engineering seeks to create functional entities for modular use in the bottom-up design of nanoassemblies that can perform complex tasks. Such systems require fuel-consuming nanomotors that can actively drive downstream passive followers. Most artificial molecular motors are driven by Brownian motion, in which, with few exceptions, the generated forces are non-directed and insufficient for efficient transfer to passive second-level components. Consequently, efficient chemical-fuel-driven nanoscale driver-follower systems have not yet been realized. Here we present a DNA nanomachine (70 nm × 70 nm × 12 nm) driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates as fuel to generate a rhythmic pulsating motion of two rigid DNA-origami arms. Furthermore, we demonstrate actuation control and the simple coupling of the active nanomachine with a passive follower, to which it then transmits its motion, forming a true driver-follower pair.

Dual-mode DNA walker-based optical fiber biosensor for ultrasensitive detection of microRNAs

We present a novel dual-mode DNA-walker based optical fiber biosensor (DMDW-Opt biosensor) for sensitive assay of micro-RNAs in bio-samples. In the sensor system, we develop a new strategy for the cascade amplification, DNA-walker/rolling cycle amplification (RCA), by the use of the residue track of the walker. The strategy can significantly improve the response of the sensor and avoid any tedious operation procedure. Dual-mode readouts, i.e., fluorescence and chemiluminescence, are measured independently without interfering with each other to achieve reliable and accurate analysis. Optical fibers with the surface modified by gold nanoparticles are utilized as the support for fabrication of the sensor, which would be benefit for developing miniaturized and portable sensing devices. The performance of the proposed method is evaluated by using micro-RNAs (MiR-155 and MiR-21) as the analytical target. The method is successfully applied for accurate determination of micoRNAs in human serum and MCF-7 cells. Our method can perform sensitive assays of MiR-155 with limit-of-detection as low as 97.72 fM and 11.22 fM, MiR-21 with limit-of-detection as low as 107.15 fM and 8.32 fM for the fluorescence- and the chemiluminescence-readout respectively, and the biosensor exhibits excellent specificity, reproducibility and storage stability, indicating its valuable potential applications for sensing trace-amount targets in complicated real samples.

Development of a DNAzyme Walker for the Detection of APE1 in Living Cancer Cells

DNAzyme walker technology is a compelling option for bioanalytical and drug delivery applications. While nucleic acid and protein targets have been used to activate DNAzyme walkers, investigations into enzyme-triggered DNAzyme walkers in living cells are still in their early stages. The base excision repair (BER) pathway presents an array of enzymes that are overexpressed in cancer cells. Here, we introduce a DNAzyme walker system that sensitively and specifically detects the BER enzyme apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1). We constructed the DNAzyme walker on the surface of 20 nm-diameter gold nanoparticles. We achieved a detection limit of 160 fM of APE1 in a buffer and in whole cell lysate equivalent to the amount of APE1 in a single HeLa cell in a sample volume of 100 μL. Confocal imaging of the DNAzyme walking reveals a cytoplasmic distribution of APE1 in HeLa cells. Walking activity is tunable to exogenous Mn2+ concentrations and the uptake of the DNAzyme walker system does not require transfection assistance. We demonstrate the investigative potential of the DNAzyme walker for up-regulated or overactive enzyme biomarkers of the BER pathway in cancer cells.

Efficient Three-Dimensional DNA Nanomachine Guided by a Robust Tetrahedral DNA Nanoarray Structure for the Rapid and Ultrasensitive Electrochemical Detection of Matrix Metalloproteinase 2

Herein, a giant-sized DNA nanoarray was subtly assembled by two kinds of independent tetrahedral DNA structures as the DNA track for a multi-armed three-dimensional (3D) DNA nanomachine to perform signal transduction and amplification efficiently, which was developed as an electrochemical biosensor for the rapid and ultrasensitive detection of matrix metalloproteinase 2 (MMP-2). Impressively, in contrast to conventional DNA walkers with inefficiency, which walked on random DNA tracks composed of a two-dimensional (2D) probe or a one-dimensional (1D) single-stranded (ss)DNA probe, the multi-armed 3D DNA nanomachine from exonuclease III (Exo III) enzyme-assisted target recycling amplification would be endowed with faster reaction speed and better walking efficiency because of the excellent rigidity and orderliness of the tetrahedral DNA nanoarray structure. Once the hairpin H3-label with the signal substance ferrocene (Fc) was added to the modified electrode surface, the multi-armed 3D DNA nanomachine would be driven to move along the well-designed nanoarray tracks by toehold-mediated DNA strand displacement, resulting in most of the ferrocene (Fc) binding to the electrode surface and a remarkable increase in electrochemical signals within 60 min. As a proof of concept, the prepared biosensor attained a low detection limit of 11.4 fg/mL for the sensitive detection of the target MMP-2 and was applied in Hela and MCF-7 cancer cell lysates. As a result, this strategy provided a high-performance sensing platform for protein detection in tumor diagnosis.

