Enzyme-Powered Three-Dimensional DNA Nanomachine for DNA Walking, Payload Release, and Biosensing

Versatile “on–off” biosensing of thrombin and miRNA based on Ag(i) ion-enhanced or Ag nanocluster-quenched electrochemiluminescence coupled with hybridization chain reaction amplification

A novel biosensing platform based on Ag(i) ion-enhanced or Ag nanoclusters (NCs)-quenched electrochemiluminescence (ECL) of CdSe quantum dots (QDs) was designed for versatile “on–off” assays of thrombin (TB) and miRNA.

BSA stabilized tetraphenylethylene nanocrystals as aggregation-induced enhanced electrochemiluminescence emitters for ultrasensitive microRNA assay

An ultrasensitive ECL biosensing platform was constructed based on BSA stabilized tetraphenylethylene nanocrystals to achieve microRNA detection in cancer cells.

A DNA walker powered by endogenous enzymes for imaging uracil-DNA glycosylase activity in living cells

A DNA walker powered by endogenous enzymes detects uracil-DNA glycosylase activity in living cells.

A dynamic 3D DNA nanostructure based on silicon-supported lipid bilayers: a highly efficient DNA nanomachine for rapid and sensitive sensing

Herein, we have developed a dynamic three-dimensional (3D) self-powered DNA nanomachine by anchoring cholesterol-labelled DNA probes to silicon-supported lipid bilayers via cholesterol–lipid interaction.

A novel fluorescent assay for the ultrasensitive detection of miRNA-21 with the use of G-quadruplex structures as an immobilization material for a signal indicator

A fluorescent assay for the ultrasensitive detection of miRNA-21 is based on immobilization of PPIX as signal indicators in massive G-quadruplex structures obtained by target recycling, three-dimensional DNA walker and RCA coupled cascade nucleic acid amplification.

A rolling circle amplification-assisted DNA walker triggered by multiple DNAzyme cores for highly sensitive electrochemical biosensing

A DNA walker triggered by multiple DNAzyme cores was constructed with the assistance of rolling circle amplification for electrochemical biosensing.

Ultrasensitive photoelectrochemical microRNA biosensor based on doxorubicin sensitized graphitic carbon nitride assisted by a target-activated enzyme-free DNA walker

Herein, a photoelectrochemical biosensor was constructed based on a sensitization strategy of doxorubicin sensitized graphitic carbon nitride for ultrasensitive detection of microRNA-141 assisted by a target-activated enzyme-free DNA walker.

Expanding DNA nanomachine functionality through binding-induced DNA output for application in clinical diagnosis

Herein, we describe two homogeneous conversion systems that can convert protein recognition into the release of predesigned output DNA for the activation of DNA nanomachines.

Programmable Target-Initiated DNAzyme Walker Walking along a Spatially Isolated and Highly Hybridizable Substrate Track on a Nanoparticle Surface

Synthetic DNA machines that operate on the nanoscale three-dimensional (3D) track have attracted rapidly increasing interest because of their potential in biocomputing, drug delivery, and biosensing applications. Current nanoscale 3D DNA tracks are typically created by self-assembling thiolated oligonucleotides at gold nanoparticle (AuNP) surfaces via the strong Au-S chemistry. However, it remains challenging to accurately control the conformation and orientation of the 3D DNA track on AuNP surfaces and finely adjust the hybridization ability of the 3D track. Herein, we describe for the first time a polyadenine (polyA)-based, spatially isolated 3D DNA track, on which a target-initiated DNAzyme walker moves by a burnt-bridge mechanism with improved efficiency and processivity. PolyA serves as an anchoring block for preferential binding with the AuNP surface, and the appended substrate block adopts an upright conformation that favors the hybridization and subsequent DNAzyme-mediated cleavage. The operation of this target-initiated DNAzyme walker was monitored in real time and at a single-particle level. We tested the cleavage efficiency of 3D substrates with various polyA block lengths, which displayed that the DNAzyme activity was remarkably improved as compared with a thiol-based 3D track. We also explored bioanalytical applications of this DNAzyme nanomachine by movement-triggered cascade signal amplification.

