DNA materials: bridging nanotechnology and biotechnology

DNA-Based Networks Formed by Coordination Cross-Linking of DNA with Metal-Organic Polyhedra: From Gels to Aerogels to Hydrogels

Herein, we introduce a supramolecular method to form DNA-based networks by cross-linking DNA with Rh(II)-based metal-organic polyhedra (MOPs), which entails coordination of DNA to the exohedral Rh(II) axial sites of the MOP. The resultant highly connected networks can then be processed into gels, porous aerogels, or hydrogels, exhibiting properties suitable for pollutant removal and drug release.

DNA as a promising biomaterial for bone regeneration and potential mechanisms of action

DNA nanotechnology has created new possibilities for the use of DNA in tissue regeneration - an important advance for DNA use beyond its paradigmatic role as the hereditary biomacromolecule. Biomaterials containing synthetic or natural DNA have been proposed for several applications including drug and gene delivery, and more recently, as osteoconductive biomaterials. This review provides an in-depth discussion of studies that have used DNA-based materials for biomineralization and/or bone repair, with expansion on the topic of DNA hydrogels specifically, and the advantages they offer for advancing the field of bone regeneration. Four mechanisms of action for the osteoconductive capabilities of DNA-based materials are discussed, and a proposed model for degradation of these materials and its link to their osteoconductive properties is later presented. Finally, the review considers current limitations of DNA-based materials and summarizes important aspects that need to be addressed for future application of DNA nanotechnology in tissue repair. STATEMENT OF SIGNIFICANCE: Herein we summarize the developing field of DNA-based materials for biomineralization and bone repair, with a focus on DNA hydrogels. We first provide a comprehensive review of different forms of DNA-based materials described thus far which have been shown to enhance bone repair and mineralization (namely DNA coatings, DNA-containing pastes, DNA nanostructures and DNA hydrogels). Next, we describe four different mechanisms by which DNA-based materials could be exerting their osteogenic effect. Then, we propose a novel model that links DNA degradation and osteoconductivity. Lastly, we suggest possible research directions to enhance DNA-based materials for future clinical application. The suggested mechanisms and the proposed model can guide future research to better understand how DNA functions as a mineral- and bone-promoting molecule.

DNA Hydrogels in Tissue Engineering: From Molecular Design to Next-Generation Biomedical Applications

DNA hydrogels have emerged as promising materials in tissue engineering due to their biocompatibility, programmability, and responsiveness to stimuli. Synthesized through physical and chemical crosslinking, these hydrogels can be categorized into functionalized types, such as those based on aptamers, and stimuli-responsive types that react to pH, temperature, and light. This review highlights their applications in tissue engineering, including drug delivery, cell culture, biosensing, and gene editing. DNA hydrogels can encapsulate therapeutic agents, support cell growth, and respond dynamically to environmental changes, making them ideal for tissue engineering. A comprehensive bibliometric analysis is included, identifying key research trends and emerging areas of interest in DNA hydrogel design, synthesis, and biomedical applications. The analysis provides a deeper understanding of the field's development and future research directions. Challenges such as mechanical strength, stability, and biosafety persist, but the integration of AI in hydrogel design shows promise for advancing their functionality in clinical applications.

Intra- and Interbead Communications by an Anchored DNA Structure and Cascaded DNA Reactions

In nature, communication between compartments, such as cells and organelles, gives rise to biological complexity. Two types of chemical communication play important roles in achieving this complexity: intra- and intercompartment communication. Building a bioinspired synthetic system that can exhibit such communication is of interest for realizing microscale artificial robots with the complexity of actual cells. In this study, we aimed to demonstrate intra- and interbead communication using microbeads made of hydrogels as compartments. We employed the diffusion and reaction of programmed DNA molecules as a medium for chemical communication. As a result of the reaction-diffusion dynamics of DNA, the spatiotemporal development of fluorophore-labeled DNAs was observed under fluorescence microscopy, showing both intra- and interbead communication. Our simple, robust, and scalable methodology will accelerate the fabrication of synthetic microsystems that may have complex functionalities from various local interactions.

DNA-encoded dynamic hydrogels for 3D bioprinted cartilage organoids

Articular cartilage, composed of chondrocytes within a dynamic viscoelastic matrix, has limited self-repair capacity, posing a significant challenge for regeneration. Constructing high-fidelity cartilage organoids through three-dimensional (3D) bioprinting to replicate the structure and physiological functions of cartilage is crucial for regenerative medicine, drug screening, and disease modeling. However, commonly used matrix bioinks lack reversible cross-linking and precise controllability, hindering dynamic cellular regulation. Thus, encoding bioinks adaptive for cultivating cartilage organoids is an attractive idea. DNA, with its ability to be intricately encoded and reversibly cross-linked into hydrogels, offers precise manipulation at both molecular and spatial structural levels. This endows the hydrogels with viscoelasticity, printability, cell recognition, and stimuli responsiveness. This paper elaborates on strategies to encode bioink via DNA, emphasizing the regulation of predictable dynamic properties and the resulting interactions with cell behavior. The significance of these interactions for the construction of cartilage organoids is highlighted. Finally, we discuss the challenges and future prospects of using DNA-encoded hydrogels for 3D bioprinted cartilage organoids, underscoring their potential impact on advancing biomedical applications.