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.

A photoelectrochemical biosensor based on ZnIn2S4@AuNPs coupled with circular bipedal DNA walker for signal-on detection of circulating tumor DNA

The circulating tumor DNA (ctDNA) is a crucial cancer marker, its sensitive monitoring is useful for early diagnose and therapy of tumor-related diseases. Herein, a bipedal DNA walker with multiple recognition sites is designed through the transition of dumbbell-shaped DNA nanostructure to realize the dual amplification of the signal and achieve ultrasensitive photoelectrochemical (PEC) detection of ctDNA. Initially, the ZnIn₂S₄@AuNPs is obtained by combining the drop coating method with electrodeposition method. When the target is present, the dumbbell-shaped DNA structure transforms into an annular bipedal DNA walker that can walk unrestrictedly on the modified electrode. After the cleavage endonuclease (Nb.BbvCI) was added to the sensing system, the ferrocene (Fc) on the substrate is released from the electrode surface, and the transfer efficiency of photogenerated electron-hole pairs is extremely improved, enabling the "signal on" testing of ctDNA. The detection limit of the prepared PEC sensor is 0.31 fM, and the recovery of actual samples varied between 96.8 and 103.6% with an average relative standard deviation of about 8%. Meaningfully, the prepared PEC biosensor with an innovative bipedal DNA walker has potential application value for ultrasensitive detection of other nucleic acid-related biomarker.

High-Efficiency 3D DNA Walker Immobilized by a DNA Tetrahedral Nanostructure for Fast and Ultrasensitive Electrochemical Detection of MiRNA

Herein, by directly limiting the reaction space, an ingenious three-dimensional (3D) DNA walker (IDW) with high walking efficiency is developed for rapid and sensitive detection of miRNA. Compared with the traditional DNA walker, the IDW immobilized by the DNA tetrahedral nanostructure (DTN) brings stronger kinetic and thermodynamic favorability resulting from its improved local concentration and space confinement effect, accompanied by a quite faster reaction speed and much better walking efficiency. Once traces of target miRNA-21 react with the prelocked IDW, the IDW could be largely activated and walk on the interface of the electrode to trigger the cleavage of H2 with the assistance of Mg²⁺, resulting in the release of amounts of methylene blue (MB) labeled on H2 from the electrode surface and the obvious decrease of the electrode signal. Impressively, the IDW reveals a conversion efficiency as high as 9.33 × 10⁸ in 30 min with a much fast reaction speed, which is at least five times beyond that of typical DNA walkers. Therefore, the IDW could address the inherent challenges of the traditional DNA walker easily: slow walking speed and low efficiency. Notably, the IDW as a DNA nanomachine was utilized to construct a sensitive sensing platform for rapid miRNA-21 detection with a limit of detection (LOD) of 19.8 aM and realize the highly sensitive assay of biomarker miRNA-21 in the total RNA lysates of cancer cell. The strategy thus helps in the design of a versatile nucleic acid conversion and signal amplification approach for practical applications in the areas of biosensing assay, DNA nanotechnology, and clinical diagnosis.

Electrostatic Interaction-Induced Aggregation-Induced Emission-Type AgAu Bimetallic Nanoclusters as a Highly Efficient Electrochemiluminescence Emitter for Ultrasensitive Detection of Glial Fibrillary Acidic Protein

