An Exonuclease III‐Powered,On‐Particle Stochastic DNA Walker

DNA‐based machines have attracted rapidly growing interest owing to their potential in drug delivery, biocomputing, and diagnostic applications. Herein, we report a type of exonuclease III (Exo III)‐powered stochastic DNA walker that can autonomously move on a spherical nucleic acid (SNA)‐based 3D track. The motion is propelled by unidirectional Exo III digestion of hybridized DNA tracks in a burnt‐bridge mechanism. The operation of this Exo III‐propelled DNA walker was monitored in real time and at the single‐particle resolution using total internal reflection fluorescence microscopy (TIRF). We further interrogated the morphological effect of the 3D track on the nuclease activity, which suggested that the performance of the DNA walker was critically dependent upon the DNA density and the track conformation. Finally, we demonstrated potential bioanalytical applications of this SNA‐based stochastic DNA walker by exploiting movement‐triggered cascade signal amplification.     

An Exonuclease III‐Powered,On‐Particle Stochastic DNA Walker

DNA‐based machines have attracted rapidly growing interest owing to their potential in drug delivery, biocomputing, and diagnostic applications. Herein, we report a type of exonuclease III (Exo III)‐powered stochastic DNA walker that can autonomously move on a spherical nucleic acid (SNA)‐based 3D track. The motion is propelled by unidirectional Exo III digestion of hybridized DNA tracks in a burnt‐bridge mechanism. The operation of this Exo III‐propelled DNA walker was monitored in real time and at the single‐particle resolution using total internal reflection fluorescence microscopy (TIRF). We further interrogated the morphological effect of the 3D track on the nuclease activity, which suggested that the performance of the DNA walker was critically dependent upon the DNA density and the track conformation. Finally, we demonstrated potential bioanalytical applications of this SNA‐based stochastic DNA walker by exploiting movement‐triggered cascade signal amplification.     

Orthogonally Photocontrolled Non‐Autonomous DNA Walker

There is considerable interest in developing progressively moving devices on the nanoscale, with the aim of using them as parts of programmable therapeutics, smart materials, and nanofactories. Present here is an entirely light‐induced DNA walker based on orthogonal photocontrol. Implementing two azobenzene derivatives, S‐DM‐Azo and DM‐Azo, enabled precise coordination of strand displacement reactions that powered a biped walker and guided it along a defined track in a non‐autonomous way. This unprecedented type of molecular walker design offers high precision control over the movement in back‐and‐forth directions as desired, and is regulated solely by the sequence of the irradiation wavelengths. This concept may open new avenues for advancing non‐autonomous progressive molecular motors, ultimately facilitating their application at the nanoscale.     

A bipedal DNA nanowalker fueled by catalytic assembly for imaging of base-excision repairing in living cells

DNA nanowalkers moving progressively along a prescribed DNA track are useful tools in biosensing, molecular theranostics and biosynthesis. However, stochastic DNA nanowalkers that can perform in living cells have been largely unexplored. We report the development of a novel stochastic bipedal DNA walker that, for the first time, realizes direct intracellular base excision repair (BER) fluorescence activation imaging. In our design, the bipedal walker DNA was generated by BER-related human apurinic/apyrimidinic endonuclease 1 (APE1)-mediated cleavage of DNA sequences at an abasic site in the intracellular environment, and it autonomously travelled on spherical nucleic acid (SNA) surfaces via catalyzed hairpin assembly (CHA). Our nanomachine outperforms the conventional single leg-based DNA walker with an improved sensitivity, kinetics and walking steps. Moreover, in contrast to the single leg-based DNA walker, the bipedal DNA walker is capable of monitoring the fluorescence signal of reduced APE1 activity, thus indicating amplified intracellular imaging. This bipedal DNA-propelled DNA walker presents a simple and modular amplification mechanism for intracellular biomarkers of interest, providing an invaluable platform for low-abundance biomarker discovery leading to the accurate identification and effective treatment of cancers.

The developed DNA bipedal walker represents improved sensitivity, kinetics and walking steps for intracellular fluorescence imaging of base-excision repairing.     

A stimuli responsive DNA walking device

A pH responsive DNA walker has been designed. The walker can reversibly transport specific molecules along an assembled track under environmental stimuli.     

