Towards DNA Nanomachines for Cancer Treatment: Achieving Selective and Efficient Cleavage of Folded RNA

Cleaving Folded RNA by Multifunctional DNAzyme Nanomachines

Both tight and specific binding of folded biological mRNA is required for gene silencing by oligonucleotide gene therapy agents. However, this is fundamentally impossible using the conventional oligonucleotide probes according to the affinity/specificity dilemma. This study addresses this problem for cleaving folded RNA by using multicomponent agents (dubbed 'DNA nanomachine' or DNM). DNMs bind RNA by four short RNA binding arms, which ensure tight and highly selective RNA binding. Along with the improved affinity, DNM maintain the high sequence selectivity of the conventional DNAzymes. DNM enabled up to 3-fold improvement in DNAzymes catalytic efficiency (kcat/Km) by facilitating both RNA substrate binding and product release steps of the catalytic cycle. This study demonstrates that multicomponent probes organized in sophisticated structures can help to achieve the balance between affinity and selectivity in recognizing folded RNA and thus creates a foundation for applying complex DNA nanostructures derived by DNA nanotechnology in gene therapy.

Multivalent DNAzyme agents for cleaving folded RNA

Multivalent recognition and binding of biological molecules is a natural phenomenon that increases the binding stability (avidity) without decreasing the recognition specificity. In this study, we took advantage of this phenomenon to increase the efficiency and maintain high specificity of RNA cleavage by DNAzymes (Dz). We designed a series of DNA constructs containing two Dz agents, named here bivalent Dz devices (BDD). One BDD increased the cleavage efficiency of a folded RNA fragment up to 17-fold in comparison with the Dz of a conventional design. Such an increase was achieved due to both the improved RNA binding and the increased probability of RNA cleavage by the two catalytic cores. By moderating the degree of Dz agent association in BDD, we achieved excellent selectivity in differentiating single-base mismatched RNA, while maintaining relatively high cleavage rates. Furthermore, a trivalent Dz demonstrated an even greater efficiency than the BDD in cleaving folded RNA. The data suggests that the cooperative action of several RNA-cleaving units can significantly improve the efficiency and maintain high specificity of RNA cleavage, which is important for the development of Dz-based gene knockdown agents.

RNase H-dependent DNA thresholder modulated by cancer marker concentration

Threshold antisense oligonucleotide constructs were designed to cleave mRNA within different biomarker concentrations. The mRNA cleavage is activated by 2.6, 7.5 or 39.5 nM of biomarker depending on the construct design. The constructs can be used to differentiate cancer from normal cells by the level of oncogene expression followed by silencing of a targeted gene.

Towards the development of a DNA automaton: modular RNA-cleaving deoxyribozyme logic gates regulated by miRNAs

Advancements in DNA computation have unlocked molecular-scale information processing possibilities, utilizing the intrinsic properties of DNA for complex logical operations with transformative applications in biomedicine. DNA computation shows promise in molecular diagnostics, enabling precise and sensitive detection of genetic mutations and disease biomarkers. Moreover, it holds potential for targeted gene regulation, facilitating personalized therapeutic interventions with enhanced efficacy and reduced side effects. Herein, we have developed six DNAzyme-based logic gates able to process YES, AND, and NOT Boolean logic. The novelty of this work lies in their additional functionalization with a common DNA scaffold for increased cooperativity in input recognition. Moreover, we explored hierarchical input binding to multi-input logic gates, which helped gate optimization. Additionally, we developed a new design of an allosteric hairpin switch used to implement NOT logic. All DNA logic gates achieved the desired true-to-false output signal when detecting a panel of miRNAs, known for their important role in malignancy regulation. This is the first example of DNAzyme-based logic gates having all input-recognizing elements integrated in a single DNA nanostructure, which provides new opportunities for building DNA automatons for diagnosis and therapy of human diseases.

Cleaving Folded RNA with DNAzyme Agents

Cleavage of biological mRNA by DNAzymes (Dz) has been proposed as a variation of oligonucleotide gene therapy (OGT). The design of Dz-based OGT agents includes computational prediction of two RNA-binding arms with low affinity (melting temperatures (Tm ) close to the reaction temperature of 37 °C) to avoid product inhibition and maintain high specificity. However, RNA cleavage might be limited by the RNA binding step especially if the RNA is folded in secondary structures. This calls for the need for two high-affinity RNA-binding arms. In this study, we optimized 10-23 Dz-based OGT agents for cleavage of three RNA targets with different folding energies under multiple turnover conditions in 2 mM Mg2+ at 37 °C. Unexpectedly, one optimized Dz had each RNA-binding arm with a Tm ≥60 °C, without suffering from product inhibition or low selectivity. This phenomenon was explained by the folding of the RNA cleavage products into stable secondary structures. This result suggests that Dz with long (high affinity) RNA-binding arms should not be excluded from the candidate pool for OGT agents. Rather, analysis of the cleavage products' folding should be included in Dz selection algorithms. The Dz optimization workflow should include testing with folded rather than linear RNA substrates.