Herein, the aggregation-induced emission (AIE)-type carboxymethyl chitosan (CMCS)@6-aza-2-thiothymine (ATT) templated AgAu bimetallic nanoclusters (CMCS@ATT-AgAu BMNCs) with superior electrochemiluminescence (ECL) emission were first synthesized to construct a biosensor for the ultrasensitive detection of glial fibrillary acidic protein (GFAP). Impressively, unlike the traditional AIE-type bimetallic nanoclusters (BMNCs) obtained by complicated multi-step synthesis, the AIE-type CMCS@ATT-AgAu BMNCs were prepared by the electrostatic interaction between the negatively charged ATT and positively charged CMCS, in which the molecule ATT was served as a capping and reducing agent of bimetal ions. In addition, a rapidly moving cholesterol labeled DNA walker was constructed to move freely on the lipid bilayer to increase its moving efficiency, and the well-regulated DNA was intelligently designed to further improve its walking efficiency for rapid and ultrasensitive detection of GFAP with a limit of detection (LOD) as low as 73 ag/mL. This strategy proposed an avenue to synthesize highly efficient BMNCs-based ECL emitters, which have great potential in ultrasensitive biosensing for early diagnosis of diseases.

A Telomerase-Assisted Strategy for Regeneration of DNA Nanomachines in Living Cells

DNA nanomachines have been engineered into diverse personalized devices for diagnostic imaging of biomarkers; however, the regeneration of DNA nanomachines in living cells remains challenging. Here, we report an ingenious DNA nanomachine that can implement telomerase (TE)-activated regeneration in living cells. Upon apurinic/apyrimidinic endonuclease 1 (APE1)-responsive initiation of the nanomachine, the walker of the nanomachine moves along tracks regenerated by TE, generating multiply amplified signals through which APE1 can be imaged in situ. Additionally, augmentation of the signal due to the regeneration of the nanomachines could reveal differential expression of TE in different cell lines. To the best of our knowledge, this is the first proof-of-concept demonstration of the use of biomarkers to assist in the regeneration of nanomachines in living cells. This study offers a new paradigm for the development of more applicable and efficient DNA nanomachines.

Reconfigurable Nanopolygons Made of DNA Catenanes

The development of new types of bonds and linkages that can reversibly tune the geometry and structural features of molecules is an elusive goal in chemistry. Herein, we report the use of catenated DNA structures as nanolinkages that can reversibly switch their angle and form different kinds of polygonal nanostructures. We designed a reconfigurable catenane that can self-assemble into a triangular or hexagonal structure upon addition of programmable DNA strands that function via toehold strand-displacement. The nanomechanical and structural features of these catenated nanojoints can be applied for the construction of dynamic systems such as molecular motors with switchable functionalities.

DNA Walkers for Biosensing Development

The ability to design nanostructures with arbitrary shapes and controllable motions has made DNA nanomaterials used widely to construct diverse nanomachines with various structures and functions. The DNA nanostructures exhibit excellent properties, including programmability, stability, biocompatibility, and can be modified with different functional groups. Among these nanoscale architectures, DNA walker is one of the most popular nanodevices with ingenious design and flexible function. In the past several years, DNA walkers have made amazing progress ranging from structural design to biological applications including constructing biosensors for the detection of cancer-associated biomarkers. In this review, the key driving forces of DNA walkers are first summarized. Then, the DNA walkers with different numbers of legs are introduced. Furthermore, the biosensing applications of DNA walkers including the detection- of nucleic acids, proteins, ions, and bacteria are summarized. Finally, the new frontiers and opportunities for developing DNA walker-based biosensors are discussed.

Distinctive features and challenges in catenane chemistry

From being an aesthetic molecular object to a building block for the construction of molecular machines, catenanes and related mechanically interlocked molecules (MIMs) continue to attract immense interest in many research areas. Catenane chemistry is closely tied to that of rotaxanes and knots, and involves concepts like mechanical bonds, chemical topology and co-conformation that are unique to these molecules. Yet, because of their different topological structures and mechanical bond properties, there are some fundamental differences between the chemistry of catenanes and that of rotaxanes and knots although the boundary is sometimes blurred. Clearly distinguishing these differences, in aspects of bonding, structure, synthesis and properties, between catenanes and other MIMs is therefore of fundamental importance to understand their chemistry and explore the new opportunities from mechanical bonds.

Biosupramolecular networks: Taking inspiration from nature to create powerful synthetic platforms

Nature is predicated on the ability to process large number of parallel signals to produce specific downstream outputs. Biosupramolecular networks are beginning to allow such processing power in synthetic systems, particularly through harnessing the recognition power of biomolecules. Such systems can be summarised through the reductionist view of containing inputs, circuitry motifs and functional outputs, with each of these elements able to be readily combined in a modular approach. Through the inherent 'plug and play' nature of these systems the field continues to rapidly expand, providing a wealth of new smart diagnostic and therapeutic systems.

