Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications

Advances in novel biosensors in biomedical applications

Biosensors, devices capable of detecting biomolecules or bioactive substances, have recently become one of the important tools in the fields of bioanalysis and medical diagnostics. A biosensor is an analytical system composed of biosensitive elements and signal-processing elements used to detect various biological and chemical substances. Biomimetic elements are key to biosensor technology and are the components in a sensor that are responsible for identifying the target analyte. The construction methods and working principles of biosensors based on synthetic biomimetic elements, such as DNAzyme, molecular imprinted polymers and aptamers, and their updated applications in biomedical analysis are summarised. Finally, the technical bottlenecks and future development prospects for biomedical analysis are summarised and discussed.

L-Histidine Modulates the Catalytic Activity and Conformational Changes of the HD3 Deoxyribozyme

Background/Objectives: Riboswitches are functional nucleic acids that regulate biological processes by interacting with small molecules, such as metabolites, influencing gene expression. Artificial functional nucleic acids, including deoxyribozymes, have been developed through in vitro selection for various catalytic functions. In a previous study, an l-histidine-dependent deoxyribozyme was identified, exhibiting RNA cleavage activity in the presence of l-histidine resembling ribonuclease catalytic mechanisms. This study aims to clarify the role of l-histidine in the activity and structural formation of the l-histidine-dependent deoxyribozyme (HD), focusing on the binding properties and conformational changes of its derivative HD3. Methods: Conformational changes in HD3 were analyzed using circular dichroism (CD) under varying concentrations of l-histidine. Direct binding analysis was conducted using carbon-14 (14C)-labeled l-histidine and a liquid scintillation counter. The catalytic activity of HD3 in the presence of different l-histidine concentrations was measured. Results: The binding constant for l-histidine-induced conformational changes (Ka(CD)) was found to be 2.0 × 103 (M-1), whereas for catalytic activity (Ka(Rxn)) and scintillation counting (Ka(RI)), it was approximately 1.0 × 103 (M-1). Conclusions: l-Histidine plays an essential role in both the catalytic activity and structural formation of the HD3 deoxyribozyme. The consistent binding constants across different experimental methods highlight the significant contribution of l-histidine to the active folding of deoxyribozymes.

Carbon dots for pathogen detection and imaging: recent breakthroughs and future trends

As a class of carbon-based nanomaterials, carbon dots (CDs) have gained a lot of interest for a variety of applications. They offer distinctive optical, chemical, and structural characteristics along with favourable attributes such as low cost, availability of abundant functional groups, remarkable chemical inertness, high stability, exceptional biocompatibility, and ecofriendliness. This review discusses synthesis methods, structural characteristics, and surface modifications of CDs, specific for pathogen detection. Furthermore, it delves into the mechanisms that govern the interaction between pathogens and CDs. In addition, the study explores the use of CDs in a number of detection modalities, such as optical, electrochemical, and electrochemiluminescence, emphasising real-time pathogen monitoring. Moreover, both the challenges and opportunities related to the application of CDs-based detection and imaging methods are highlighted in field and clinical contexts.

Recent advances in DNAzymes for bioimaging, biosensing and cancer therapy

DNAzymes, a class of single-stranded catalytic DNA with good stability, high catalytic activity, and easy synthesis, functionalization and modification properties, have garnered significant interest in the realm of biosensing and bioimaging. Their integration with fluorescent dyes or chemiluminescent moieties has led to remarkable bioimaging outcomes, while DNAzyme-based biosensors have demonstrated robust sensitivity and selectivity in detecting metal ions, nucleic acids, proteins, enzyme activities, exosomes, bacteria and microorganisms. In addition, by delivering DNAzymes into tumor cells, the mRNA therein can be cleaved to regulate the expression of corresponding proteins, which has further propelled the application of DNAzymes in cancer gene therapy and synergistic therapy. This paper reviews the strategies for screening attractive DNAzymes such as SELEX and high-throughput sequencing, and briefly describes the amplification strategies of DNAzymes, which mainly include catalytic hairpin assembly (CHA), DNA walker, hybridization chain reaction (HCR), DNA origami, CRISPR-Cas12a, rolling circle amplification (RCA), and aptamers. In addition, applications of DNAzymes in bioimaging, biosensing, and cancer therapy are also highlighted. Subsequently, the possible challenges of these DNAzymes in practical applications are further pointed out, and future research directions are suggested.