Multicomponent DNAzyme Nanomachines: Structure, Applications, and Prospects

Nucleic acids (NAs) are important components of living organisms responsible for the storage and transmission of hereditary information. They form complex structures that can self-assemble and bind to various biological molecules. DNAzymes are NAs capable of performing simple chemical reactions, which makes them potentially useful elements for creating DNA nanomachines with required functions. This review focuses on multicomponent DNA-based nanomachines, in particular on DNAzymes as their main functional elements, as well as on the structure of DNAzyme nanomachines and their application in the diagnostics and treatment of diseases. The article also discusses the advantages and disadvantages of DNAzyme-based nanomachines and prospects for their future applications. The review provides information about new technologies and the possibilities of using NAs in medicine.

Visual Detection of Stem-Loop Primer Amplification (SPA) Products without Denaturation Using Peroxidase-like DNA Machines (PxDM)

Rapid, inexpensive, and accurate determination of nucleic acids is a decisive factor in evaluating population's health and monitoring treatment at point-of-care (POC) settings. Testing systems with visual outputs can provide instrument-free signal detection. Isothermal amplification technologies can substitute conventional polymerase chain reaction (PCR) testing due to compatibility with the POC diagnostic. Here, we have visually detected DNA fragments obtained by stem-loop-primer-assisted isothermal amplification (SPA), but not those obtained by PCR or LAMP amplification using DNA nanomachines with peroxidase-like activity (PxDM) with sensitivity to a single nucleotide substitution. Compared to the diagnostics with conventional loop-mediated isothermal amplification (LAMP), the PxDM method produces no false positive signals with the non-specific amplification products. The study suggests that PxDM, in conjunction with SPA isothermal amplification, can become a valid platform for POC testing systems.

Ultrasensitive Electrochemiluminescence Biosensor Based on 2D Co3O4 Nanosheets as a Coreaction Accelerator and Highly Ordered Rolling DNA Nanomachine as a Signal Amplifier for the Detection of MicroRNA

A novel ultrasensitive electrochemiluminescence (ECL) biosensor was constructed using two-dimensional (2D) Co₃O₄ nanosheets as a novel coreaction accelerator of the luminol/H₂O₂ ECL system for the detection of microRNA-21 (miRNA-21). Impressively, coreaction accelerator 2D Co₃O₄ nanosheets with effective mutual conversion of the Co²⁺/Co³⁺ redox pair and abundant active sites could promote the decomposition of coreactant H₂O₂ to generate more superoxide anion radicals (O₂^•-), which reacted with luminol for significantly enhancing ECL signals. Furthermore, the trace target miRNA-21 was transformed into a large number of G-wires through the strand displacement amplification (SDA) process to self-assemble the highly ordered rolling DNA nanomachine (HORDNM), which could tremendously improve the detection sensitivity of biosensors. Hence, on the basis of the novel luminol/H₂O₂/2D Co₃O₄ nanosheet ternary ECL system, the biosensor implemented ultrasensitive detection of miRNA-21 with a detection limit as low as 4.1 aM, which provided a novel strategy to design an effective ECL emitter for ultrasensitive detection of biomarkers for early disease diagnosis.

Construction and Application of DNAzyme-based Nanodevices

The development of stimuli-responsive nanodevices with high efficiency and specificity is very important in biosensing, drug delivery, and so on. DNAzymes are a class of DNA molecules with the specific catalytic activity. Owing to their unique catalytic activity and easy design and synthesis, the construction and application of DNAzymes-based nanodevices have attracted much attention in recent years. In this review, the classification and properties of DNAzyme are first introduced. The construction of several common kinds of DNAzyme-based nanodevices, such as DNA motors, signal amplifiers, and logic gates, is then systematically summarized. We also introduce the application of DNAzyme-based nanodevices in sensing and therapeutic fields. In addition, current limitations and future directions are discussed.

A novel FRET-based dendritic hybridization chain reaction for tumour-related mRNA imaging

A novel FRET-based dendritic hybridization chain reaction (D-HCR) for TK1 mRNA imaging in living cells was developed. Compared with traditional complex D-HCR methods, it includes the advantages of having a simple design, an accurate signal and is suitable for use with living cells.