DNA-Walker-Induced Allosteric Switch for Tandem Signal Amplification with Palladium Nanoparticles/Metal-Organic Framework Tags in Electrochemical Biosensing

A DNA walker as a new molecular machine can walk on defined tracks to directly generate signal indicators in biosensing and biomedical applications. In this work, a tandem signal amplification strategy was developed on the basis of the DNA-walker-induced conformation switch for bridging palladium nanoparticles/metal-organic framework tags in ultrasensitive electrochemical DNA biosensing. The signal tags were synthesized by in situ reduction of Pd nanocrystals on porphyrinic metal-organic frameworks (PCN-224), followed by conjugation with streptavidin (SA). The as-prepared Pd/PCN-224-SA tag could electrocatalyze the oxidation of NaBH₄ with high efficiency for signal readout. The presence of target DNA released swing arms that were each silenced by a blocker, and then the activated swing arms could hybridize with hairpin DNA. The movement of swing arms was powered by enzymatic cleavage of conjugated oligonucleotides, inducing the allosteric switch from hairpin to SA aptamer. Therefore, Pd/PCN-224-SA tags were brought onto the electrode surface via SA-aptamer biorecognition to generate the enhanced electrochemical signal. The DNA walker-based electrochemical biosensor demonstrated good performance such as 6 orders of magnitude linear range, femtomolar detection limit, and single mismatch differentiation ability. Moreover, the feasibility of the biosensor was identified in serum matrixes. The tandem signal amplification of metal-organic frameworks and DNA walkers provided a new avenue in trace electrochemical biosensing.

Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging

Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.

A new electrochemical aptasensor for sensitive assay of a protein based on the dual-signaling electrochemical ratiometric method and DNA walker strategy

Herein, a new electrochemical aptamer-based biosensor for highly sensitive assay of thrombin has been developed based on the dual-signaling electrochemical ratiometric method and the DNA walker strategy, and shows a low detection limit of about 56 fM.

Stepwise nanoassembly of a single hairpin probe and its biosensing

Herein, we describe a novel trigger-induced DNA nanoassembly method using only one loop-stem shaped hairpin probe (HP) that consists of three different functional regions as a single building unit. The Region I is designed complementary to the trigger, while the Region II and Region III are projected to complementary with each other. When hybridized with the trigger, a toehold mediated strand displacement (TMSD) occurred on the strand of Region I, leading to the release of Region III for further hybridization with the Region II on another HP molecule and in turn inducing a stepwise growth of HP with the aid of polymerase. Unlike the conventional assembly approaches that rely on the sophisticated sequence design and complex operation, the single-HP nanoassembly is easy and fast. Moreover, because many HPs are opened during the assembly process, we exemplified the nanoassembly strategy by re-designing a new labeled hairpin probe to analyze the Kras oncogene with a high sensitivity and specificity. The present study demonstrated a novel promising DNA nanoassembly strategy for biological applications.

Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants

Single nucleotide variants (SNVs) are important both clinically and biologically because of their profound biological consequences. Herein, we engineered a nicking endonuclease-powered three dimensional (3D) DNA nanomachine for discriminating SNVs with high sensitivity and specificity. Particularly, we performed a simulation-guided tuning of sequence designs to achieve the optimal trade-off between device efficiency and specificity. We also introduced an auxiliary probe, a molecular fuel capable of tuning the device in solution via noncovalent catalysis. Collectively, our device produced discrimination factors comparable with commonly used molecular probes but improved the assay sensitivity by ∼100 times. Our results also demonstrate that rationally designed DNA probes through computer simulation can be used to quantitatively improve the design and operation of complexed molecular devices and sensors.

Multipedal DNA Walker Biosensors Based on Catalyzed Hairpin Assembly and Isothermal Strand-Displacement Polymerase Reaction for the Chemiluminescent Detection of Proteins

