Design Principles of DNA Enzyme-Based Walkers: Translocation Kinetics and Photoregulation

A Universal Paper-Based Electrochemical Sensor for Zero-Background Assay of Diverse Biomarkers

This paper describes a universal paper-based electrochemical sensing platform that uses a paper modified with signal molecule-labeled DNA and a screen-printed electrode along with target recognition solutions to achieve the detection of multiple types of biomarkers. These assays rely on the target-induced synthesis of Mg²⁺-dependent DNAzyme for catalyzing the cleavage of substrate DNA from paper, which have been demonstrated by using microRNA recognition probe for miR-21, a phosphorylated hairpin probe for alkaline phosphatase, and a DNA aptamer for carcinoembryonic antigen assays, respectively. Taking advantages of the high specific target-triggered polymerization/nicking and DNAzyme-catalyzed signal amplification, the present assays enable highly sensitive and selective detection of these targets with zero-background. These assays can also be applied to detect target in spiked serum samples, demonstrating the potential for point-of-care detection of clinical samples.

Base excision repair-inspired DNA motor powered by intracellular apurinic/apyrimidinic endonuclease

The transition of DNA nanomachines from test tubes to living cells would realize the ultimate goal of smart therapeutic dynamic DNA nanotechnology. The operation of DNA nanomachines in living cells remains challenging because it is difficult to utilize an endogenous driving force. Inspired by the base excision repair (BER) process, we demonstrate a 'burnt-bridge' DNA motor system powered by intracellular apurinic/apyrimidinic (AP) endonuclease APE1. The high specificity of APE1 to the AP site in double-stranded DNA permits directional and autonomous movement. The advanced single-molecule fluorescence technique was utilized to directly monitor the stepwise movement of the motor strand, confirming the excellent controllability and processivity of this system. The speed of this DNA motor relies highly on APE1 concentration, allowing discrimination by APE1 level against cancer cells and normal cells. Western blot was used to confirm APE1 expression level. Successful operation of the DNA motor in living cells demonstrates that an endogenous enzyme can operate the rationally designed DNA nanostructures in a programmable way, rather than digesting simple molecular probes. This is useful and practicable for broad application, such as for cellular diagnostic tools, gene regulators for DNA repair, and enzyme-mediated drug delivery.

A review on optical imaging of DNA nanostructures and dynamic processes

DNA self-assembly offers a powerful means to construct complex nanostructures and program dynamic molecular processes such as strand displacement. DNA nanosystems pack high structural complexity in a small scale (typically, <100 nm) and span dynamic features over long periods of time, which bring new challenges for characterizations. The spatial and temporal features of DNA nanosystems require novel experimental methods capable of high resolution imaging over long time periods. This article reviews recent advances in optical imaging methods for characterizing self-assembled DNA nanosystems, with particular emphasis on super-resolved fluorescence microscopy. Several advanced strategies are developed to obtain accurate and detailed images of intricate DNA nanogeometries and to perform precise tracking of molecular motions in dynamic processes. We present state-of-the-art instruments and imaging strategies including localization microscopy and spectral imaging. We discuss how they are used in biological studies and biomedical applications, and also provide current challenges and future outlook. Overall, this review serves as a practical guide in optical microscopy for the field of DNA nanotechnology.

Stimuli-Responsive DNA-Switchable Biointerfaces

Switchable interfaces, also known as smart interfaces, can alter their macroscopic properties in response to external stimuli. Compared to an artificial switchable interface, DNA-based switchable biointerfaces have high diversity, uniformity, reproducibility, and functionality and are easily designed and developed with atomic precision because the sequence of the DNA strand strictly governs the structural and active properties of its assembly. Moreover, various structures such as double strands based on the Watson-Crick base-pairing rule, G-quadruplexes, i-Motifs, triplexes, and parallel-stranded duplexes exist between or among DNA strands to enrich the structures of DNA biointerfaces. In this article, the design, stimulus responses, and applications of switchable DNA biointerfaces were discussed in terms of single-switch, dual-response, and sequential operation. The applications related to sensing, imaging, delivery, logic gates, and nanomechines were introduced in terms of the design and construction of DNA biointerfaces. Future directions and challenges were also outlined for this rapidly emerging field.

