Nonviolent Self-Catabolic DNAzyme Nanosponges for Smart Anticancer Drug Delivery

The development of self-assembled DNA nanomedicine requires a facile and accurate DNA degradation strategy for precisely programmable drug release. Conventional DNA catabolic strategies are restrained with the fragile and unclear enzymatic reactions that might lead to inefficient and uncontrollable digestion of DNA scaffolds and thus might bring undesirable side effects to the sophisticated biosystems. Herein we reported a versatile self-sufficient DNAzyme-driven drug delivery system consisting of the rolling circle polymerized DNAzyme-substrate scaffolds and the encapsulated pH-responsive ZnO nanoparticles (NPs). The full DNAzyme nanosponges (NSs) were also encoded with multivalent tandem aptamer sequences to facilitate their efficient delivery into cancer cells, where the acidic endo/lysosomal microenvironment stimulates the dissolution of ZnO into Zn²⁺ ions as DNAzyme cofactors and therapeutic reactive oxygen species generators. The supplement Zn²⁺ cofactors mediated the nonviolent DNAzyme-catalyzed cleavage of DNA scaffolds for precise and efficient drug administrations with synergistically enhanced therapeutic performance. The facile design of DNAzyme, together with their cost-effective and intrinsic robust features, is anticipated to provide extensive insights for the development of DNA-based therapeutic platforms by activating the specific intracellular biocatalytic reactions. As an intelligent and nonviolent self-driven drug delivery platform, the present DNAzyme NS system could be engineered with more therapeutic sequences and agents and was anticipated to show exceptional promise and versatility for applications in biomedicine and bioengineering.

Dynamically Programmed Switchable DNA Hydrogels Based on a DNA Circuit Mechanism

Biological stimuli-responsive DNA hydrogels have attracted much attention in the field of medical engineering owing to their unique phase transitions from gel to sol through cleavage of DNA cross-linking points in response to specific biomolecular inputs. In this paper, a new class of biological stimuli-responsive DNA hydrogels with a dynamically programmed DNA system that relies on a DNA circuit system through cascading toehold-mediated DNA displacement reactions is constructed, allowing the catalytic cleavage of cross-linking points and main chains in response to an appropriate DNA input. The dynamically programmed DNA hydrogels exhibit a significant sharp phase transition from gel to sol in comparison to another DNA hydrogel showing noncatalytic cleavage of cross-linking points due to synchronization of the catalytic cleavage of cross-linking points and the main chains. Further, the sol-gel phase transitions of the DNA hydrogels in response to the DNA input are easily tunable by changing the cross-linking density. Additionally, with a structure-switching aptamer, DNA hydrogels encapsulating PEGylated gold nanoparticles can be used as enzyme-free signal amplifiers for the colorimetric detection of adenosine 5'-triphosphate (ATP); this detection system provides simplicity and higher sensitivity (limit of detection: 5.6 × 10^-6 m at 30 min) compared to other DNA hydrogel-based ATP detection systems.

Oligonucleotide Cross-Linked Hydrogel for Recognition and Quantitation of MicroRNAs Based on a Portable Glucometer Readout

A novel sensing platform for recognition and quantification of target microRNAs (miRNAs) was developed by combining an amylase-trapped DNA hydrogel, multicomponent nucleic acid enzymes (MNAzymes), and a portable glucometer (PGM) readout. First, the amylase was encapsulated inside the DNA hydrogel and physically separated from its substrate of amylose, which was in a solution outside the hydrogel. After addition of the target miRNA, the activity of the MNAzyme was restored, which cuts off the substrate linker strand. The active MNAzyme can catalytically act upon multiple substrate strands through diffusion, leading to the collapse of the hydrogel and the release of amylase, which catalyzes the hydrolysis of amylose to produce a large amount of glucose and generate a high PGM signal. The smart usage of the PGM enables simple portable detection of miR-21, with a detection limit as low as 0.325 fmol. Additionally, through the simple rational design of the target-binding sensor arms, the amylase-trapped DNA hydrogel sensing platform was successfully applied in the detection of multiple endogenous miRNAs (including miR-21, miR-335, miR-155, and miR-122) extracted from HeLa cells, HepG2 cells, MCF-7 cells, and L02 cells.