In this study, two kinds of sensitive biosensors based on a multipedal DNA walker along a three-dimensional DNA functional magnet particles track for the chemiluminescent detection of streptavidin (SA) are constructed and compared. In the presence of SA, a multipedal DNA walker was constructed by a biotin-modified catalyst as a result of the terminal protection to avoid being digested by exonuclease I. Then, through a toehold-mediated strand exchange, a "leg" of a multipedal DNA walker interacted with a toehold of a catalyzed hairpin assembly (CHA)-H1 coupled with magnetic microparticles (MMPs) and opened its hairpin structure. The newly open stem in CHA-H1 was hybridized with a toehold of biotin-labeled H2. Via the strand displacement process, H2 displaced one "leg" of a multipedal DNA walker, and the other "leg" continued to interact with the neighboring H1 to initiate the next cycle. In order to solve the high background caused by the hybridization between CHA-H1 and H2 without a CHA-catalyst, the other model was designed. The principle of the other model (isothermal strand-displacement polymerase reaction (ISDPR)-DNA walker) was similar to that of the above one. After the terminal protection of SA, a "leg" of a multipedal DNA walker was triggered to open the hairpin of the ISDPR-H1 conjugated with MMPs. Then, the biotin-modified primer hybridized with the newly exposed DNA segment, triggering the polymerization reaction with the assistance of dNTPs/polymerase. As for the extension of the primer, the "leg" of a multipedal DNA walker was displaced so that the other "leg" could trigger the proximal H1 to go onto the next cycle. Due to its lower background and stronger signal, a multipedal DNA walker based on an ISDPR had a lower limit of detection for SA. The limit of detection for SA was 6.5 pM, and for expanding the application of the method, the detections of the folate receptor and thrombin were explored. In addition, these DNA walker methods were applied in complex samples successfully.

Double Photosystems-Based 'Z-Scheme' Photoelectrochemical Sensing Mode for Ultrasensitive Detection of Disease Biomarker Accompanying Three-Dimensional DNA Walker

A new double photosystems-based 'Z-scheme' photoelectrochemical (PEC) sensing platform is designed for ultrasensitive detection of prostate-specific antigen (PSA) by coupling with a three-dimensional (3D) DNA walker. Two photosystems consist of CdS quantum dots (photosystem I; PS I) and BiVO4 photoactive materials (photosystem II; PS II), whereas gold nanoparticles (AuNPs) photodeposited on high-active {010} facets of BiVO4 are used as the electron mediators to promote electron transfer from conduction band of PS II to valence band of PS I. 3D DNA walker-based amplification strategy is carried out between hairpin DNA1 conjugated onto the AuNP, hairpin DNA2 labeled with CdS quantum dot (QD-H2), and DNA walker complementary with the PSA aptamer modified to a magnetic bead (Apt-MB). Upon addition of target, DNA walker strand is displaced from DNA walker/Apt-MB to open hairpin DNA1 on AuNP@BiVO4. In the presence of QD-H2, DNA walker induces the hybridization of DNA1 with DNA2 on the gold nanoparticles step by step, thereby resulting in the assembly of CdS QDs on the AuNP@BiVO4 to form Z-scheme double photosystems with strong photocurrent. Under optimum conditions, the Z-scheme PEC sensing system exhibits good photocurrent responses toward target PSA within the working range of 0.01-50 ng mL-1 at a low detection limit of 1.5 pg mL-1. Good reproducibility and accuracy are acquired for analysis of target PSA and human serum specimens relative to the commercial PSA ELISA kit. Importantly, our strategy provides a new horizon for photoelectrochemical in vitro diagnostics.

A highly integrated DNA nanomachine operating in living cells powered by an endogenous stimulus

Synthetic molecular machines have received increasing attention because of their great ability to mimic natural biological motors and create novel modes of motion. However, very few examples have been implemented with real autonomous movement inside living cells, due to the challenges of the driving force and highly integrated system design. In this work, we report an elegant, highly integrated DNA nanomachine that can be powered by endogenous ATP molecules and autonomously operated inside living cells without any auxiliary additives. It assembles all components on a single gold nanoparticle (AuNP) including a hairpin-locked swing arm encoding a start triggered by an intracellular target molecule and a two-stranded DNA track responding to the motion of the swing arm. When the intracellular target activates the nanomachine via the unlocking swing arm, the machine autonomously and progressively operates on the established DNA track via intramolecular toehold-mediated strand migration and internal ATP binding. This paper also demonstrates the machine's bioanalytical application for specific microRNA (miRNA) imaging in living cells.