Opportunities and Challenges of DNA Materials toward Sustainable Development Goals

Sustainable development represents a significant and pressing challenge confronting the global community at present. A wide variety of macroscopic engineering systems has been developed to promote sustainable development. Recent advancements in DNA materials have showcased their substantial contributions toward achieving sustainable development goals (SDGs). Compared to nonbiological materials, DNA materials possess exceptional properties such as genetic functionality, molecular programmability, recognition capabilities, and biocompatibility. These unique characteristics enable DNA materials to serve as general and versatile substrates beyond their genetic role. Consequently, they can be used to develop DNA-based engineering systems that offer versatile solutions to support sustainable development. In this Perspective, we critically examine the opportunities that DNA-based engineering systems present in contributing to the achievement of the SDGs within various real-world scenarios. We establish direct relationships between DNA-based engineering systems and the SDGs, highlighting their inherent merits in accelerating sustainable development. Furthermore, in order to successfully achieve SDGs, we address the challenges associated with these systems and emphasize the urgent need for developing multifunctional, reliable, biosafe, and intelligent DNA-based engineering systems to overcome these challenges.

An Optimization Generator of Synthetic DNA Fragments for the Rational Design of Environmental Tracers

Chemically synthesized DNA fragments are increasingly recognized as highly valuable tracers for investigating environmental pollution due to their inherent high specificity, sequence diversity, environmental friendliness, stable migration, and high detection sensitivity, outperforming traditional ion and dye tracers. Despite their advantages, a systematic approach for generating suitable DNA sequences, which is a critical requirement for preparing DNA tracers, remains not fully developed. This study introduces an optimization generator of synthetic DNA sequences guided by seven principles, which enables the concurrent generation of multiple sequences with enhanced stability, specificity, and detectability. The DNA sequences produced by our optimization generator display a balanced base distribution, uniform melting temperatures, and reduced formation of hairpin and dimer structures. The necessity of the established principles was further validated through PCR and qPCR detection, showing that noncompliance led to unstable or undetectable DNA amplification. The column and sandbox injection experiments also demonstrated that the generated DNA sequences can be clearly distinguished and effectively used for hydrological multitracing applications. Our research underscores the importance of established principles in creating suitable DNA sequences and offers valuable insights for the efficient preparation of DNA tracers.

Important applications of DNA nanotechnology combined with CRISPR/Cas systems in biotechnology

DNA nanotechnology leverages the specificity of Watson-Crick base pairing and the inherent attributes of DNA, enabling the exploitation of molecular characteristics, notably self-assembly, in nucleic acids to fabricate novel, controllable nanoscale structures and mechanisms. In the emerging field of DNA nanotechnology, DNA is not only a genetic material, but also a versatile multifunctional polymer, comprising deoxyribonucleotides, and facilitating the construction of precisely dimensioned and precise shaped two-dimensional (2D) and three-dimensional (3D) nanostructures. DNA molecules act as carriers of biological information, with notable advancements in bioimaging, biosensing, showing the profound impact. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated systems (Cas) constitute self-defense mechanisms employed by bacteria and archaea to defend against viral invasion. With the discovery and modification of various functional Cas proteins, coupled with the identification of increasingly designable and programmable CRISPR RNAs (crRNAs), the potential of the CRISPR/Cas system in the field of molecular diagnostics is steadily being realized. Structural DNA nanotechnology provides a customizable and modular platform for accurate positioning of nanoscopic materials, for e.g., biomedical uses. This addressability has just recently been applied in conjunction with the newly developed gene engineering tools to enable impactful, programmable nanotechnological applications. As of yet, self-assembled DNA nanostructures have been mainly employed to enhance and direct the delivery of CRISPR/Cas, but lately the groundwork has also been laid out for other intriguing and complex functions. These recent advances will be described in this perspective. This review explores biosensing detection methods that combine DNA nanotechnology with CRISPR/Cas systems. These techniques are used in biosensors to detect small molecules such as DNA, RNA, and etc. The combination of 2D and 3D DNA nanostructures with the CRISPR/Cas system holds significant value and great development prospects in the detection of important biomarkers, gene editing, and other biological applications in fields like biosensing.