Development of a FRET aptasensor based on MoS2-doped Zn-MOF as luminophore for selective detection of cadmium in aqueous solutions

A robust "on-off" fluorescent aptasensor was developed using nanohybrids of molybdenum sulfide (MoS2) quantum dot (QD)-doped zinc metal-organic frameworks (Zn-MOF) for selective and sensitive detection of cadmium ions (Cd2+) in water. This nanohybrid (MoS2@Zn-MOF), synthesized via "bottle around the ship" methodology, exhibited a high-intensity fluorescence emission centered at 430 nm (λEm) (blue) on excitation at 320 nm (λEx). Further, the conjugation of this fluorophore to phosphate-modified cadmium aptamer (Cd-2-2) was achieved through carbodiimide reaction. The hybridization of prepared sensing probe (MoS2@Zn-MOF/Cd-2-2 aptamer) was done with dabcyl-conjugated complementary DNA (cDNA), acting as energy donor-acceptor pair in the fluorescence resonance energy transfer (FRET) system. This hybridization causes the fluorescence quenching of the nanohybrid. In the presence of Cd2+, the aptamer from the fabricated nano-biosensing probe binds to these ions, resulting in release of dabcyl-cDNA oligomer. This release of dabcyl-cDNA oligomer from the sensing probes restores the fluorescence of the nanohybrid. Under optimized conditions (sensing probe/dabcyl-cDNA ratio 1/7, pH 7.4, and temp 28 °C), the sensing probe showed a fast response time of 1 min. The fluorescence intensity of the nanohybrid can be utilized to determine the concentration of Cd2+. The proposed aptasensor achieved highly sensitive detection of Cd2+ with a limit of detection (LOD) of 0.24 ppb over the range of 1 × 10-9 to 1 × 10-4 M along with minimal effects of interferences (e.g., Hg2+, Pb2+, and Zn2+) and good reproducibility. The designed aptasensor based on MoS2@Zn-MOF nanofluorophore offers a highly sensitive and selective approach for rapid screening of metal ions in aqueous environments.

Current developments and future perspectives of nanotechnology in orthopedic implants: an updated review

Orthopedic implants are the most commonly used fracture fixation devices for facilitating the growth and development of incipient bone and treating bone diseases and defects. However, most orthopedic implants suffer from various drawbacks and complications, including bacterial adhesion, poor cell proliferation, and limited resistance to corrosion. One of the major drawbacks of currently available orthopedic implants is their inadequate osseointegration at the tissue-implant interface. This leads to loosening as a result of immunological rejection, wear debris formation, low mechanical fixation, and implant-related infections. Nanotechnology holds the promise to offer a wide range of innovative technologies for use in translational orthopedic research. Nanomaterials have great potential for use in orthopedic applications due to their exceptional tribological qualities, high resistance to wear and tear, ability to maintain drug release, capacity for osseointegration, and capability to regenerate tissue. Furthermore, nanostructured materials possess the ability to mimic the features and hierarchical structure of native bones. They facilitate cell proliferation, decrease the rate of infection, and prevent biofilm formation, among other diverse functions. The emergence of nanostructured polymers, metals, ceramics, and carbon materials has enabled novel approaches in orthopaedic research. This review provides a concise overview of nanotechnology-based biomaterials utilized in orthopedics, encompassing metallic and nonmetallic nanomaterials. A further overview is provided regarding the biomedical applications of nanotechnology-based biomaterials, including their application in orthopedics for drug delivery systems and bone tissue engineering to facilitate scaffold preparation, surface modification of implantable materials to improve their osteointegration properties, and treatment of musculoskeletal infections. Hence, this review article offers a contemporary overview of the current applications of nanotechnology in orthopedic implants and bone tissue engineering, as well as its prospective future applications.