Accurate and Efficient Lipoprotein Detection Based on the HCR-DNAzyme Platform

Cardiovascular disease is one of the main causes of death in the world, which is closely associated with dyslipidemia. Dyslipidaemia is usually manifested as a relatively higher level of low-density lipoprotein (LDL) and lower level of high-density lipoprotein (HDL). Thus, the quantitative detection of the LDL and HDL particles is of great importance to predict the risk of cardiovascular diseases. However, the traditional methods can only indirectly reflect the HDL/LDL particle concentrations by detecting the cholesterol or proteins in HDL/LDL particles and are always laborious and time-consuming. Thus, the accurate and efficient approach for the detection of intact HDL and LDL particles is still lacking so far. We developed an enzyme- and isolation-free method to measure the concentration of HDL and LDL based on DNAzyme and hybridization chain reaction (HCR)-based signal amplification. This method can be used to directly and accurately detect the concentration of "actual" HDL and LDL particles instead of the cholesterol in HDL and LDL, with limits of detection of 10 and 30 mg/dL, respectively, which also satisfied the lipoprotein analysis in clinical samples. Therefore, this HCR-DNAzyme platform has great potential in clinical applications and health management.

In Situ Modulating DNAzyme Activity and Internalization Behavior with Acid-Initiated Reconfigurable DNA Nanodevice for Activatable Theranostic

DNAzyme-mediated gene silencing was still challenged by off-target toxicity. In this study, we developed a split DNAzyme-based nanodevice (sDz-ND) that leveraged acidic tumor microenvironments to drive in situ assembly, thus modulating internalization behavior and silencing activity of DNAzymes. sDz-ND consisted of two different modules, which functionalized with split DNAzyme fragments, respectively. At psychological pH (∼7.4), the two modules were monodispersed, showing cleavage anergy and quenched fluorescence. At pH 6.3, the separated modules could cross-link with each other to form integrated sDz-ND, resulting activation of theranostic function. Meanwhile, the increased particle size and acquired multivalent effect favored 2.1-fold enhanced binding ability, which further facilitated rapid endocytosis of sDz-ND into target cancer cells, then allowing DNAzyme mediated gene silencing. The strategy provides a promising and general concept for precise tumor imaging and gene therapy.

DNAzyme Walker for Homogeneous Detection of Enterovirus EV71 and CVB3

When dealing with infectious pathogens, the risk of contamination or infection in the process of detecting them is nonnegligible. Separation-free detection will be beneficial in operation and safety. In this work, we proposed a DNAzyme walker for homogeneous and isothermal detection of enterovirus. The DNAzyme is divided into two inactivate subunits. When the subunit-conjugated antibody binds to the target virus, the activity of the DNAzyme recovers as a result of spatial proximity. The walker propels, and the fluorescence recovers. The final fluorescence intensity of the reaction mixture is related to the concentration of the target virus. The detection limit of this proposed method is 6.6 × 10⁴ copies/mL for EV71 and 4.3 × 10⁴ copies/mL for CVB3, respectively. Besides, this method was applied in detection of EV71 in clinical samples with a satisfactory result. The entire experiment is easy to operate, and the proposed method has great potential for practical use.

Interrogation of highly structured RNA with multicomponent deoxyribozyme probes at ambient temperatures

Molecular analysis of RNA through hybridization with sequence-specific probes is challenging due to the intrinsic ability of RNA molecules to form stable secondary and tertiary structures. To overcome the energy barrier toward the probe-RNA complex formation, the probes are made of artificial nucleotides, which are more expensive than their natural counterparts and may still be inefficient. Here, we propose the use of a multicomponent probe based on an RNA-cleaving deoxyribozyme for the analysis of highly structured RNA targets. Efficient interrogation of two native RNA from Saccharomyces cerevisiae-a transfer RNA (tRNA) and 18S ribosomal RNA (rRNA)-was achieved at ambient temperature. We achieved detection limits of tRNA down to ∼0.3 nM, which is two orders of magnitude lower than that previously reported for molecular beacon probes. Importantly, no probe annealing to the target was required, with the hybridization assay performed at 37°C. Excess of nonspecific targets did not compromise the performance of the probe, and high interrogation efficiency was maintained by the probes even in complex matrices, such as cell lysate. A linear dynamic range of 0.3-150 nM tRNA was demonstrated. The probe can be adapted for differentiation of a single mismatch in the tRNA-probe complex. Therefore, this study opens a venue toward highly selective, sensitive, robust, and inexpensive assays for the interrogation of biological RNA.