Highly Stable and Multiemissive Silver Nanoclusters Synthesized in Situ in a DNA Hydrogel and Their Application for Hydroxyl Radical Sensing

Oligonucleotide-stabilized silver nanoclusters (AgNCs) show promising applications in bioimaging and bio-/chemo-sensing. However, their unsatisfactory photostability limits their practical applications. In this work, fluorescent AgNCs were synthesized in situ in a DNA hydrogel, consisting of cross-linked enzymatically amplified polymeric DNAs with cytosine-rich sequences in the presence of Ag⁺. The fluorescence property of the resultant AgNCs was optimized by a rational design of the DNA sequences to cover a broad spectrum with comparable green and red emissions. Under the protection of the DNA hydrogel, the AgNCs showed significantly improved photostability in an ambient oxygen environment, as well as low cytotoxicity even at a high concentration. Therefore, these properties show the rolling-circle-amplification-stabilized AgNCs to be a promising possible fluorescent probe for the detection of reactive oxygen/nitrogen species (ROS/RNS) in live cells because red-emitting species are susceptible to oxidation and consequently convert to green-emitting species. Finally, the as-prepared AgNCs were demonstrated to be a sensitive and specific probe for cellular imaging and the monitoring of ROS/RNS levels, which broadens the applications of AgNCs and provides a new tool for related biological investigations.

Tuning the Mechanical Properties of a DNA Hydrogel in Three Phases Based on ATP Aptamer

By integrating ATP aptamer into the linker DNA, a novel DNA hydrogel was designed, with mechanical properties that could be tuned into three phases. Based on the unique interaction between ATP and its aptamer, the mechanical strength of the hydrogel increased from 204 Pa to 380 Pa after adding ATP. Furthermore, with the addition of the complementary sequence to the ATP aptamer, the mechanical strength could be increased to 570 Pa.

Designable Immune Therapeutical Vaccine System Based on DNA Supramolecular Hydrogels

Immunotherapy is believed to be an ideal method to treat cancer because it can break the immunotolerance of tumor and induce robust immunoresponse. However, constructing a wide antigen-adaptive, easy-handling, and biodegradable system that can recruit and activate antigen-presenting cells (APCs) much effectively is still a challenge. Herein, we show an injectable DNA supramolecular hydrogel vaccine (DSHV) system which could efficiently recruit and activate APCs in vitro and in vivo. The in vitro processes have been visualized by fluorescence microscopy. Through intraperitoneal or subcutaneous injection, the DSHV system can mimic the function of a lymph node where the APCs are recruited and activated by the high local concentration of cytosine-phosphate-guanine. Subsequently, strong immune response and obvious antitumor effects have been obtained. Our findings demonstrated that the DSHV system could serve as a general platform for tumor vaccination and benefit the personalized cancer therapy in the near future.

DNA Hydrogel with Aptamer-Toehold-Based Recognition, Cloaking, and Decloaking of Circulating Tumor Cells for Live Cell Analysis

Circulating tumor cells (CTCs) contain molecular information on the primary tumor and can be used for predictive cancer diagnostics. Capturing rare live CTCs and their quantification in whole blood remain technically challenging. Here we report an aptamer-trigger clamped hybridization chain reaction (atcHCR) method for in situ identification and subsequent cloaking/decloaking of CTCs by porous DNA hydrogels. These decloaked CTCs were then used for live cell analysis. In our design, a DNA staple strand with aptamer-toehold biblocks specifically recognizes epithelial cell adhesion molecule (EpCAM) on the CTC surface that triggers subsequent atcHCR via toehold-initiated branch migration. Porous DNA hydrogel based-cloaking of single/cluster of CTCs allows capturing of living CTCs directly with minimal cell damage. The ability to identify a low number of CTCs in whole blood by DNA hydrogel cloaking would allow high sensitivity and specificity for diagnosis in clinically relevant settings. More significantly, decloaking of CTCs using controlled and defined chemical stimuli can release living CTCs without damages for subsequent culture and live cell analysis. We expect this liquid biopsy tool to open new powerful and effective routes for cancer diagnostics and therapeutics.