Molecular Machine Powered Surface Programmatic Chain Reaction for Highly Sensitive Electrochemical Detection of Protein

A bipedal molecular machine powered surface programmatic chain reaction was designed for electrochemical signal amplification and highly sensitive electrochemical detection of protein. The bipedal molecular machine was built through aptamer-target specific recognition for the binding of one target protein with two DNA probes, which hybridized with surface-tethered hairpin DNA 1 (H1) via proximity effect to expose the prelocked toehold domain of H1 for the hybridization of ferrocene-labeled hairpin DNA 2 (H2-Fc). The toehold-mediated strand displacement reaction brought the electrochemical signal molecule Fc close to the electrode and meanwhile released the bipedal molecular machine to traverse the sensing surface by the surface programmatic chain reaction. Eventually, a large number of duplex structures of H1-H2 with ferrocene groups facing to the electrode were formed on the sensor surface to generate an amplified electrochemical signal. Using thrombin as a model target, this method showed a linear detection range from 2 pM to 20 nM with a detection limit of 0.76 pM. The proposed detection strategy was enzyme-free and allowed highly sensitive and selective detection of a variety of protein targets by using corresponding DNA-based affinity probes, showing potential application in bioanalysis.

Bioderived DNA Nanomachines for Potential Uses in Biosensing, Diagnostics, and Therapeutic Applications

Beside its genomic properties, DNA is also recognized as a novel material in the field of nanoengineering. The specific bonding of base pairs can be used to direct the assembly of highly structured materials with specific nanoscale features such as periodic 2D arrays, 3D nanostructures, assembly of nanomaterials, and DNA nanomachines. In recent years, a variety of DNA nanomachines are developed because of their many potential applications in biosensing, diagnostics, and therapeutic applications. In this review, the fuel-powered motors and secondary structure motors, whose working mechanisms are inspired or derived from natural phenomena and nanomachines, are discussed. The combination of DNA motors with other platforms is then discussed. In each section of these motors, their mechanisms and their usage in the biomedical field are described. Finally, it is believed that these DNA-based nanomachines and hybrid motifs will become an integral point-of-care diagnostics and smart, site-specific therapeutic delivery.

An electrochemiluminescence biosensor for Kras mutations based on locked nucleic acid functionalized DNA walkers and hyperbranched rolling circle amplification

Herein, an electrochemiluminescence (ECL) biosensor for ultrasensitive and specific detection of Kras mutant genes has been developed on the basis of the high discrimination capability of locked nucleic acid (LNA) and dual signal amplification techniques including DNA walkers and hyperbranched rolling circle amplification (HRCA).

Programmable DNA switches and their applications

DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.

Stochastic DNA walker for electrochemical biosensing sensitized with gold nanocages@graphene nanoribbons

A target-driven stochastic DNA walking electrochemical biosensor sensitized with gold nanocages@graphene nanoribbons (Au NCs@GNRs) was explored for sensitive detection of target DNA. Benefited from the large surface area and excellent conductivity of Au NCs and GNRs, the proposed sensing platform not only improved the electron transfer kinetics involved in electrochemical reactions, but also enhanced the loading capability for stem-loop structural DNA segment (H). Upon the addition of target DNA, the hairpin structure of H was opened and H:target DNA duplex was formed based on toehold-mediated DNA strand displacement. In the presence of exonuclease III (Exo III), the H:target DNA duplex was digested. As a result, target DNA spontaneously dissociated from H:target DNA duplex and then hybridized with another H strand. Therefore, the continuous locomotion of target DNA unceasingly triggered new digestion process from near to far along the electrode surface, resulting in great signal amplification. The proposed strategy exhibited excellent detection performances for DNA analysis in complex matrix such as human serum, which illuminated the practical application field of the sensing platform.

Encapsulation of Gold Nanoparticles into DNA Minimal Cages for 3D-Anisotropic Functionalization and Assembly

Gold nanoparticles (AuNPs) endowed with anisotropic DNA valency are an important class of materials, as they can assemble into complex structures with a minimal number of DNA strands. However, methods to encode 3D DNA strand patterns on AuNPs with a controlled number of unique DNA strands in a predesigned spatial arrangement remain elusive. In this work, a simple one-step method to yield such DNA-decorated AuNPs is demonstrated, through encapsulating AuNPs into DNA minimal nanocages. The AuNP@DNA cage encapsulation complex inherits the 3D anisotropic molecular information from the DNA nanocage with enhanced structural stability. The DNA nanocage can be further functionalized and used as a building block for the self-assembly of complex architectures, such as dimers and trimers, programmed assemblies with sequential growth DNA backbones and DNA origami.