Diverse methods of reducing and confirming false-positive results of loop-mediated isothermal amplification assays: A review

Loop-mediated isothermal amplification (LAMP), a rapid and sensitive isothermal nucleic acid amplification method, is a promising alternative to other molecular amplification techniques due to its superior specificity and sensitivity. However, due to primer dimerization, LAMP results in nonspecific and nontemplate amplification. And during the amplification confirmation process, there is carry-over contamination. These factors can result in false-positive results that overestimate the amount of DNA, preventing accurate detection. This review outlined several techniques for reducing false-positive LAMP results before amplification and confirming false-positive results after amplification. Before the amplification step, DNA polymerase activity can be decreased with organic additives such as dimethyl sulfoxide, betaine, and pullulan to prevent nonspecific amplification. The enzyme uracil-DNA-glycosylase (UDG) can eliminate false-positive results caused by carry-over contamination, and the hot-start effect with gold nanoparticles can reduce nonspecific amplification. When confirming false-positive results using clustered regularly interspaced short palindromic repeats, guide RNA accurately detects LAMP amplification, allowing differentiation from nonspecific amplification. By confirming amplification, the colorimetric change in the deoxyribozyme (DNAzyme) formed by the reaction of the G-quadruplex sequence of the LAMP amplicon and hemin can distinguish false-positive results. Lateral flow immunoassay can distinguish false-positive results by accurately recognizing hybridized probes to LAMP amplicons.

Translation of nanotechnology-based implants for orthopedic applications: current barriers and future perspective

The objective of bioimplant engineering is to develop biologically compatible materials for restoring, preserving, or altering damaged tissues and/or organ functions. The variety of substances used for orthopedic implant applications has been substantially influenced by modern material technology. Therefore, nanomaterials can mimic the surface properties of normal tissues, including surface chemistry, topography, energy, and wettability. Moreover, the new characteristics of nanomaterials promote their application in sustaining the progression of many tissues. The current review establishes a basis for nanotechnology-driven biomaterials by demonstrating the fundamental design problems that influence the success or failure of an orthopedic graft, cell adhesion, proliferation, antimicrobial/antibacterial activity, and differentiation. In this context, extensive research has been conducted on the nano-functionalization of biomaterial surfaces to enhance cell adhesion, differentiation, propagation, and implant population with potent antimicrobial activity. The possible nanomaterials applications (in terms of a functional nanocoating or a nanostructured surface) may resolve a variety of issues (such as bacterial adhesion and corrosion) associated with conventional metallic or non-metallic grafts, primarily for optimizing implant procedures. Future developments in orthopedic biomaterials, such as smart biomaterials, porous structures, and 3D implants, show promise for achieving the necessary characteristics and shape of a stimuli-responsive implant. Ultimately, the major barriers to the commercialization of nanotechnology-derived biomaterials are addressed to help overcome the limitations of current orthopedic biomaterials in terms of critical fundamental factors including cost of therapy, quality, pain relief, and implant life. Despite the recent success of nanotechnology, there are significant hurdles that must be overcome before nanomedicine may be applied to orthopedics. The objective of this review was to provide a thorough examination of recent advancements, their commercialization prospects, as well as the challenges and potential perspectives associated with them. This review aims to assist healthcare providers and researchers in extracting relevant data to develop translational research within the field. In addition, it will assist the readers in comprehending the scope and gaps of nanomedicine's applicability in the orthopedics field.

Electrochemical DNAzyme-based biosensors for disease diagnosis

DNAzyme-based electrochemical biosensors provide exceptional analytical sensitivity and high target recognition specificity for disease diagnosis. This review provides a critical perspective on the fundamental and applied impact of incorporating DNAzymes in the field of electrochemical biosensing. Specifically, we highlight recent advances in creating DNAzyme-based electrochemical biosensors for diagnosing infectious diseases, cancer and regulatory diseases. We also develop an understanding of challenges around translating the research in the field of DNAzyme-based electrochemical biosensors from labs to clinics, followed by a discussion on different strategies that can be applied to enhance the performance of the currently existing technologies to create truly point-of-care electrochemical DNAzyme biosensors.