Rapid and annealing-free self-assembly of DNA building blocks for 3D hydrogel chaperoned by cationic comb-type copolymers

The construction and self-assembly of DNA building blocks are the foundation of bottom-up development of three-dimensional DNA nanostructures or hydrogels. However, most self-assembly from DNA components is impeded by the mishybridized intermediates or the thermodynamic instability. To enable rapid production of complicated DNA objects with high yields no need for annealing process, herein different DNA building blocks (Y-shaped, L- and L'-shaped units) were assembled in presence of a cationic comb-type copolymer, poly (L-lysine)-graft-dextran (PLL-g-Dex), under physiological conditions. The results demonstrated that PLL-g-Dex not only significantly promoted the self-assembly of DNA blocks with high efficiency, but also stabilized the assembled multi-level structures especially for promoting the complicated 3D DNA hydrogel formation. This study develops a novel strategy for rapid and high-yield production of DNA hydrogel even derived from instable building blocks at relatively low DNA concentrations, which would endow DNA nanotechnology for more practical applications.

Constructing Tissuelike Complex Structures Using Cell-Laden DNA Hydrogel Bricks

Tissue engineering has long been a challenge because of the difficulty of addressing the requirements that such an engineered tissue must meet. In this paper, we developed a new "brick-to-wall" based on unique properties of DNA supramolecular hydrogels to fabricate three-dimensional (3D) tissuelike structures: different cell types are encapsulated in DNA hydrogel bricks which are then combined to build 3D structures. Signal responsiveness of cells through the DNA gels was evaluated and it was discovered that the gel permits cell migration in 3D. The results demonstrated that this technology is convenient, effective and reliable for cell manipulation, and we believe that it will benefit artificial tissue fabrication and future large-scale production.

Remote Controlling DNA Hydrogel by Magnetic Field

DNA hydrogel has aroused widespread attention because of its unique properties. In this work, the DNA-modified magnetic nanoparticles were integrated into the mainframe of DNA hydrogel, resulting in DNA-MNP hydrogel. Under the magnetic field, this hydrogel can be remotely deformed into various shapes, driven to jump between two planes and even climb the hill. By applying various triggers, such as temperature, enzyme, and magnetic field, DNA-MNP hydrogel can specifically undergo sol-gel transition. This work not only imparts DNA hydrogel with a new fold of property but also opens a unique platform of such smart materials for its further applications.

Generation of Large-Scale DNA Hydrogels with Excellent Blood and Cell Compatibility

Hemocompatibility and cytocompatibility of biomaterials codetermine the success of tissue engineering applications. DNA, the natural component of our cells, is an auspicious biomaterial for the generation of designable scaffolds with tailorable characteristics. In this study, a combination of rolling circle amplification and multiprimed chain amplification is used to generate hydrogels at centimeter scale consisting solely of DNA. Using an in vitro rotation model and fresh human blood, the reaction of the hemostatic system on DNA hydrogels is analyzed. The measurements of hemolysis, platelets activation, and the activation of the complement, coagulation, and neutrophils using enzyme-linked immunosorbent assays demonstrate excellent hemocompatibility. In addition, the cytocompatibility of the DNA hydrogels is tested by indirect contact (agar diffusion tests) and material extract experiments with L929 murine fibroblasts according to the ISO 10993-5 specifications and no negative impact on the cell viability is detected. These results indicate the promising potential of DNA hydrogels as biomaterials for versatile applications in the field of regenerative medicine.