Design and Synthesis of a Reconfigurable DNA Accordion Rack

DNA nanostructure-based mechanical systems or DNA nanomachines, which produce complex nanoscale motion in 2D and 3D in the nanometer to ångström resolution, show great potential in various fields of nanotechnology such as the molecular reactors, drug delivery, and nanoplasmonic systems. The reconfigurable DNA accordion rack, which can collectively manipulate a 2D or 3D nanoscale network of elements, in multiple stages in response to the DNA inputs, is described. The platform has potential to increase the number of elements that DNA nanomachines can control from a few elements to a network scale with multiple stages of reconfiguration. In this protocol, we describe the entire experimental process of the reconfigurable DNA accordion rack of 6 by 6 meshes. The protocol includes a design rule and simulation procedure of the structures and a wet-lab experiment for synthesis and reconfiguration. In addition, analysis of the structure using TEM (transmission electron microscopy) and FRET (fluorescence resonance energy transfer) is included in the protocol. The novel design and simulation methods covered in this protocol will assist researchers to use the DNA accordion rack for further applications.

A pH-controlled bidirectionally pure DNA hydrogel: reversible self-assembly and fluorescence monitoring

A concept for a pure DNA hydrogel has been demonstrated in which triplex structures act as the core components and are assisted by single strands and artfully designed Y-shaped structures. Typically, the triplex structure which is based on protonated cytosine-guanine-cytosine (C-G·C+) is formed at pH 5.0 and disassembles at pH 7.0, whereas the thymine-adenine-thymine (T-A·T)-based triplex structure is formed at pH 7.0 and disassembles at pH 10.0. Therefore, such triplex DNA structure-based pure DNA hydrogels provide pH-controlled reversible self-assembly of DNA structures with a transition between gel and liquid states. More significantly, the introduction of both a fluorophore (FAM) and a quencher (BHQ1) to the hydrogels provides an innovative method for monitoring the self-assembly and disassembly processes through a fluorescence technology.

Azobenzene as a photoregulator covalently attached to RNA: a quantum mechanics/molecular mechanics-surface hopping dynamics study

Azobenzene covalently attached to RNA undergoes trans-to-cis photo-switching on a time scale of ∼15 picoseconds – 30 times slower than in vacuo.

The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA–azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a β-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ∼10–15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA–azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.

Recent developments in reversible photoregulation of oligonucleotide structure and function

There is a growing interest in the photoregulation of biological functions, due to the high level of spatiotemporal precision achievable with light. Additionally, light is non-invasive and waste-free. In particular, the photoregulation of oligonucleotide structure and function is a rapidly developing study field with relevance to biological, physical and material sciences. Molecular photoswitches have been incorporated in oligonucleotides for 20 years, and the field has currently grown beyond fundamental studies on photochemistry of the switches and DNA duplex stability, and is moving towards applications in chemical biology, nanotechnology and material science. Moreover, the currently emerging field of photopharmacology indicates the relevance of photocontrol in future medicine. In recent years, a large number of publications has appeared on photoregulation of DNA and RNA structure and function. New strategies are evaluated and novel, exciting applications are shown. In this comprehensive review, the key strategies for photoswitch inclusion in oligonucleotides are presented and illustrated with recent examples. Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design. Finally, we identify the challenges that the field currently faces and look forward to future applications.

Autonomous DNA nanomachine based on cascade amplification of strand displacement and DNA walker for detection of multiple DNAs

DNA can be modified to function as a scaffold for the construction of a DNA nanomachine, which can then be used in analytical applications if the DNA nanomachine can be triggered by the presence of a diagnostic DNA or some other analyte. We herein propose a novel and powerful DNA nanomachine that can detect DNA via combining the tandem strand displacement reactions and a DNA walker. Three different DNA sensing platforms are described, where the whole DNA machine was constructed on a gold electrode (GE). This cascade multiple amplification strategy exhibited an excellent sensitivity. Under optimal conditions, the electrochemical sensor could achieve a detection limit of 36 fM with a linear range from 50 to 500 fM. In particular, the electrochemical sensor could easily distinguish the base mutations. More interestingly, the DNA nanomachine could be used to construct analog AND and OR logic gates. We demonstrate that electrochemical signals generated from the different input combinations can be used to distinguish multiple target DNAs. The practical applicability of the present biosensor is demonstrated by the detection of target DNA in human serum with satisfactory results, which holds great potential for a future application in clinical diagnosis.

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.