Altering gene expression using antisense oligonucleotide therapy for hearing loss

Hearing loss affects more than 430 million people, worldwide, and is the third most common chronic physical condition in the United States and Europe (GBD Hearing Loss Collaborators, 2021; NIOSH, 2021; WHO, 2021). The loss of hearing significantly impacts motor and cognitive development, communication, education, employment, and overall quality of life. The inner ear houses the sensory organs for both hearing and balance and provides an accessible target for therapeutic delivery. Antisense oligonucleotides (ASOs) use various mechanisms to manipulate gene expression and can be tailor-made to treat disorders with defined genetic targets. In this review, we discuss the preclinical advancements within the field of the highly promising ASO-based therapies for hereditary hearing loss disorders. Particular focus is on ASO mechanisms of action, preclinical studies on ASO treatments of hearing loss, timing of therapeutic intervention, and delivery routes to the inner ear.

Recent Advances and Perspective of Nanotechnology-Based Implants for Orthopedic Applications

Bioimplant engineering strives to provide biological replacements for regenerating, retaining, or modifying injured tissues and/or organ function. Modern advanced material technology breakthroughs have aided in diversifying ingredients used in orthopaedic implant applications. As such, nanoparticles may mimic the surface features of real tissues, particularly in terms of wettability, topography, chemistry, and energy. Additionally, the new features of nanoparticles support their usage in enhancing the development of various tissues. The current study establishes the groundwork for nanotechnology-driven biomaterials by elucidating key design issues that affect the success or failure of an orthopaedic implant, its antibacterial/antimicrobial activity, response to cell attachment propagation, and differentiation. The possible use of nanoparticles (in the form of nanosized surface or a usable nanocoating applied to the implant’s surface) can solve a number of problems (i.e., bacterial adhesion and corrosion resilience) associated with conventional metallic or non-metallic implants, particularly when implant techniques are optimised. Orthopaedic biomaterials’ prospects (i.e., pores architectures, 3D implants, and smart biomaterials) are intriguing in achieving desired implant characteristics and structure exhibiting stimuli-responsive attitude. The primary barriers to commercialization of nanotechnology-based composites are ultimately discussed, therefore assisting in overcoming the constraints in relation to certain pre-existing orthopaedic biomaterials, critical factors such as quality, implant life, treatment cost, and pain alleviation.

DNA-based enzymatic systems and their applications

DNA strands with unique secondary structures can catalyze various chemical reactions and mimic natural enzymes with the assistance of cofactors, which have attracted much research attention. At the same time, the emerging DNA nanotechnology provides an efficient platform to organize functional components of the enzymatic systems and regulate their catalytic performances. In this review, we summarize the recent progress of DNA-based enzymatic systems. First, DNAzymes (Dzs) are introduced, and their versatile utilities are summarized. Then, G-quadruplex/hemin (G4/hemin) Dzs with unique oxidase/peroxidase-mimicking activities and representative examples where these Dzs served as biosensors are explicitly elaborated. Next, the DNA-based enzymatic cascade systems fabricated by the structural DNA nanotechnology are depicted. In addition, the applications of catalytic DNA nanostructures in biosensing and biomedicine are included. At last, the challenges and the perspectives of the DNA-based enzymatic systems for practical applications are also discussed.

Photoelectrochemical aptasensors for detection of viruses

Photoelectrochemistry (PEC) is a dynamic discipline studying the effect of light on photoelectrode or photosensitive material, and the conversion from solar energy into electrical power. The basic PEC process refers to the oxidation or reduction reactions between electrochemical active species in solution and photoactive materials that occurred at the electrode/electrolyte interface during illumination. In recent years, the PEC biosensing approaches have also been developed by the combination of the PEC technique with bioanalysis, where the interaction between biological recognition element and analyte influences a photocurrent signal. This involves the charge and energy transfer of PEC reaction between electron donor/acceptor and photoactive material upon light irradiation. Coupling the advantages of PEC bioanalysis and aptamers has provided new concepts for highly selective and sensitive biosensors development, applicable in human health monitoring and environmental protection. In a typical assay, a photoactive material converts the affinity binding properties of aptamers into a detectable electrical signal, presenting an innovative method for probing numerous aptamer-analyte interactions. Using different aptamer probes aiming for specific purposes, more sensing strategies with rational design and exquisite signaling mechanisms have been proposed. This review concentrated on the current topic of PEC aptasensors that are used for the detection of viruses. The prospects in this area are also discussed.