Advanced Pt hollow nanospheres/rubrene nanoleaves coupled with M-shaped DNA walker for ultrasensitive electrochemiluminescence bioassay

Herein, an intense electrochemiluminescence (ECL) was achieved based on Pt hollow nanospheres/rubrene nanoleaves (Pt HNSs/Rub NLs) without the addition of any coreactant, which was employed for ultrasensitive detection of carcinoembryonic antigen (CEA) coupled with an M-shaped DNA walker (M-DNA walker) as signal switch. Specifically, in comparison with platinum nanoparticles (Pt NPs), Pt HNSs revealed excellent catalytic performance and pore confinement-enhanced ECL, which could significantly amplify ECL intensity of Rub NLs/dissolved O₂ (DO) binary system. Then, the tracks and M-DNA walker were confined on the Pt HNSs simultaneously to promote the reaction efficiency, whose M-structure boosted the interaction sites between walking strands and tracks and reduced the rigidity of their recognition. Once the CEA approached the sensing interface, the M-DNA walker was activated based on highly specific aptamer recognition to recover ECL intensity with the assistance of exonuclease Ⅲ (Exo Ⅲ). As proof of concept, the “on-off-on” switch aptasensor was constructed for CEA detection with a low detection limit of 0.20 fg/mL. The principle of the constructed ECL aptasensor also enables a universal platform for sensitive detection of other tumor markers.     

Integration of exonuclease III-powered three-dimensional DNA walker with single-molecule detection for multiple initiator caspases assay

Initiator caspases are important components of cellular apoptotic signaling and they can activate effector caspases in extrinsic and intrinsic apoptotic pathways. The simultaneous detection of multiple initiator caspases is essential for apoptosis mechanism studies and disease therapy. Herein, we develop a sensitive nanosensor based on the integration of exonuclease III (Exo III)-powered three-dimensional (3D) DNA walker with single-molecule detection for the simultaneous measurement of initiator caspase-8 and caspase-9. This assay involves two peptide–DNA detection probe-conjugated magnetic beads and two signal probe-conjugated gold nanoparticles (signal probes@AuNPs). The presence of caspase-8 and caspase-9 can induce the cleavage of peptides in two peptide–DNA detection probes, releasing two trigger DNAs from the magnetic beads, respectively. The two trigger DNAs can serve as the walker DNA to walk on the surface of the signal probes@AuNPs powered by Exo III digestion, liberating numerous Cy5 and Texas Red fluorophores which can be quantified by single-molecule detection, with Cy5 indicating caspase-8 and Texas Red indicating caspase-9. Notably, the introduction of the AuNP-based 3D DNA walker greatly reduces the background signal and amplifies the output signals, and the introduction of single-molecule detection further improves the detection sensitivity. This nanosensor is very sensitive with a detection limit of 2.08 × 10⁻⁶ U μL⁻¹ for caspase-8 and 1.71 × 10⁻⁶ U μL⁻¹ for caspase-9, and it can be used for the simultaneous screening of caspase inhibitors and the measurement of endogenous caspase activity in various cell lines at the single-cell level. Moreover, this nanosensor can be extended to detect various proteases by simply changing the peptide sequences of the detection probes.

We demonstrate the simultaneous detection of multiple initiator caspases by integrating exonuclease III-powered three-dimensional DNA walker with single-molecule detection.     

DNA-based machines

Nucleic acids include substantial information in their base sequence and their hybridization-complexation motifs. Recent research efforts attempt to utilize this biomolecular information to develop DNA nanostructures exhibiting machine-like functions. DNA nano-assemblies revealing tweezers, motor, and walker activities exemplify a few such machines. The DNA-based machines provide new components that act as sensitive sensors, transporters, or drug delivery systems.     

A NIR Programmable In Vivo miRNA Magnifier for NIR-II Imaging of Early Stage Cancer

Aberrant expressions of biomolecules occur much earlier than tumor visualized size and morphology change, but their common measurement strategies such as biopsy suffer from invasive sampling process. In vivo imaging of slight biomolecule expression difference is urgently needed for early cancer detection. Fluorescence of rare earth nanoparticles (RENPs) in second near-infrared (NIR-II) region makes them appropriate tool for in vivo imaging. However, the incapacity to couple with signal amplification strategies, especially programmable signal amplification strategies, limited their application in lowly expressed biomarkers imaging. Here we develop a 980/808 nm NIR programmed in vivo microRNAs (miRNAs) magnifier by conjugating activatable DNAzyme walker set to RENPs, which achieves more effective NIR-II imaging of early stage tumor than size monitoring imaging technique. Dye FD1080 (FD1080) modified substrate DNA quenches NIR-II downconversion emission of RENPs under 808 nm excitation. The miRNA recognition region in DNAzyme walker is sealed by a photo-cleavable strand to avoid “false positive” signal in systemic circulation. Upconversion emission of RENPs under 980 nm irradiation activates DNAzyme walker for miRNA recognition and amplifies NIR-II fluorescence recovery of RENPs via DNAzyme catalytic reaction to achieve in vivo miRNA imaging. This strategy demonstrates good application potential in the field of early cancer detection.     