A ratiometric electrochemical biosensor for the exosomal microRNAs detection based on bipedal DNA walkers propelled by locked nucleic acid modified toehold mediate strand displacement reaction

Sensitive and selective detection of microRNAs (miRNAs) in cancer cells derived exosomes have attracted rapidly growing interest owing to their potential in diagnostic and prognostic applications. Here, we design a ratiometric electrochemical biosensor based on bipedal DNA walkers for the attomolar detection of exosomal miR-21. In the presence of miR-21, DNA walkers are activated to walk continuously along DNA tracks, resulting in conformational changes as well as considerable increases of the signal ratio produced by target-respond and target-independent reporters. With the signal cascade amplification of DNA walkers, the biosensor exhibits ultrahigh sensitivity with the limit of detection (LOD) down to 67 aM. Furthermore, owing to the background-correcting function of target-independent reporters termed as reference reporters, the biosensor is robust and stable enough to be applied in the detection of exosomal miR-21 extracted from breast cancer cell lines and serums. In addition, because locked nucleic acid (LNA) modified toehold mediate strand displacement reaction (TMSDR) has extraordinary discriminative ability, the biosensor displays excellent selectivity even against the single-base-mismatched target. It is worth mentioning that our sensor is regenerative and stable for at least 5 cycles without diminution in sensitivity. In brief, the high sensitivity, selectivity and reproducibility, together with cheap, make the proposed biosensor a promising approach for exosomal miRNAs detection, in conjunction with early point-of-care testing (POCT) of cancer.

A microRNA-initiated DNAzyme motor operating in living cells

Synthetic DNA motors have great potential to mimic natural protein motors in cells but the operation of synthetic DNA motors in living cells remains challenging and has not been demonstrated. Here we report a DNAzyme motor that operates in living cells in response to a specific intracellular target. The whole motor system is constructed on a 20 nm gold nanoparticle (AuNP) decorated with hundreds of substrate strands serving as DNA tracks and dozens of DNAzyme molecules each silenced by a locking strand. Intracellular interaction of a target molecule with the motor system initiates the autonomous walking of the motor on the AuNP. An example DNAzyme motor responsive to a specific microRNA enables amplified detection of the specific microRNA in individual cancer cells. Activated by specific intracellular targets, these self-powered DNAzyme motors will have diverse applications in the control and modulation of biological functions.

Synthetic DNA nanomachines have been designed to perform a variety of tasks in vitro. Here, the authors build a nanomotor system that integrates a DNAzyme and DNA track on a gold nanoparticle, to facilitate cellular uptake, and apply it as a real-time miRNA imaging tool in living cells.

DNA Walkers as Transport Vehicles of Nanoparticles Along a Carbon Nanotube Track

DNA-based molecular motors are synthetic analogs of naturally occurring protein motors. Typical DNA walkers are constructed from synthetic short DNA strands and are powered by various free energy changes during hybridization reactions. Due to the constraints set by their small physical dimension and slow kinetics, most DNA walkers are characterized by ensemble measurements that result in averaged kinetics data. Here we present a synthetic DNA walker system that exploits the extraordinary physicochemical properties of nanomaterials and the functionalities of DNA molecules, which enables real-time control and monitoring of single-DNA walkers over an extended period.

Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers

DNA walkers are designed with the structural specificity and functional diversity of oligonucleotides to actively convert chemical energy into mechanical translocation. Compared to natural protein motors, DNA walkers' small translocation distance (mostly <100 nm) and slow reaction rate (<0.1 nm s^-1) make single-molecule characterization of their kinetics elusive. An important indication of single-walker kinetics is the rate-limiting reactions that a particular walker design bears. We introduce an integrated super-resolved fluorescence microscopy approach that is capable of long-term imaging to investigate the stochastic behavior of DNA walkers. Subdiffraction tracking and imaging in the visible and second near-infrared spectra resolve walker structure and reaction rates. The distributions of walker kinetics are analyzed using a stochastic model to reveal reaction randomness and the rate-limiting biochemical reaction steps.

DNA-based nanoscale walking devices and their applications

Herein we review DNA-based nanoscale walking devices including unipedal, bipedal, multipedal, and other novel walking devices and their applications.

A catalytic assembled enzyme-free three-dimensional DNA walker and its sensing application

A novel and enzyme-free three-dimensional DNA walker powered by catalytic assembly has been constructed.