A nonenzymatic DNA nanomachine for biomolecular detection by target recycling of hairpin DNA cascade amplification

Synthetic enzyme-free DNA nanomachine performs quasi-mechanical movements in response to external intervention, suggesting the promise of constructing sensitive and specific biosensors. Herein, a smart DNA nanomachine biosensor for biomolecule (such as nucleic acid, thrombin and adenosine) detection is developed by target-assisted enzyme-free hairpin DNA cascade amplifier. The whole DNA nanomachine system is constructed on gold nanoparticle which decorated with hundreds of locked hairpin substrate strands serving as DNA tracks, and the DNA nanomachine could be activated by target molecule toehold-mediated exchange on gold nanoparticle surface, resulted in the fluorescence recovery of fluorophore. The process is repeated so that each copy of the target can open multiplex fluorophore-labeled hairpin substrate strands, resulted in amplification of the fluorescence signal. Compared with the conventional biosensors of catalytic hairpin assembly (CHA) without substrate in solution, the DNA nanomachine could generate 2-3 orders of magnitude higher fluorescence signal. Furthermore, the DNA nanomachine could be used for nucleic acid, thrombin and adenosine highly sensitive specific detection based on isothermal, and homogeneous hairpin DNA cascade signal amplification in both buffer and a complicated biomatrix, and this kind of DNA nanomachine could be efficiently applied in the field of biomedical analysis.

mRNA-Initiated, Three-Dimensional DNA Amplifier Able to Function inside Living Cells

DNA molecular machines show great promise in fields such as biomarker discovery and biological activity regulation, but operating DNA machines with specific functions within living systems remains extremely challenging. Although DNA machines have been engineered with exact molecular-level specifications, some intrinsic imperfections such as poor cell permeation and fragility in complex cytoplasmic milieu persist due to the well-established character of nucleic acid molecules. To circumvent these problems, we herein report a molecularly engineered, entropy-driven three-dimensional DNA amplifier (EDTD) that can operate inside living cells in response to a specific mRNA target. In particular, mRNA target/EDTD interaction can specifically initiate an autonomous DNA circuit inside living cells owing to the exclusive entropy-driven force, thus providing enormous signal amplification for ultrasensitive detection of the mRNA. Moreover, owing to molecular engineering of a unique DNA tetrahedral framework into the DNA amplifier, EDTD exhibits significantly enhanced biostability and cellular uptake efficiency, which are prerequisites for DNA machines used for in vivo applications. This programmable DNA machine presents a simple and modular amplification mechanism for the detection of intracellular biomarkers. Moreover, this study provides a potentially valuable molecular tool for understanding the chemistry of cellular systems and offers a design blueprint for further expansion of DNA nanotechnology in living systems.

A biosensor based on a 3D-DNA walking machine network and distance-controlled electrochemiluminescence energy transfer for ultrasensitive detection of tenascin C and lead ions

An electrochemiluminescence biosensor was proposed based on distance-controlled energy transfer and a 3D-DNA walking machine network.

Recent progress in live cell mRNA/microRNA imaging probes based on smart and versatile nanomaterials

We summarize the recent progress in live cell mRNA/miRNA imaging probes based on various versatile nanomaterials, describing their structures and their working principles of bio-imaging applications.

Nicking enzyme-controlled toehold regulation for DNA logic circuits

DNA strand displacement is widely used in DNA-related nanoengineering for its remarkable specificity and predictability. We report a nicking enzyme-assisted mechanism to regulate strand displacement, where DNA toeholds are dynamically controlled. To demonstrate the strategy, a protein/DNA-based Boolean operation system is constructed and based on it a two-channel multiplexer controlled by three different nicking enzymes is realized. The proposed regulatory mechanism can be used for switch logic statement and bridges protein and DNA logic circuits.

Collapse of DNA Tetrahedron Nanostructure for "Off-On" Fluorescence Detection of DNA Methyltransferase Activity