Graphical abstract

Fluorescence-Based Kinetic Measurements for RNA-Cleaving DNAzymes

Studying the catalytic behavior of biocatalysts under different conditions including temperature, buffer conditions, and cofactor concentrations is an important tool to understand their reaction mechanism. We describe two protocols that allow for the investigation of the catalysis of RNA-cleaving DNAzymes. The techniques include the use of FRET-labeled RNA substrates for studying the RNA-cleavage reaction in real-time under high throughput as well as RNA substrates labeled with a fluorescein molecule at the 5' end for gel-based assays. Both methods allow for an accurate determination of rate constants given a reaction model.

Delivery of therapeutic oligonucleotides in nanoscale

Therapeutic oligonucleotides (TOs) represent one of the most promising drug candidates in the targeted cancer treatment due to their high specificity and capability of modulating cellular pathways that are not readily druggable. However, efficiently delivering of TOs to cancer cellular targets is still the biggest challenge in promoting their clinical translations. Emerging as a significant drug delivery vector, nanoparticles (NPs) can not only protect TOs from nuclease degradation and enhance their tumor accumulation, but also can improve the cell uptake efficiency of TOs as well as the following endosomal escape to increase the therapeutic index. Furthermore, targeted and on-demand drug release of TOs can also be approached to minimize the risk of toxicity towards normal tissues using stimuli-responsive NPs. In the past decades, remarkable progresses have been made on the TOs delivery based on various NPs with specific purposes. In this review, we will first give a brief introduction on the basis of TOs as well as the action mechanisms of several typical TOs, and then describe the obstacles that prevent the clinical translation of TOs, followed by a comprehensive overview of the recent progresses on TOs delivery based on several various types of nanocarriers containing lipid-based nanoparticles, polymeric nanoparticles, gold nanoparticles, porous nanoparticles, DNA/RNA nanoassembly, extracellular vesicles, and imaging-guided drug delivery nanoparticles.

A Novel DNAzyme Signal Amplification-based Colorimetric Method for RNase H Assays

A simple visual strategy was developed for the RNase H colorimetric measurement using DNAzyme-mediated signal amplification. When RNase H was presented, the RNA strand of the duplex formed by the G-rich DNA sequence (G-Rich) and its complementary RNA sequence (cp-RNA) was digested, releasing G-Rich to form HRP-mimicking DNAzymes of the G-quadruplex/hemin complexes in the presence of hemin. These DNAzymes catalyze the oxidation reaction of the substrate of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) to produce green-color products of ABTS^•-, allowing for the detection of RNase H. A horseradish peroxidase (HRP)-mimicking DNAzyme of the G-quadruplex/hemin complex was used to mediate the signal amplification in the sensing strategy, resulting in high selectivity and sensitivity. This proposed colorimetric method shows a low detection limit of 0.04 U/mL, with a detection range of 0.1 to 3 U/mL. Moreover, this colorimetric method has been successfully used for RNase H assays in complicated biosamples, such as cell lysates. These results indicate that our colorimetric method not only detects RNase H in an ideal system, but also in real samples.

DNAzyme-Based Biosensors: Immobilization Strategies, Applications, and Future Prospective

Since their discovery almost three decades ago, DNAzymes have been used extensively in biosensing. Depending on the type of DNAzyme being used, these functional oligonucleotides can act as molecular recognition elements within biosensors, offering high specificity to their target analyte, or as reporters capable of transducing a detectable signal. Several parameters need to be considered when designing a DNAzyme-based biosensor. In particular, given that many of these biosensors immobilize DNAzymes onto a sensing surface, selecting an appropriate immobilization strategy is vital. Suboptimal immobilization can result in both DNAzyme detachment and poor accessibility toward the target, leading to low sensing accuracy and sensitivity. Various approaches have been employed for DNAzyme immobilization within biosensors, ranging from amine and thiol-based covalent attachment to non-covalent strategies involving biotin-streptavidin interactions, DNA hybridization, electrostatic interactions, and physical entrapment. While the properties of each strategy inform its applicability within a proposed sensor, the selection of an appropriate strategy is largely dependent on the desired application. This is especially true given the diverse use of DNAzyme-based biosensors for the detection of pathogens, metal ions, and clinical biomarkers. In an effort to make the development of such sensors easier to navigate, this paper provides a comprehensive review of existing immobilization strategies, with a focus on their respective advantages, drawbacks, and optimal conditions for use. Next, common applications of existing DNAzyme-based biosensors are discussed. Last, emerging and future trends in the development of DNAzyme-based biosensors are discussed, and gaps in existing research worthy of exploration are identified.