Photocaged G-Quadruplex DNAzyme and Aptamer by Post-Synthetic Modification on Phosphodiester Backbone

G-quadruplex-containing DNAzymes and aptamers are widely applied in many research fields because of their high stability and prominent activities versus the protein counterparts. In this work, G-quadruplex DNAs were equipped with photolabile groups to construct photocaged DNAzymes and aptamers. We incorporated TEEP-OH (thioether-enol phosphate, phenol substituted) into phosphodiester backbone of G-quadruplex DNA by a facile post-synthetic method to achieve efficient photocaging of their activities. Upon light irradiation, the peroxidase-mimicking activity of the caged G-quadruplex DNAzyme was activated, through the transformation of TEEP-OH into a native DNA phosphodiester without any artificial scar. Similarly, the caged G-quadruplex thrombin-binding aptamer also showed light-induced activation of thrombin inhibition activity. This method could serve as a general strategy to prepare photocaged G-quadruplex DNA with other activities for noninvasive control of their functions.

Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity

Because oligonucleotides are short sequences of nucleic acid bases, their association in solution with complementary strands (hybridization) is often seen to conform to a simple two-state model. However, experimental evidence suggests that, despite their short length, oligonucleotides may hybridize through multiple states involving intermediates. We investigate whether these apparently contradictory scenarios are possible by imposing different levels of sequence specificity on a lattice model of oligonucleotides in solution, which we introduced in Part I [J. C. Araque et al., J. Chem. Phys. 134, 165103 (2011)]. We find that both multiple-intermediate (weakly cooperative) and two-state (strongly cooperative) transitions are possible and that these are directly linked to the level of sequence specificity. Sequences with low specificity hybridize (base-by-base) by way of multiple stable intermediates with increasing number of paired bases. Such intermediate states are weakly cooperative because the energetic gain from adding an additional base pair is outweighed by the conformational entropy loss. Instead, sequences with high specificity hybridize through multiple metastable intermediates which easily bridge the configurational and energetic gaps between single- and double-stranded states. These metastable intermediates interconvert with minimal loss of conformational entropy leading to a strongly cooperative hybridization. The possibility of both scenarios, multiple- and two-states, is therefore encoded in the specificity of the sequence which in turn defines the level of cooperativity.

Catalytic Hairpin Assembly Actuated DNA Nanotweezer for Logic Gate Building and Sensitive Enzyme-Free Biosensing of MicroRNAs

A target-switched DNA nanotweezer is designed for AND logic gate operation and enzyme-free detection of microRNAs (miRNAs) by catalytic hairpin assembly (CHA) and proximity-dependent DNAzyme formation. The double crossover motif-based nanotweezer consists of an arched structure as the set strand for target inputs and two split G-rich DNAs at the termini of two arms for signal output. Upon a CHA, a small amount of binary target inputs can switch numerous open nanotweezers to a closed state, which leads to the formation of proximity-dependent DNAzyme in the presence of hemin to produce a highly sensitive biosensing system. The binary target inputs can be used for successful building of AND logic gate, which is validated by polyacrylamide gel electrophoresis, surface plasmon resonance and the biosensing signal. The developed biosensing system shows a linear response of the output chemiluminescence signal to input binary miRNAs with a detection limit of 30 fM. It can be used for miRNAs analysis in complex sample matrix. This system provides a simple and reusable platform for logic gate operation and enzyme-free, highly sensitive, and specific multianalysis of miRNAs.

DNA Walker-Regulated Cancer Cell Growth Inhibition

We demonstrate a DNAzyme-based walker system as a controlled oligonucleotide drug AS1411 release platform for breast cancer treatment. In this system, AS1411 strands are released from fuel strands as a walker moves along its carbon nanotube track. The release rate and amount of anticancer oligonucleotides are controlled by the walker operation. With a walker system embedded within the collagen extracellular matrix, we show that this drug release system can be used for in situ cancer cell growth inhibition.

Postsynthetic Modification of DNA Phosphodiester Backbone for Photocaged DNAzyme

Photocaged (photoactivatable) biomolecules are powerful tools for noninvasive control of biochemical activities by light irradiation. DNAzymes (deoxyribozymes) are single-stranded oligonucleotides with a broad range of enzymatic activities. In this work, to construct photocaged DNAzymes, we developed a facile and mild postsynthetic method to incorporate an interesting photolabile modification (thioether-enol phosphate, phenol substituted, TEEP-OH) into readily available phosphorothioate DNA. Upon light irradiation, TEEP-OH transformed into a native DNA phosphodiester, and accordingly the DNAzymes with RNA-cleaving activities were turned "on" from its inactive and caged form. Activation of the TEEP-OH-caged DNAzyme by light was also successful inside live cells.