As a potential detection technique, highly rigid and versatile functionality of DNA tetrahedron nanostructures is often used in biosensing systems. In this work, a novel multifunctional nanostructure has been developed as an "off-on" fluorescent probe for detection of target methyltransferase by integrating the elements of DNA tetrahedron, target recognition, and dual-labeled reporter. This sensing system is initially in an "OFF" state owing to the close proximity of fluorophores and quenchers. After the substrate is recognized by target methyltransferase, the DNA tetrahedron can be methylated to produce methylated DNA sites. These sites can be recognized and cut by the restriction endonuclease DpnI to bring about the collapse of the DNA tetrahedron, which leads to the separation of the dual-labeled reporters from the quenchers, and thus the recovery of fluorescence signal to produce an "ON" state. The proposed DNA tetrahedron-based sensing method can detect Dam methyltransferase in the range of 0.1-90 U mL^-1 with a detection limit of 0.045 U mL^-1 and shows good specificity and reproducibility for detection of Dam methyltransferase in a real sample. It has been successfully applied for screening various methylation inhibitors. Thus, this work possesses a promising prospect for detection of DNA methyltransfrase in the field of clinical diagnostics.

A Target-Triggered DNAzyme Motor Enabling Homogeneous, Amplified Detection of Proteins

We report here the concept of a self-powered, target-triggered DNA motor constructed by engineering a DNAzyme to adapt into binding-induced DNA assembly. An affinity ligand was attached to the DNAzyme motor via a DNA spacer, and a second affinity ligand was conjugated to the gold nanoparticle (AuNP) that was also decorated with hundreds of substrate strands serving as a high-density, three-dimensional track for the DNAzyme motor. Binding of a target molecule to the two ligands induced hybridization between the DNAzyme and its substrate on the AuNP, which are otherwise unable to spontaneously hybridize. The hybridization of DNAzyme with the substrate initiates the cleavage of the substrate and the autonomous movement of the DNAzyme along the AuNP. Each moving step restores the fluorescence of a dye molecule, enabling monitoring of the operation of the DNAzyme motor in real time. A simple addition or depletion of the cofactor Mg²⁺ allows for fine control of the DNAzyme motor. The motor can translate a single binding event into cleavage of hundreds of substrates, enabling amplified detection of proteins at room temperature without the need for separation.

DNA Implementation of Fuzzy Inference Engine: Towards DNA Decision-Making Systems

Decision-making systems are an integral part of any autonomous device. With the recent developments in bio-nanorobots, smart drugs, and engineered viruses, there is an immediate need of decision-making systems which are bio-compatible in nature. DNA is considered a perfect candidate for designing the computing systems in such decision-making systems because of their bio-compatibility and programmability. Complex biological systems can be easily modeled/controlled using fuzzy logic operations with the help of linguistic rules. In this paper, we propose an enzyme-free DNA strand displacement-based architecture of fuzzy inference engine using the fuzzy operators, such as fuzzy intersection and union. The basic building blocks of this architecture are minimum, maximum, and fan-out gates. All these gates are analog in nature, which means that the input/output values of the gates are represented by the concentration of the input/output DNA strands. To demonstrate the performance of the proposed architecture, a detailed design, analysis, and kinetic simulation of each gate were carried out. Finally, the minimum and maximum gates are cascaded according to the pre-defined rules to design the fuzzy inference engine. All these DNA circuits are implemented and simulated in Visual DSD software.

A Simple, Cleated DNA Walker That Hangs on to Surfaces

We designed and demonstrated a single-legged or unipedal walker that has a "cleat" that allows it to persistently associate with a track and make autonomous decisions about movement. The walker is highly processive over long periods of time, as shown by its movement over a microparticle surface suffused with substrate. The simple design can be readily optimized on the basis of simple energetic considerations. The walker can be used for signal amplification and should prove especially valuable for programming amorphous computations within chemical reaction networks.

Rational Engineering of a Dynamic, Entropy-Driven DNA Nanomachine for Intracellular MicroRNA Imaging

We rationally engineered an elegant entropy-driven DNA nanomachine with three-dimensional track and applied it for intracellular miRNAs imaging. The proposed nanomachine is activated by target miRNA binding to drive a walking leg tethered to gold nanoparticle with a high density of DNA substrates. The autonomous and progressive walk on the DNA track via the entropy-driven catalytic reaction of intramolecular toehold-mediated strand migration leads to continuous disassembly of DNA substrates, accompanied by the recovery of fluorescence signal due to the specific release of a dye-labeled substrate from DNA track. Our nanomachine outperforms the conventional intermolecular reaction-based gold nanoparticle design in the context of an improved sensitivity and kinetics, attributed to the enhanced local effective concentrations of working DNA components from the proximity-induced intramolecular reaction. Moreover, the nanomachine was applied for miRNA imaging inside living cells.