Supramolecular adhesives inspired from adhesive proteins and nucleic acids: molecular design, properties, and applications

Bioinspired supramolecular adhesives have been recently emerging as novel functional materials, which have shown a wide range of applications in wearable sensors and tissue engineering such as tissue adhesives and wound dressings. In this review, we summarize and discuss two main types of biologically inspired supramolecular adhesives from adhesive proteins and nucleic acids. The widely studied catechol-based adhesives, that originated from adhesive proteins of marine organisms such as mussels, and recently emerging nucleobase-containing supramolecular adhesives are both introduced and discussed. Both bioinspired adhesives from nucleic acids and adhesive proteins involve multiple supramolecular interactions such as hydrogen bonding, hydrophobic interactions, π-π stacking, and so on. Several major types of these bioinspired adhesives are summarized, respectively, including polymer-based, hydrogel-based, and other types of adhesives. The novel molecular design and adhesion properties are focused on and highlighted for each type of bioinspired adhesive. In addition, the potential applications of these bioinspired supramolecular adhesives in different realms including tissue engineering and biomedical devices are discussed. This review concludes with issues and challenges in the area of the bioinspired adhesives, hopefully promoting further developments and broader applications of novel supramolecular adhesives.

Nanoscale self-assembly and water retention properties of silk fibroin-riboflavin hydrogel

Silk-fibroin hydrogels have gained considerable attention in recent years for their versatile biomedical applications. The physical properties of a complex hydrogel, comprising silk fibroin and riboflavin, surpass those of the silk fibroin-hydrogel without additives. This study investigates silk fibroin-riboflavin (silk-RIB) hydrogel at the atomistic level to uncover molecular structures and chemical characteristics specific to silk fibroin and riboflavin molecules in an aqueous medium. The interplay between hydrophilic riboflavin and hydrophobic silk fibroin polymers facilitates the formation of solubilized silk fiber, which subsequently evolves into a nano-scale hydrogel over time. Eventually, the interlinked RIB stacks form a scaffold that not only accommodates silk fibroin aggregates but also encloses water pockets, preserving the moisture level and enhancing the thermal conductivity of the hydrogel. To explore water retention properties and the role of ions, two sets of simulations of semi-hydrated hydrogel in the presence and absence of ions are conducted. The presence of ions significantly influences the dynamics of RIB and silk fibroin. Favorable interactions with the ions impede the unrestricted diffusion of these larger molecules, potentially leading to a stable structure capable of retaining water for a prolonged duration. The complete removal of water results in further shrinkage of the anhydrous silk-RIB hydrogel or xerogel (XG), yet its porosity and structural integrity remain intact. These findings offer valuable insights into the behavior of silk fibroin hydrogel and XG, paving the way for materials engineering in aqueous environments to develop biomedical devices with customized functional properties.

A Critical View on the Use of DNA Hydrogels in Cell-Free Protein Synthesis

Numerous studies have reported in the past that the use of protein-encoding DNA hydrogels as templates for cell-free protein synthesis (CFPS) leads to better yields than the use of conventional templates such as plasmids or PCR fragments. Systematic investigation of different types of bulk materials from pure DNA hydrogels and DNA hydrogel composites using a commercially available CFPS kit showed no evidence of improved expression efficiency. However, protein-coding DNA hydrogels were advantageously used in microfluidic reactors as immobilized templates for repetitive protein production, suggesting that DNA-based materials offer potential for future developments in high-throughput profiling or rapid in situ characterization of proteins.

Counterintuitive DNA destabilization by monovalent salt at high concentrations due to overcharging

Monovalent salts are generally believed to stabilize DNA duplex by weakening inter-strand electrostatic repulsion. Unexpectedly, our force-induced hairpin unzipping experiments and thermal melting experiments show that LiCl, NaCl, KCl, RbCl, and CsCl at concentrations beyond ~1 M destabilize DNA, RNA, and RNA-DNA duplexes. The two types of experiments yield different changes in free energy during melting, while the results that high concentration monovalent salts destabilize duplexes are common. The effects of these monovalent ions are similar but also have noticeable differences. From 1 M to 4 M, DNA duplex is destabilized by about 0.3 kBT/bp and the melting temperature decreases by about 10 oC. Our all-atom simulations reveal this effect is caused by overcharging, where excessive ion absorption inverts the effective DNA charge from negative to positive. Furthermore, our coarse-grained simulations obtain a phase diagram that indicates whether DNA overcharging occurs at a given cation valence and concentration. These findings challenge the traditional belief that DNA overcharging occurs only with multivalent ions and have significant implications for polyelectrolyte theory, DNA nanomaterials, DNA nanotechnology, and DNA biophysics.