Walking molecules

Movement is intrinsic to life. Biologists have established that most forms of directed nanoscopic, microscopic and, ultimately, macroscopic movements are powered by molecular motors from the dynein, myosin and kinesin superfamilies. These motor proteins literally walk, step by step, along polymeric filaments, carrying out essential tasks such as organelle transport. In the last few years biological molecular walkers have inspired the development of artificial systems that mimic aspects of their dynamics. Several DNA-based molecular walkers have been synthesised and shown to walk directionally along a track upon sequential addition of appropriate chemical fuels. In other studies, autonomous operation--i.e. DNA-walker migration that continues as long as a complex DNA fuel is present--has been demonstrated and sophisticated tasks performed, such as moving gold nanoparticles from place-to-place and assistance in sequential chemical synthesis. Small-molecule systems, an order of magnitude smaller in each dimension and 1000× smaller in molecular weight than biological motor proteins or the walker systems constructed from DNA, have also been designed and operated such that molecular fragments can be progressively transported directionally along short molecular tracks. The small-molecule systems can be powered by light or chemical fuels. In this critical review the biological motor proteins from the kinesin, myosin and dynein families are analysed as systems from which the designers of synthetic systems can learn, ratchet concepts for transporting Brownian substrates are discussed as the mechanisms by which molecular motors need to operate, and the progress made with synthetic DNA and small-molecule walker systems reviewed (142 references).     

General mechanism for inchworm nanoscale track walkers: analytical theory and realistic simulation

Nanomotors capable of directed transportation along an unlimited linear track are being vigorously pursued both theoretically and experimentally. This study generalizes a previously proposed mechanism for nanoscale track walkers by explicitly treating key molecular details of the walker-track systems. An energy-diagram analysis identifies pathways of energy flow through the walker's movement cycle, and thereby enables us to develop an analytical theory for the track-walking mechanism. Realistic simulations of the walker's movement cycles are also conducted. The results show that the walker's directionality, run length, and speed depend critically on several key dimensional parameters of the walker-track systems. Most notably, the walker's performance as a function of the binding site interval of the track exhibits an oscillating pattern, which is accurately reproduced by the analytical theory. The wealth of nanocontrol mechanisms identified in the proposed track-walker systems not only provides a framework for optimizing performance of the walker, but also clarifies major requirements for future experimental implementation.     

Mechanisms,Methods of Tracking and Applications of DNA Walkers: A Review

In recent years, DNA nanotechnology expanded its scope from structural DNA nanoarchitecture towards designing dynamic and functional nanodevices. This progress has been evident in the development of an advanced class of DNA nanomachines, the so-called DNA walkers. They represent an evolution of basic switching between distinctly defined states into continuous motion. Inspired by the naturally occurring walkers such as kinesin, research on DNA walkers has focused on developing new ways of powering them and investigating their walking mechanisms and advantages. New techniques allowing the visualization of walkers as single molecules and in real time have provided a deeper insight into their behavior and performance. The construction of novel DNA walkers bears great potential for applications in therapeutics, nanorobotics or computation. This review will cover the various examples and breakthrough designs of recently reported DNA walkers that pushed the limits of their performance. It will also mention the techniques that have been used to investigate walker nanosystems, as well as discuss the applications that have been explored so far.     

Monte Carlo simulation of freely jointed chains with variable bond lengths

Monte Carlo simulation of freely jointed off-lattice chains with variable bond length is usually done with local random displacements of beads and with reptation moves (displacements of a bead along a chain). In dense systems, the acceptance ratio of reptations decreases strongly with density. We discuss versions of reptation moves, which are effective in dense systems. The idea, which comes from lattice systems, is to use a pseudovacancy (walker), which has the same size as a bead of a chain. The walker is attached to a neighbor chain and then another bead of that chain is cleaved. This is equivalent to a reptation move and a nonlocal displacement of the walker and since no free volume is needed, the move can be used with advantage in dense systems. A related technique are cooperative motions, which were introduced by T. Pakula for lattice models, where several chains change their conformation concomitantly. Such cooperative loops are implemented in the Monte Carlo algorithm by creating a temporary walker by cleaving a bead from a chain, moving it with reptations and finally annihilating the walker by attaching it to the same chain it was cleaved from. These moves and the condition of detailed balance are discussed in detail. As an example, we study the integrated autocorrelation time τ_int for the radius of gyration for a two-dimensional system. For reduced densities larger than 0,4, we find that with standard reptations and local bead displacements τ_int increases strongly with density. If reptations with either a permanent or a temporary walker are used in addition to local moves, the integrated autocorrelation time changes only very little with density and very dense systems can still be simulated efficiently.     

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.     