Self-Assembled DNA Hydrogel Based on Enzymatically Polymerized DNA for Protein Encapsulation and Enzyme/DNAzyme Hybrid Cascade Reaction

DNA hydrogel is a promising biomaterial for biological and medical applications due to its native biocompatibility and biodegradability. Herein, we provide a novel, versatile, and cost-effective approach for self-assembly of DNA hydrogel using the enzymatically polymerized DNA building blocks. The X-shaped DNA motif was elongated by terminal deoxynucleotidyl transferase (TdT) to form the building blocks, and hybridization between dual building blocks via their complementary TdT-polymerized DNA tails led to gel formation. TdT polymerization dramatically reduced the required amount of original DNA motifs, and the hybridization-mediated cross-linking of building blocks endows the gel with high mechanical strength. The DNA hydrogel can be applied for encapsulation and controllable release of protein cargos (for instance, green fluorescent protein) due to its enzymatic responsive properties. Moreover, this versatile strategy was extended to construct a functional DNAzyme hydrogel by integrating the peroxidase-mimicking DNAzyme into DNA motifs. Furthermore, a hybrid cascade enzymatic reaction system was constructed by coencapsulating glucose oxidase and β-galactosidase into DNAzyme hydrogel. This efficient cascade reaction provides not only a potential method for glucose/lactose detection by naked eye but also a promising modular platform for constructing a multiple enzyme or enzyme/DNAzyme hybrid system.

DhITACT: DNA Hydrogel Formation by Isothermal Amplification of Complementary Target in Fluidic Channels

DNA hydrogel formation by isothermal amplification of complementary targets in microfluidic channels (DhITACT) is a new platform for rapid and accurate detection of infectious pathogens. DNA hydrogel is formed in situ within microfluidic channels by the isothermal rolling circle amplification process upon the selective binding of target strands from the biological fluid. Once the volume of DNA hydrogel sufficiently enlarges, it can selectively block the matching channels with target pathogens.

Design and synthesis of target-responsive aptamer-cross-linked hydrogel for visual quantitative detection of ochratoxin A

A target-responsive aptamer-cross-linked hydrogel was designed and synthesized for portable and visual quantitative detection of the toxin Ochratoxin A (OTA), which occurs in food and beverages. The hydrogel network forms by hybridization between one designed DNA strand containing the OTA aptamer and two complementary DNA strands grafting on linear polyacrylamide chains. Upon the introduction of OTA, the aptamer binds with OTA, leading to the dissociation of the hydrogel, followed by release of the preloaded gold nanoparticles (AuNPs), which can be observed by the naked eye. To enable sensitive visual and quantitative detection, we encapsulated Au@Pt core-shell nanoparticles (Au@PtNPs) in the hydrogel to generate quantitative readout in a volumetric bar-chart chip (V-Chip). In the V-Chip, Au@PtNPs catalyzes the oxidation of H2O2 to generate O2, which induces movement of an ink bar to a concentration-dependent distance for visual quantitative readout. Furthermore, to improve the detection limit in complex real samples, we introduced an immunoaffinity column (IAC) of OTA to enrich OTA from beer. After the enrichment, as low as 1.27 nM (0.51 ppb) OTA can be detected by the V-Chip, which satisfies the test requirement (2.0 ppb) by the European Commission. The integration of a target-responsive hydrogel with portable enrichment by IAC, as well as signal amplification and quantitative readout by a simple microfluidic device, offers a new method for portable detection of food safety hazard toxin OTA.

A triggered DNA hydrogel cover to envelop and release single cells

We develop an enzyme-triggered permeable DNA hydrogel cover to envelop and release single cells in microwells. The porous structure of the DNA hydrogel allows nutrients and waste to pass through, leading to a cell viability as high as 98%. The design provides a general method to culture, monitor, and manipulate single cells, and has potential applications in cell patterning and studying cell communication.