Engineering Phi29-DNAP Variants for Customized DNA Hydrogel Materials

DNA hydrogels, which hold potential for use in medicine, biosensors, and tissue engineering, can be produced through enzymatic rolling circle amplification (RCA) using phi29 DNA polymerase (DNAP). This paper introduces new DNAP variants designed for RCA-based DNA hydrogel production, featuring enzymes with modified DNA binding, enhanced thermostability, reduced exonuclease activity, and protein tags for fluorescence detection or specific immobilization. We evaluated these enzymes by quantifying DNA output via quantitative PCR (qPCR) and assessing hydrogel mechanical properties through micromechanical indentation. The results showed that most variants generated similar DNA amounts and hydrogels with comparable mechanical properties. Additionally, all variants successfully incorporated non-natural nucleotides, such as base-modified dGTP derivatives and 2'fluoro-dGTP, during RCA. This study's robust analytical approach offers a strong foundation for selecting new enzymes and producing DNA hydrogels with tailored material properties.

Micromechanical Indentation Platform for Rapid Analysis of Viscoelastic Biomolecular Hydrogels

The advent of biomedical applications of soft bioinspired materials has entailed an increasing demand for streamlined and expedient characterization methods meant for both research and quality control objectives. Here, a novel measurement system for the characterization of biological hydrogels with volumes as low as 75 µL was developed. The system is based on an indentation platform equipped with micrometer drive actuators that allow the determination of both the fracture points and Young's moduli of relatively stiff polymers, including agarose, as well as the measurements of viscosity for exceptionally soft and viscous hydrogels, such as DNA hydrogels. The sensitivity of the method allows differentiation between DNA hydrogels produced by rolling circle amplification based on different template sequences and synthesis protocols. In addition, the polymerization kinetics of the hydrogels can be determined by time-resolved measurements, and the apparent viscosities of even more complex DNA-based nanocomposites can be measured. The platform presented here thus offers the possibility to characterize a broad variety of soft biomaterials in a targeted, fast, and cost-effective manner, holding promises for applications in fundamental materials science and ensuring reproducibility in the handling of complex materials.

DNA-templated fluorescent metal nanoclusters and their illuminating applications

After the discovery of DNA during the mid-20th century, a multitude of novel methodologies have surfaced which exploit DNA for its various properties. One such recently developed application of DNA is as a template in metal nanocluster formation. In the early years of the new millennium, a group of researchers found that DNA can be adopted as a template for the binding of metal nanoparticles that ultimately form nanoclusters. Three metal nanoclusters have been studied so far, including silver, gold, and copper, which have a plethora of biological applications. This review focuses on the synthesis, mechanisms, and novel applications of DNA-templated metal nanoclusters, including the therapies that have employed them for their wide range of fluorescent properties, and the future perspectives related to their development by exploiting machine learning algorithms and molecular dynamics simulation studies.

DNA hydrogels and their derivatives in biomedical engineering applications

Deoxyribonucleotide (DNA) is uniquely programmable and biocompatible, and exhibits unique appeal as a biomaterial as it can be precisely designed and programmed to construct arbitrary shapes. DNA hydrogels are polymer networks comprising cross-linked DNA strands. As DNA hydrogels present programmability, biocompatibility, and stimulus responsiveness, they are extensively explored in the field of biomedicine. In this study, we provide an overview of recent advancements in DNA hydrogel technology. We outline the different design philosophies and methods of DNA hydrogel preparation, discuss its special physicochemical characteristics, and highlight the various uses of DNA hydrogels in biomedical domains, such as drug delivery, biosensing, tissue engineering, and cell culture. Finally, we discuss the current difficulties facing DNA hydrogels and their potential future development.

Self-Replicating DNA-Based Nanoassemblies

The properties of DNA that make it an effective genetic material also allow it to be ideal for programmed self-assembly. Such DNA-programmed assembly has been utilized to construct responsive DNA origami and wireframe nanoassemblies, yet replicating these hybrid nanomaterials remains challenging. Here we report a strategy for replicating DNA wireframe nanoassemblies using the isothermal ligase chain reaction lesion-induced DNA amplification (LIDA). We designed a triangle wireframe structure that can be formed in one step by ring-closing of its linear analog. Introducing a small amount of the wireframe triangle to an excess of the linear analog and complementary fragments, one of which contains a destabilizing abasic lesion, leads to rapid, sigmoidal self-replication of the wireframe triangle via cross-catalysis. Using the same cross-catalytic strategy we also demonstrate rapid self-replication of a hybrid wireframe triangle containing synthetic vertices as well as the self-replication of circular DNA. This work reveals the suitability of isothermal ligase chain reactions such as LIDA to self-replicate complex DNA architectures, opening the door to incorporating self-replication, a hallmark of life, into biomimetic DNA nanotechnology.