A core-brush 3D DNA nanostructure: the next generation of DNA nanomachine for ultrasensitive sensing and imaging of intracellular microRNA with rapid kinetics

A highly loaded and integrated core–brush three-dimensional (3D) DNA nanostructure is constructed by programmatically assembling a locked DNA walking arm (DA) and hairpin substrate (HS) into a repetitive array along a well-designed DNA track generated by rolling circle amplification (RCA) and is applied as a 3D DNA nanomachine for rapid and sensitive intracellular microRNA (miRNA) imaging and sensing. Impressively, the homogeneous distribution of the DA and HS at a ratio of 1 : 3 on the DNA track provides a specific walking range for the DA to avoid invalid and random self-walking and notably improve the executive ability of the core–brush 3D DNA nanomachine, which easily solves the major technical challenges of traditional Au-based 3D DNA nanomachines: low loading capacity and low executive efficiency. As a proof of concept, the interaction of miRNA with the 3D DNA nanomachine could initiate the autonomous and progressive operation of the DA to cleave the HS for ultrasensitive ECL detection of target miRNA-21 with a detection limit as low as 3.57 aM and rapid imaging in living cells within 15 min. Therefore, the proposed core–brush 3D DNA nanomachine could not only provide convincing evidence for sensitive detection and rapid visual imaging of biomarkers with tiny change, but also assist researchers in investigating the formation mechanism of tumors, improving their recovery rates and reducing correlative complications. This strategy might enrich the method to design a new generation of 3D DNA nanomachine and promote the development of clinical diagnosis, targeted therapy and prognosis monitoring.

This study designed a highly loaded and integrated core–brush 3D DNA nanomachine for miRNA imaging and sensing, which easily solves the major technical challenges of traditional Au-based 3D nanomachines: low loading capacity and low executive efficiency.

Sequence-dependent twist-bend coupling in DNA minicircles

Looping of double-stranded DNA molecules with 100-200 base pairs into minicircles, catenanes, and rotaxanes has been suggested as a potential tool for DNA nanotechnologies. However, sharp DNA bending into a minicircle with a diameter of several to ten nanometers occurs with alterations in the DNA helical structure and may lead to defective kink formation that hampers the use of DNA minicircles, catenanes, and rotaxanes in nanoscale DNA applications. Here, we investigated local variations of a helical twist in sharply bent DNA using microsecond-long all-atom molecular dynamics simulations of six different DNA minicircles, focusing on the sequence dependence of the coupling between DNA bending and its helical twist. Twist angles between consecutive base pairs were analyzed at different locations relative to the direction of DNA bending and, among 10 unique dinucleotide steps, we identified four dinucleotide steps with strong twist-bend coupling, the pyrimidine-purine dinucleotide steps of TA/TA, CG/CG, and CA/TG and the purine-purine dinucleotide step of GA/TC. This work suggests the sequence-dependent structural responses of DNA to strong mechanical deformation, providing new molecular-level insights into the structure and stability of sharply bent DNA minicircles for nanoscale applications.

A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy

Nature-inspired molecular machines can exert mechanical forces by controlling and varying the distance between two molecular subunits in response to different inputs. Here, we present an automated molecular linear actuator composed of T7 RNA polymerase (T7RNAP) and a DNA [2]rotaxane. A T7 promoter region and terminator sequences are introduced into the rotaxane axle to achieve automated and iterative binding and detachment of T7RNAP in a self-controlled fashion. Transcription by T7RNAP is exploited to control the release of the macrocycle from a single-stranded (ss) region in the T7 promoter to switch back and forth from a static state (hybridized macrocycle) to a dynamic state (movable macrocycle). During transcription, the T7RNAP keeps restricting the movement range on the axle available for the interlocked macrocycle and prevents its return to the promotor region. Since this range is continuously depleted as T7RNAP moves along, a directional and active movement of the macrocycle occurs. When it reaches the transcription terminator, the polymerase detaches, and the system can reset as the macrocycle moves back to hybridize again to the ss-promoter docking site. The hybridization is required for the initiation of a new transcription cycle. The rotaxane actuator runs autonomously and repeats these self-controlled cycles of transcription and movement as long as NTP-fuel is available.