Rapid detection of Pseudomonas aeruginosa using a DNAzyme-based sensor

In the present study, a DNAzyme was screened in vitro through the use of a DNA library and crude extracellular mixture (CEM) of Pseudomonas aeruginosa. Following eight rounds of selection, a DNAzyme termed PAE-1 was obtained, which displayed high rates of cleavage with strong specificity. A fluorescent biosensor was designed for the detection of P. aeruginosa in combination with the DNAzyme. A detection limit as low as 1.2 cfu/ml was observed. Using proteases and filtration, it was determined that the target was a protein with a molecular weight of 10 kDa-50 kDa. The DNAzyme was combined with a polystyrene board to construct a simple indicator plate sensor which produced a color that identified the target within 10 min. The results were reliable when tap water and food samples were tested. The present study provides a novel experimental strategy for the development of sensors based on a DNAzyme to rapidly detect P. aeruginosa in the field.

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.

Zn2+-dependent DNAzymes that cleave all combinations of ribonucleotides

Although several DNAzymes are known, their utility is limited by a narrow range of substrate specificity. Here, we report the isolation of two zinc-dependent DNAzymes, ZincDz1 and ZincDz2, which exhibit compact catalytic core sequences with highly versatile hydrolysis activity. They were selected through in vitro selection followed by deep sequencing analysis. Despite their sequence similarity, each DNAzyme showed different Zn²⁺-concentration and pH-dependent reaction profiles, and cleaved the target RNA sequences at different sites. Using various substrate RNA sequences, we found that the cleavage sequence specificity of ZincDz2 and its highly active mutant ZincDz2-v2 to be 5'-rN↓rNrPu-3'. Furthermore, we demonstrated that the designed ZincDz2 could cut microRNA miR-155 at three different sites. These DNAzymes could be useful in a broad range of applications in the fields of medicine and biotechnology.

Toward Sub-Diffraction Imaging of Single-DNA Molecule Sensors Based on Stochastic Switching Localization Microscopy

The natural characteristics of deoxyribonucleic acid (DNA) enable its advanced applications in nanotechnology as a special tool that can be detected by high-resolution imaging with precise localization. Super-resolution (SR) microscopy enables the examination of nanoscale molecules beyond the diffraction limit. With the development of SR microscopy methods, DNA nanostructures can now be optically assessed. Using the specific binding of fluorophores with their target molecules, advanced single-molecule localization microscopy (SMLM) has been expanded into different fields, allowing wide-range detection at the single-molecule level. This review discusses the recent progress in the SR imaging of DNA nano-objects using SMLM techniques, such as direct stochastic optical reconstruction microscopy, binding-activated localization microscopy, and point accumulation for imaging nanoscale topography. Furthermore, we discuss their advantages and limitations, present applications, and future perspectives.

Co-delivery of doxorubicin and DNAzyme using ZnO@polydopamine core-shell nanocomposites for chemo/gene/photothermal therapy