Piggybacking functionalized DNA nanostructures into live-cell nuclei

DNA origami nanostructures (DOs) are promising tools for applications including drug delivery, biosensing, detecting biomolecules, and probing chromatin substructures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches for probing, visualizing, and controlling biomolecular processes within live cells. We present an approach to deliver DOs into live-cell nuclei. We show that these DOs do not undergo detectable structural degradation in cell culture media or cell extracts for 24 hours. To deliver DOs into the nuclei of human U2OS cells, we conjugated 30-nanometer DO nanorods with an antibody raised against a nuclear factor, specifically the largest subunit of RNA polymerase II (Pol II). We find that DOs remain structurally intact in cells for 24 hours, including inside the nucleus. We demonstrate that electroporated anti-Pol II antibody-conjugated DOs are piggybacked into nuclei and exhibit subdiffusive motion inside the nucleus. Our results establish interfacing DOs with a nuclear factor as an effective method to deliver nanodevices into live-cell nuclei.

Liquid Metal Nanocores Initiated Construction of Smart DNA-Polymer Microgels with Programmable and Regulable Functions and Near-Infrared Light-Driven Locomotion

Due to their sequence-directed functions and excellent biocompatibility, smart DNA microgels have attracted considerable research interest, and the combination of DNA microgels with functional nanostructures can further expand their applications in biosensing and biomedicine. Gallium-based liquid metals (LMs) exhibiting both fluidic and metallic properties hold great promise for the development of smart soft materials; in particular, LM particles upon sonication can mediate radical-initiated polymerization reactions, thus allowing the combination of LMs and polymeric matrix to construct "soft-soft" materials. Herein, by forming active surfaces under sonication, LM nanoparticles (LM NPs) initiated localized radical polymerization reactions allow the combination of functional DNA units and different polymeric backbones to yield multifunctional core/shell microgels. The localized polymerization reaction allows fine control of the microgel compositions, and smart DNA microgels with tunable catalytic activities can be constructed. Moreover, due to the excellent photothermal effect of LM NPs, the resulting temperature gradient between microgels and surrounding solution upon NIR light irradiation can drive the oriented locomotion of the microgels, and remote control of the activity of these smart microgels can be achieved. These microgels may hold promise for various applications, such as the development of in vivo and in vitro biosensing and drug delivery systems.

Piggybacking functionalized DNA nanostructures into live cell nuclei

DNA origami (DO) are promising tools for in vitro or in vivo applications including drug delivery; biosensing, detecting biomolecules; and probing chromatin sub-structures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches for probing visualizing and controlling important biological processes in live cells. Here we present an approach to deliver DO strucures into live cell nuclei. We show that labelled DOs do not undergo detectable structural degradation in cell culture media or human cell extracts for 24 hr. To deliver DO platforms into the nuclei of human U2OS cells, we conjugated 30 nm long DO nanorods with an antibody raised against the largest subunit of RNA Polymerase II (Pol II), a key enzyme involved in gene transcription. We find that DOs remain structurally intact in cells for 24hr, including within the nucleus. Using fluorescence microscopy we demonstrate that the electroporated anti-Pol II antibody conjugated DOs are efficiently piggybacked into nuclei and exihibit sub-diffusive motion inside the nucleus. Our results reveal that functionalizing DOs with an antibody raised against a nuclear factor is a highly effective method for the delivery of nanodevices into live cell nuclei.

Programmable all-DNA hydrogels based on rolling circle and multiprimed chain amplification products

Soft, biocompatible, and tunable materials offer biomedical engineers and material scientists programmable matrices for a variety of biomedical applications. In this regard, DNA hydrogels have emerged as highly promising biomaterials that offer programmable self-assembly, superior biocompatibility, and the presence of specific molecular identifiable structures. Many types of DNA hydrogels have been developed, yet the programmability of the DNA building blocks has not been fully exploited, and further efforts must be directed toward understanding how to finely tune their properties in a predictable manner. Herein, we develop physically crosslinked all-DNA hydrogels with tunable morphology and controllable biodegradation, based on rolling circle amplification and multiprimed chain amplification products. Through molecular engineering of the DNA sequences and their nano-/microscale architectures, the precursors self-assemble in a controlled manner to produce soft hydrogels in an efficient, cost-effective, and highly tunable manner. Notably, we develop a novel DNA microladder architecture that serves as a framework for modulating the hydrogel properties, including over an order of magnitude change in pore size and up to 50% change in biodegradation rate. Overall, we demonstrate how the properties of this DNA-based biomaterial can be tuned by modulating the amounts of rigid double-stranded DNA chains compared to flexible single-stranded DNA chains, as well as through the precursor architecture. Ultimately, this work opens new avenues for the development of programmable and biodegradable soft materials in which DNA functions not only as a store of genetic information but also as a versatile polymeric biomaterial and molecularly engineered macroscale scaffold.