Fluorescence Signal Amplification Strategies Based on DNA Nanotechnology for miRNA Detection

In this review,the most recent progresses in the field of fluorescence signal amplification strategies based on DNA nanotechnology for miRNA are summarized.The types of signal amplification are given and the principles of amplification strategies are explained,including rolling circle amplification(RCA),catalytic hairpin assembly(CHA),hybridization chain reaction(HCR)and DNA walker.Subsequently,the application of these signal amplification methods in biosensing and bioimaging are covered and described.Finally,the challenges and the outlook of fluorescence signal amplification methods for miRNA detection are briefly commented.     

正常及肿瘤染色质的荧光寿命法、精确量热法和荧光能量转换

量热法;荧光寿命;正常及肿瘤染色质的荧光寿命法、精确量热法和荧光能量转换     

A Reagentless Electrochemical DNA Sensor Based on a Self-powered DNA Machine

Herein, a reagentless electrochemical DNA sensor based on a self-powered DNA machine for detecting survivin mRNA in cells is developed. The metal-organic framework (MOFs) loaded with DNAzyme cofactors (Mn²⁺) is coated on PTFE rods on the Au surface and assembled with the DNA walker, overcoming the complexity of adding metal ions from the external environment. In addition, the orbital chain is modified by a synthetic bisferrocene signal marker, which further enables signal amplification. Under optimal conditions, the sensor exhibits a range from 1×10⁻¹⁴ mol/L to 1×10⁻⁸ mol/L with a detection limit (S/N=3) of 1.28 fM.     

A DNA nanopillar as a scaffold to regulate the ratio and distance of mimic enzymes for an efficient cascade catalytic platform

Herein, a rigid 3D DNA nanopillar was used to investigate the influence of spatial organization on the cascade activity in multienzyme systems, realizing controllable regulation of the mimic enzyme ratio and spacing for acquiring a high-efficiency enzyme cascade catalytic platform. Initially, the ratio of mimic enzyme AuNPs (glucose oxidase-like activity) and hemin/G-quadruplex DNAzyme (peroxidase-like activity) fixed at the designed position was adjusted by changing the number of edges in a DNA polyhedron, resulting in an optimal mimic enzyme ratio of 1 : 4 with a quadrangular prism as the scaffold. Notably, the DNA nanopillar formed by quadrangular prism layer-by-layer assembly acted as a track for directional and controllable movement of a bipedal DNA walker based on the toehold mediated strand displacement reaction (TSDR), which endowed the assay system with continuous enzyme spacing regulation compared with previous enzyme cascade systems that induced inflexible operation. Furthermore, enzyme mimetics in this work circumvented the drawbacks of natural enzymes, such as time-consuming purification processes and poor thermal stability. As a proof of concept, the proposed dual regulation strategy of cascade enzymes was applied in the ultrasensitive electrochemical detection of Pb²⁺, which provided a new route to fabrication of high-performance artificial enzyme cascade platforms for ultimate application in bioanalysis and biodiagnostics.

A rigid 3D DNA nanopillar was used to investigate the influence of spatial organization on the cascade activity in multienzyme systems, realizing controllable regulation of the mimic enzyme ratio and spacing for efficient cascade catalytic platform.     

Design, synthesis, and operation of small molecules that walk along tracks

The synthesis and system dynamics of a series of small-molecule walker-track conjugates, 3,4-C(n) (n = 2, 3, 4, 5, and 8), based on dynamic covalent linkages between the "feet" of the walkers and the "footholds" of the track, is described. Each walker has one acyl hydrazide and one sulfur-based foot separated by a spacer chain of "n" methylene groups, while the track consists of four footholds of alternating complementary functionalities (aldehydes and masked thiols). Upon repeatedly switching between acid and base, the walker moiety can be exchanged between the footholds on the track, primarily through a "passing-leg gait" mechanism, until a steady state, minimum energy, distribution is reached. The introduction of a kinetically controlled step in the reaction sequence (redox-mediated breaking and reforming of the disulfide linkages) can cause a directional bias in the distribution of the walker on the track. The different length walker molecules exhibit very different walking behaviors: Systems n = 2 and 3 cannot actually "walk" along the track because their stride lengths are too short to bridge the internal footholds. The walkers with longer spacers (n = 4, 5, and 8) do step up and down the track repeatedly, but a directional bias under the acid-redox conditions is only achieved for the C(4) and C(5) systems, interestingly in opposite directions (the C(8) walker has insufficient ring strain with the track). Although they are extremely rudimentary systems, the C(4) and C(5) walker-track conjugates exhibit four of the essential characteristics of linear molecular motor dynamics: processive, directional, repetitive, and progressive migration of a molecular unit up and down a molecular track.