Cascade Strand Displacement and Bipedal Walking Based DNA Logic System for miRNA Diagnostics

DNA logic gated operations empower the highly efficient analysis of multiplex nucleic acid inputs, which have attracted extensive attention. However, the integration of DNA logic gates with abundant computational functions and signal amplification for biomedical diagnosis is far from being fully achieved. Herein, we develop a bipedal DNA walker based amplified electrochemical method for miRNA detection, which is then used as the basic unit for the construction of various logic circuits, enabling the analysis of multiplex miRNAs. In the bipedal walking process, target triggered strand displacement polymerization is able to produce a large number of strands for the fabrication of three-way junction-structured bipedal walkers. The following catalytic hairpin assembly ensures the walking event and the immobilization of signal probes for output. Ultrahigh sensitivity is realized due to the integration of dual signal amplification. In addition, under logic function controls by input triggered cascade strand displacement reactions, NOT, AND, OR, NAND, NOR, XOR, and XNOR logic gates are successfully established. The as-developed DNA logic system can also be extended to multi-input modes, which holds great promise in the fields of DNA computing, multiplex analysis, and clinical diagnosis.

Recent advances in DNA walker machines and their applications coupled with signal amplification strategies: A critical review

DNA walkers, a type of dynamic nanomachines, have become the subject of burgeoning research in the field of biology. These walkers are powered by driving forces based on strand displacement reactions, protein enzyme/DNAzyme reactions and conformational transitions. With the unique properties of high directionality, flexibility and efficiency, DNA walkers move progressively and autonomously along multiple dimensional tracks, offering abundant and promising applications in biosensing, material assembly and synthesis, and early cancer diagnosis. Notably, DNA walkers identified as signal amplifiers can be combined with various amplification approaches to enhance signal transduction and amplify biosensor sensing signals. Herein, we systematically and comprehensively review the walking principles of various DNA walkers and the recent progress on multiple dimensional tracks by presenting representative examples and an insightful discussion. We also summarized and categorized the diverse signal amplification strategies with which DNA walkers have coupled. Finally, we outline the challenges and future trends of DNA walker machines in emerging analytical fields.

Substrate stiffness tunes the dynamics of polyvalent rolling motors

Nature has evolved many mechanisms for achieving directed motion on the subcellular level. The burnt-bridges ratchet (BBR) is one mechanism used to achieve superdiffusive molecular motion over long distances through the successive cleavage of surface-bound energy-rich substrate sites. This mechanism has been associated with both nanoscale and microscale movement, with the latter accomplished through polyvalent interactions between a large hub (e.g. influenza virus) and substrate (e.g. cell surface receptors). Experimental successes in achieving superdiffusive motion by synthetic polyvalent BBRs have raised questions about the dynamics of their motility, including whether rolling or translation is better able to direct motion of microscale spherical hubs. Here we simulate the three-dimensional dynamics of a polyvalent sphere moving on and cleaving an elastic substrate. We find that substrate stiffness plays an important role in controlling both the motor's mode of motility and its directional persistence. As we tune lateral substrate stiffness from soft to stiff we find there exists an intermediate value that optimizes rolling behaviour. We also find that there is an optimal substrate stiffness for maximizing persistence length, while stiffness does not influence as strongly the superdiffusive dynamics of the particle. Lastly, we examine the effect of substrate density, and show that softer landscapes are better able to buffer against decreases in substrate occupancy, with the spherical motor maintaining superdiffusive motion more on softer landscapes than on stiff landscapes as occupancy drops. Our results highlight the importance of surface in controlling the motion of polyvalent BBRs.

Regeneration of Burnt Bridges on a DNA Catenane Walker

DNA walkers are molecular machines that can move with high precision onthe nanoscale due to their structural and functional programmability. Despite recent advances in the field that allow exploring different energy sources, stimuli, and mechanisms of action for these nanomachines, the continuous operation and reusability of DNA walkers remains challenging because in most cases the steps, once taken by the walker, cannot be taken again. Herein we report the path regeneration of a burnt-bridges DNA catenane walker using RNase A. This walker uses a T7RNA polymerase that produces long RNA transcripts to hybridize to the path and move forward while the RNA remains hybridized to the path and blocks it for an additional walking cycle. We show that RNA degradation triggered by RNase A restores the path and returns the walker to the initial position. RNase inhibition restarts the function of the walker.