Electrospun composite nanofibers of deoxyribonucleic acid and polylactic acid for skincare applications

The development of useful biomaterials has resulted in significant advances in various fields of science and technology. The demand for new biomaterial designs and manufacturing techniques continues to grow, with the goal of building a sustainable society. In this study, two types of DNA-cationic surfactant complexes were synthesized using commercially available deoxyribonucleic acid from herring sperm DNA (hsDNA, <50 bp) and deoxyribonucleic acid from salmon testes DNA (stDNA, ~2000 bp). The DNA-surfactant complexes were blended with a polylactic acid (PLA) biopolymer and electrospun to obtain nanofibers, and then copper nanoparticles were synthesized on nanofibrous webs. Scanning electron microscopic images showed that all nanofibers possessed uniform morphology. Interestingly, different diameters were observed depending on the base pairs in the DNA complex. Transmission electron microscopy showed uniform growth of copper nanoparticles on the nanofibers. Fourier-transform infrared spectroscopy spectra confirmed the uniform blending of both types of DNA complexes in PLA. Both stDNA- and hsDNA-derived nanofibers showed greater biocompatibility than native PLA nanofibers. Furthermore, they exerted significant antibacterial activity in the presence of copper nanoparticles. This study demonstrates that DNA is a potentially useful material to generate electrospun nanofibrous webs for use in biomedical sciences and technologies.

Accurate quantification of DNA content in DNA hydrogels prepared by rolling circle amplification

Accurate quantification of polymerized DNA in rolling circle amplification (RCA)-based hydrogels is challenging due to the high viscosity of these materials, however, it can be achieved with a photometric nucleotide depletion assay or qPCR. We show that the DNA content strongly depends on the template sequence and correlates with the mechanical properties of the hydrogels.

Detection of long mRNA sequences by a Y-shaped DNA probe with three target-binding segments

Tumor-related mRNA detection is significant and interesting. The current mRNA detection method has the challenge of quantifying long mRNA sequences. Herein, a Y-shaped DNA probe with three target-binding segments was developed to detect tumor-related mRNA. This Y-shaped DNA probe (Y-probe) was assembled by six single DNA strands. Among these DNA strands, two DNA strands contained the split G-quadruplex sequence, and two DNA strands were modified with a pair of fluorophore and quencher, which were used to produce the detectable signal. In the presence of a long target mRNA sequence, target mRNA was hybridized with the three target-binding segments of the Y-probe, resulting in the increased fluorescence of G-quadruplex specific dye Thioflavin T and the decreased fluorescence of fluorophore, which could achieve the ratio detection of target mRNA. The Y-probe exhibited a low detection limit of 17.53 nM. Moreover, this probe showed high accuracy due to the benefits of three target-binding segments.

Optimization of aflatoxin B1 removal efficiency of DNA by resonance light scattering spectroscopy

In this paper, firstly, the resonance light scattering spectra of aflatoxin B₁ (AFB₁) and DNA were measured by resonance light scattering spectroscopy (RLS), and the DNA binding saturation value (DBSV) of AFB₁ was calculated from their spectral results. Then the interaction intensity between DNA and AFB₁ and the effects of some external factors on the interaction between DNA and AFB₁ were evaluated by corresponding DBSVs, so as to establish and optimize a way for removing AFB₁ by DNA. DBSV of AFB₁ was 2.04 at 30℃ and pH 7.40. However, after adding sodium ion, calcium ion, vitamin E, vitamin C and D-glucose, DBSV of AFB₁ was changed to 2.72, 3.17, 2.67, 1.68 and 1.33 respectively. Correspondingly, the removal efficiency of AFB₁ by DNA was changed from 90.05% to 93.25%, 95.48%, 93.08%, 82.36% and 78.90% respectively. These results indicated that the external factors had a significant impact on the interaction between DNA and AFB₁. Among them, some factors enhanced the interaction between DNA and AFB₁, while some factors weakened the interaction between DNA and AFB1. The change of these external factors led to the corresponding changes in DBSV and the removal efficiency of AFB₁. DBSV of AFB₁ could really be used as an index to evaluate the intensity of the interaction between DNA and AFB₁, and to optimize the removal efficiency of AFB₁ by DNA. The experimental data also showed that the adsorption of AFB₁ to DNA was consistent with the pseudo-second-order kinetic model and the Freundlich isothermal model, was an exothermic and spontaneous process. All these results will give good references for establishing and optimizing a way of AFB₁ removal via DNA intercalation.

Recycling of Polymerase Chain Reaction (PCR) Kits

Polymerase chain reaction (PCR) kits have been used as common diagnosing tools during the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, with daily worldwide usage in the millions. It is well known that at the beginning of the pandemic, there was a shortage of PCR kits. So far, the ecosystem of a PCR kit is linear use; that is, kits are produced, used once, and disposed of as biolab waste. Here, we show that to mitigate the risk of future shortages, it is possible to envision recyclable PCR kits based on a more sustainable use of nucleic acid resources. A PCR kit is mainly composed of primers, nucleotides, and enzymes. In the case of a positive test, the free nucleotides are polymerized onto the primers to form longer DNA strands. Our approach depolymerizes such strands, keeping the primers and regenerating the nucleotides, i.e., returning the nucleic acid materials to the original state. The polymerized long DNA strands are hydrolyzed into nucleotide monophosphates that are then phosphorylated into triphosphates using a method that is developed from a recent publication. We used oligonucleotides with a 3'-terminal phosphorothioate (PS) backbone modification as nonhydrolyzable PCR primers, which are able to undergo the recycling process unchanged. The nuclease resistance of oligonucleotides with a ribose sugar modification was also evaluated, which showed worse recycling efficiency than PS-modified oligonucleotides. We successfully recycled both PCR primers and nucleotide monomers (∼75% yield). We demonstrate that the method allows for the direct reuse of PCR kits. We also show that the recycled primers can be isolated and then added to endpoint or quantitative PCR. This recycling approach provides a new path for circularly reusing nucleic acid materials in PCR kits.