Targeted and direct intracellular delivery of native DNAzymes enables highly specific gene silencing

DNAzymes exhibit high potential as gene silencing agents for therapeutic applications. Such purposes, however, are significantly challenged by the targeted and successful delivery of unmodified DNAzymes into cells with minimal side effects. Here, we set out to formulate and demonstrate a new stimuli-responsive and constrained aptamer/DNAzyme (Apt/Dz) catenane nanostructure for highly specific gene silencing. The rational design of the Apt/Dz catenane nanostructure with the respective integration of the aptamer sequence and the completely closed catenane format enables both the targeted capability and significantly improved nuclease resistance, facilitating the stable and targeted delivery of unmodified Dz into cancer cells. Moreover, the Dz enzymatic activity in the constrained structure can only be conditionally regulated by the specific intracellular mRNA sequences to silence the target gene with highly reduced side effects. Results show that the Apt/Dz catenane nanostructure can effectively inhibit the expression of the target gene and the proliferation of cancer cells with high specificity.

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

Nowadays a variety of biosensors are widely used in different fields, including biomedical diagnostics and self-testing. Nucleic acid-based biosensors are typically applied to detect another nucleic acid, proteins, ions, and several other types of compounds. It is most promising to develop simple and effective biosensors for the use in situations where traditional methods are not available due to their complexity and laboriousness. In this project, a novel smart deoxyribozyme-based fluorescent sensor for the detection of androgen receptor mRNA was developed. It consists of several functional modules including two deoxyribozymes 10-23, an RNA-dependent split malachite green aptamer, and an oligonucleotide platform. Deoxyribozymes specifically release a 27-nucleotide RNA fragment that is readily available for the interaction with the aptamer module. This solves a problem of secondary structure in hybridization with the target sequence of full-length mRNA. It was shown that within 24 hours the proposed sensor specifically recognized both a synthetic 60-nucleotide RNA fragment (LOD is 1.4 nM of RNA fragment at 37 °C) and a full-sized mRNA molecule of the androgen receptor. The constructed sensor is easy to use, has high efficiency and selectivity for the RNA target, and can be reconstructed for the detection of various nucleic acid sequences due to its modular structure. Thus, similar biosensors may be useful for the differential diagnosis.

Bifunctional RNA-Targeting Deoxyribozyme Nanodevice as a Potential Theranostic Agent

Theranostic approaches rely on simultaneous diagnostic of a disease and its therapy. Here, we designed a DNA nanodevice, which can simultaneously report the presence of a specific RNA target through an increase in fluorescence and cleave it. High selectivity of RNA target recognition under near physiological conditions was achieved. The proposed approach can become a basis for the design of DNA nanomachines and robots for diagnostics and therapy of viral infections, cancer, and genetic disorders.

Target-Induced Cascade Amplification for Homogeneous Virus Detection

Detection of viruses with high sensitivity is critical for the prevention and treatment of the related disease. Two homogeneous target-induced cascade amplification methods were proposed for the detection of enterovirus 71 and coxsackievirus B3. These methods both employ DNAzyme but differ in the way in which the DNAzyme is amplified. In the hybridization chain reaction (HCR)-based strategy, the DNAzyme is assembled by hairpin DNA strands, while in the rolling circle amplification (RCA)-based strategy, the DNAzyme is synthesized by the polymerase. On the basis of the virion structure, we investigated the effects of using only VP1-antibody or VP1-antibody and VP2-antibody on the detection. And the combination of two kinds of antibodies was found to further improve the performance of the detection. Subsequently, the simultaneous detection of EV71 and CVB3 was achieved by the RCA-based strategy. And the proposed methods were also applied in clinical samples analysis with a satisfactory result, showing great potential for applications in virus detection.

Sensitive Oligodeoxynucleotide Synthesis Using Dim and Dmoc as Protecting Groups

In traditional oligodeoxynucleotide (ODN) synthesis, phosphate groups are protected with the 2-cyanoethyl group, and amino groups are protected with acyl groups. At the end of ODN synthesis, deprotection is achieved with strong bases and nucleophiles. Therefore, traditional technologies are not suitable for the synthesis of ODNs containing sensitive functionalities. To address the problem, we report the use of Dim and Dmoc groups, which are based on the 1,3-dithian-2-yl-methyl function, for phosphate and amine protection for the solid phase ODN synthesis. Using the new Dim-Dmoc protection, deprotection was achieved under mild oxidative conditions without using any strong bases and nucleophiles. As a result, the new technology is suitable for the synthesis of ODNs containing sensitive functions. To demonstrate feasibility, seven 20-mer ODNs including four that contain sensitive ester and alkyl chloride groups were synthesized, purified with RP HPLC, and characterized with MALDI-TOF MS and enzyme digestion essays. High purity ODNs were obtained.