Multi-modal nanomedicines that synergistically combine chemo-, gene-, and photothermal therapy have shown great potential for cancer treatment. In this study, a core-shell nanosystem-based on a zinc oxide (ZnO) nanocore and a polydopamine (PDA) shell was constructed to integrate chemo- (doxorubicin, DOX), gene- (DNAzyme, DZ), and photothermal (PDA layer) therapy in one system. Instead of small interfering RNAs, we employed DZ for tumor-related gene (survivin) regulation owing to its higher stability, biocompatibility, and predictable activity. DOX and amino-modified DZ were loaded onto the PDA shell via physisorption and covalent conjugation, respectively. Specifically, the ZnO nanocore was designed as a metal cofactor reservoir to release Zn²⁺ in response to intracellular stimuli, which triggered the activation of DZ for gene silencing after endocytosis into cells. Both in vitro and in vivo experiments demonstrated the enhanced anti-tumor efficacy of these multifunctional nanocomposites and highlighted the advantages of these nano-drug delivery systems to alleviate the side effects of DOX. This study provides a strategy for synergistic cancer therapy via chemo/gene/photothermal combination and offers a strategy to harness DZ as a gene-silencing tool for disease treatment in combination with other therapeutic modalities. STATEMENT OF SIGNIFICANCE: In this work, we constructed a core-shell nanosystem containing a zinc oxide (ZnO) nanocore and a polydopamine (PDA) outer layer, which integrated chemo- (doxorubicin, DOX), gene- (DNAzyme, DZ), and photothermal (PDA layer) therapies for multimodal cancer therapy. Specifically, the ZnO core was incorporated to solve the key issue of DZ for gene silencing applications, which acted as the metal cofactor reservoir to release Zn²⁺ inside cells for effective DZ activation. In addition, the PDA shell could detoxify the ZnO by scavenging the reactive oxygen species produced by ZnO, thus increasing the biocompatibility of the nanocarrier. This work solves the key issue of DZ for RNAi-based applications, offers a platform to combine DZ with other therapeutic modalities, and also provides a smart strategy to achieve triggered activation of biocatalytic reactions for therapeutic applications.

Nucleic acid-cleaving catalytic DNA for sensing and therapeutics

DNAzymes with nucleic acid-cleaving catalytic activity are increasing in versatility through concerted efforts to discover new sequences with unique functions, and they are generating excitement in the sensing community as cheap, stable, amplifiable detection elements. This review provides a comprehensive list and detailed descriptions of the DNAzymes identified to date, classified by their associated small molecule or ion needed for catalysis; of note, this classification clarifies conserved regions of various DNAzymes that are not obvious in the literature. Furthermore, we detail the breadth of functionality of these DNA sequences as well as the range of reaction conditions under which they are useful. In addition, the utility of the DNAzymes in a variety of sensing and therapeutic applications is presented, detailing both their advantages and disadvantages.

Hydrazone chemistry assisted DNAzyme for the analysis of double targets

In this work, a hydrazone chemistry assisted DNAzyme has been designed and constructed. The introduction of hydrazone chemistry increases the versatility of DNAzymes. With superior catalytic capability, the hydrazone chemistry assisted DNAzyme has been successfully applied for the analysis of double targets. Taking 5-hydroxymethylfurfural (HMF) and lipopolysaccharide (LPS) as samples, the hydrazone chemistry assisted DNAzyme can be used for the detection of different combinations of targets. Moreover, because hydrazone chemistry is popular in nature, this work may also provide a new insight for the development of DNAzymes and their multifunctionality.

The Two Classic Pb2+ -Selective DNAzymes Are Related: Rational Evolution for Understanding Metal Selectivity

In 1994, the first DNAzyme named GR5 was reported, which specifically requires Pb²⁺ for its RNA cleavage activity. Three years later, the 8-17 DNAzyme was isolated. The 8-17 DNAzyme and the related 17E DNAzyme are also most active with Pb²⁺ , although other divalent metals can work as well. GR5 and 17E have the same substrate sequence, and their catalytic loops in the enzyme strands also have a few similar and conserved nucleotides. Considering these, we hypothesized that 17E might be a special form of GR5. To test this hypothesis, we performed systematic rational evolution experiments to gradually mutate GR5 toward 17E. By using the activity ratio in the presence of Pb²⁺ and Mg²⁺ for defining these two DNAzymes, the critical nucleotide was identified to be T₁₂ in 17E for metal specificity. In addition, G₉ in GR5 is a position not found in most 17E or 8-17 DNAzymes, and G₉ needs to be added to rescue GR5 activity if T₁₂ becomes a cytosine. This study highlights the links between these two classic and widely used DNAzymes, and offers new insight into the sequence-activity relationship related to metal selectivity.

Synthetic evolution

The combination of modern biotechnologies such as DNA synthesis, λ red recombineering, CRISPR-based editing and next-generation high-throughput sequencing increasingly enables precise manipulation of genes and genomes. Beyond rational design, these technologies also enable the targeted, and potentially continuous, introduction of multiple mutations. While this might seem to be merely a return to natural selection, the ability to target evolution greatly reduces fitness burdens and focuses mutation and selection on those genes and traits that best contribute to a desired phenotype, ultimately throwing evolution into fast forward.