Shape control in 2D molecular nanosheets by tuning anisotropic intermolecular interactions and assembly kinetics

Since molecular materials often decompose upon exposure to radiation, lithographic patterning techniques established for inorganic materials are usually not applicable for the fabrication of organic nanostructures. Instead, molecular self-organisation must be utilised to achieve bottom-up growth of desired structures. Here, we demonstrate control over the mesoscopic shape of 2D molecular nanosheets without affecting their nanoscopic molecular packing motif, using molecules that do not form lateral covalent bonds. We show that anisotropic attractive Coulomb forces between partially fluorinated pentacenes lead to the growth of distinctly elongated nanosheets and that the direction of elongation differs between nanosheets that were grown and ones that were fabricated by partial desorption of a complete molecular monolayer. Using kinetic Monte Carlo simulations, we show that lateral intermolecular interactions alone are sufficient to rationalise the different kinetics of structure formation during nanosheet growth and desorption, without inclusion of interactions between the molecules and the supporting MoS2 substrate. By comparison of the behaviour of differently fluorinated molecules, experimentally and computationally, we can identify properties of molecules with regard to interactions and molecular packing motifs that are required for an effective utilisation of the observed effect.

Dynamic assembly of DNA-ceria nanocomplex in living cells generates artificial peroxisome

Intracellular accumulation of reactive oxygen species (ROS) leads to oxidative stress, which is closely associated with many diseases. Introducing artificial organelles to ROS-imbalanced cells is a promising solution, but this route requires nanoscale particles for efficient cell uptake and micro-scale particles for long-term cell retention, which meets a dilemma. Herein, we report a deoxyribonucleic acid (DNA)-ceria nanocomplex-based dynamic assembly system to realize the intracellular in-situ construction of artificial peroxisomes (AP). The DNA-ceria nanocomplex is synthesized from branched DNA with i-motif structure that responds to the acidic lysosomal environment, triggering transformation from the nanoscale into bulk-scale AP. The initial nanoscale of the nanocomplex facilitates cellular uptake, and the bulk-scale of AP supports cellular retention. AP exhibits enzyme-like catalysis activities, serving as ROS eliminator, scavenging ROS by decomposing H₂O₂ into O₂ and H₂O. In living cells, AP efficiently regulates intracellular ROS level and resists GSH consumption, preventing cells from redox dyshomeostasis. With the protection of AP, cytoskeleton integrity, mitochondrial membrane potential, calcium concentration and ATPase activity are maintained under oxidative stress, and thus the energy of cell migration is preserved. As a result, AP inhibits cell apoptosis, reducing cell mortality through ROS elimination.

Biomolecule-Based Optical Metamaterials: Design and Applications

Metamaterials are broadly defined as artificial, electromagnetically homogeneous structures that exhibit unusual physical properties that are not present in nature. They possess extraordinary capabilities to bend electromagnetic waves. Their size, shape and composition can be engineered to modify their characteristics, such as iridescence, color shift, absorbance at different wavelengths, etc., and harness them as biosensors. Metamaterial construction from biological sources such as carbohydrates, proteins and nucleic acids represents a low-cost alternative, rendering high quantities and yields. In addition, the malleability of these biomaterials makes it possible to fabricate an endless number of structured materials such as composited nanoparticles, biofilms, nanofibers, quantum dots, and many others, with very specific, invaluable and tremendously useful optical characteristics. The intrinsic characteristics observed in biomaterials make them suitable for biomedical applications. This review addresses the optical characteristics of metamaterials obtained from the major macromolecules found in nature: carbohydrates, proteins and DNA, highlighting their biosensor field use, and pointing out their physical properties and production paths.