Orthogonal Activation of RNA-Cleaving DNAzymes in Live Cells by Reactive Oxygen Species

RNA-cleaving DNAzymes are useful tools for intracellular metal-ion sensing and gene regulation. Incorporating stimuli-responsive modifications into these DNAzymes enables their activities to be spatiotemporally and chemically controlled for more precise applications. Despite the successful development of many caged DNAzymes for light-induced activation, DNAzymes that can be intracellularly activated by chemical inputs of biological importance, such as reactive oxygen species (ROS), are still scarce. ROS like hydrogen peroxide (H₂ O₂ ) and hypochlorite (HClO) are critical mediators of oxidative stress-related cell signaling and dysregulation including activation of immune system as well as progression of diseases and aging. Herein, we report ROS-activable DNAzymes by introducing phenylboronate and phosphorothioate modifications to the Zn²⁺ -dependent 8-17 DNAzyme. These ROS-activable DNAzymes were orthogonally activated by H₂ O₂ and HClO inside live human and mouse cells.

Evolution of Hybridization Probes to DNA Machines and Robots

Hybridization probes are RNA or DNA oligonucleotides or their analogs that bind to specific nucleotide sequences in targeted nucleic acids (analytes) via Watson-Crick base pairs to form probe-analyte hybrids. Formation of a stable hybrid would indicate the presence of a DNA or RNA fragment complementary to the known probe sequence. Some of the well-known technologies that rely on nucleic acid hybridization are TaqMan and molecular beacon (MB) probes, fluorescent in situ hybridization (FISH), polymerase chain reaction (PCR), antisense, siRNA, and CRISPR/cas9, among others. Although invaluable tools for DNA and RNA recognition, hybridization probes suffer from several common disadvantages including low selectivity under physiological conditions, low affinity to folded single-stranded RNA and double-stranded DNA, and high cost of dye-labeled and chemically modified probes. Hybridization probes are evolving into multifunctional molecular devices (dubbed here "multicomponent probes", "DNA machines", and "DNA robots") to satisfy complex and often contradictory requirements of modern biomedical applications. In the definition used here, "multicomponent probes" are DNA probes that use more than one oligonucleotide complementary to an analyzed sequence. A "DNA machine" is an association of a discrete number of DNA strands that undergoes structural rearrangements in response to the presence of a specific analyte. Unlike multicomponent probes, DNA machines unify several functional components in a single association even in the absence of a target. DNA robots are DNA machines equipped with computational (analytic) capabilities. This Account is devoted to an overview of the ongoing evolution of hybridization probes to DNA machines and robots. The Account starts with a brief excursion to historically significant and currently used instantaneous probes. The majority of the text is devoted to the design of (i) multicomponent probes and (ii) DNA machines for nucleic acid recognition and analysis. The fundamental advantage of both designs is their ability to simultaneously address multiple problems of RNA/DNA analysis. This is achieved by modular design, in which several specialized functional components are used simultaneously for recognition of RNA or DNA analytes. The Account is concluded with the analysis of perspectives for further evolution of DNA machines into DNA robots.

Symmetric exponential amplification reaction-based DNA nanomachine for the fluorescent detection of nucleic acids

By introducing palindromic sequences into the classical exponential amplification reaction (EXPAR), we constructed a new palindromic fragment-incorporated multifunctional hairpin probe (P-HP)-mediated symmetric exponential amplification reaction (S-EXPAR), to significantly reduce the background signal caused by inherent nonspecific amplification. A G-triplex/ThT complex was used as the signal reporter for the proposed label-free DNA nanomachine. The P-HP consists of five functional regions: a C-rich region (C), a target DNA recognition region (T′), two nicking sites (X′) and a palindromic fragment (P). When target DNA (T) hybridizes with P-HP, the palindromic fragment at the 3′ end of P-HP is fully exposed. Then, the P-HP/T duplexes hybridize with each other through the exposed P, and EXPAR occurs automatically and continuously on both sides of P under the synergistic effect of polymerase and nicking endonuclease. This is called the S-EXPAR assay. In this system, one T converts to a large number of G-triplex fragments, which can combine with ThT within a short time. The G-triplex/ThT complexes formed act as the signal reporter in a label-free and environmentally friendly format. In this way, the limit of detection of this method is as low as 10 pM with a dynamic response range of 10 pM to 300 nM. In addition, this method can detect other nucleic acids by simply changing the T′ region of the P-HP. Thus, the proposed DNA nanomachine is a potential alternative method for nucleic acid detection.

This label-free and ultra-low background signal DNA nanomachine was based on P-HP mediated S-EXPAR and the G-triplex/ThT complex.