Advances in regenerative medicine applications of tetrahedral framework nucleic acid-based nanomaterials: an expert consensus recommendation

With the emergence of DNA nanotechnology in the 1980s, self-assembled DNA nanostructures have attracted considerable attention worldwide due to their inherent biocompatibility, unsurpassed programmability, and versatile functions. Especially promising nanostructures are tetrahedral framework nucleic acids (tFNAs), first proposed by Turberfield with the use of a one-step annealing approach. Benefiting from their various merits, such as simple synthesis, high reproducibility, structural stability, cellular internalization, tissue permeability, and editable functionality, tFNAs have been widely applied in the biomedical field as three-dimensional DNA nanomaterials. Surprisingly, tFNAs exhibit positive effects on cellular biological behaviors and tissue regeneration, which may be used to treat inflammatory and degenerative diseases. According to their intended application and carrying capacity, tFNAs could carry functional nucleic acids or therapeutic molecules through extended sequences, sticky-end hybridization, intercalation, and encapsulation based on the Watson and Crick principle. Additionally, dynamic tFNAs also have potential applications in controlled and targeted therapies. This review summarized the latest progress in pure/modified/dynamic tFNAs and demonstrated their regenerative medicine applications. These applications include promoting the regeneration of the bone, cartilage, nerve, skin, vasculature, or muscle and treating diseases such as bone defects, neurological disorders, joint-related inflammatory diseases, periodontitis, and immune diseases.

Biosynthesis and Characterization of Co3O4NPs Utilizing Prickly Pear Fruit Extract and its Biological Activities

In the current research, there is a low level of research and information about the interaction of cobalt oxide nanoparticles (Co3O4NPs) in biological systems. This research creates a very simple and cost-effective preparation of cobalt oxide nanoparticles by using prickly pear fruit extract as a reducing agent, which may be further used for biological applications like antimicrobial, antioxidant, DNA interaction and in-vitro anticancer activity. The use of prickly pear fruit extract acts as a good reducing agent and is responsible for easy preparation and reducing the toxicity of cobalt oxide nanoparticles. The fabricated biogenic nanoparticles were confirmed by microscopic and spectroscopic analytical techniques like Ultra Violet-Visible spectrometer, Fourier transforms infrared spectrometer (FTIR), X-ray Diffraction Method (XRD), Energy-dispersive X-ray spectroscopy (EDS), Scanning electron microscopy (SEM) and Transmission electron microscopy (TEM). The average size of the synthesized nanoparticles is 36.24 nm. In the MTT assay, the prepared cobalt oxide NPs haspotential mechanisms of cytotoxicity and in-vitro anticancer activity in Hepatocellular carcinoma cancer cells (HepG2). The microbial activities like antibacterial and antifungal studies of the biosynthesized nanoparticles were performed by the Disc method. The Co3O4NPs with DNA interaction were examined by UV-Visible and fluorescence spectroscopic methods. The binding constant value of biogenic Co3O4NPs with CT-DNA was observed by UV-Visible spectroscopy with a result of 2.57x105mol-1. The binding parameters and quenching constants were observed by fluorescence spectroscopic methods having values of Ksv=7.1x103, kq=7.1x108, Ka=3.47.1x105, n=0.9119. From the findings, Co3O4NPs may be utilized as a medicinal aid for their antibacterial, antifungal, antioxidant, DNA binding and in-vitro anticancer activities.

Inhibition of Bacteria In Vitro and In Vivo by Self-Assembled DNA-Silver Nanocluster Structures

Antimicrobial nanomaterials hold great promise for bacteria-infected wound healing. However, it remains a challenge to balance antimicrobial efficacy and biocompatibility for these artificial antimicrobials. Here we employed biocompatible genetic molecule DNA as a building material to fabricate antimicrobial materials, including self-assembled Y-shaped DNA-silver nanocluster composite (Y-Ag) and Y-Ag hydrogel (Y-Ag-gel). We demonstrate that macroscopic and microcosmic DNA-Ag composites can effectively inhibit bacterial growth but do not affect cell proliferation in vitro. In particular, Y-Ag spray can speed up the process of wound healing in vivo. Considering the efficacy and advantages of DNA-based materials, our findings provide a promising route to fabricate a novel wound dressing such as spray and hydrogel for therapeutic wound healing.

Programmable DNA Hydrogels as Artificial Extracellular Matrix

The cell microenvironment plays a crucial role in regulating cell behavior and fate in physiological and pathological processes. As the fundamental component of the cell microenvironment, extracellular matrix (ECM) typically possesses complex ordered structures and provides essential physical and chemical cues to the cells. Hydrogels have attracted much attention in recapitulating the ECM. Compared to natural and synthetic polymer hydrogels, DNA hydrogels have unique programmable capability, which endows the material precise structural customization and tunable properties. This review focuses on recent advances in programmable DNA hydrogels as artificial extracellular matrix, particularly the pure DNA hydrogels. It introduces the classification, design, and assembly of DNA hydrogels, and then summarizes the state-of-the-art achievements in cell encapsulation, cell culture, and tissue engineering with DNA hydrogels. Ultimately, the challenges and prospects for cellular applications of DNA hydrogels are delivered.

Nanomaterial based PVA nanocomposite hydrogels for biomedical sensing: Advances toward designing the ideal flexible/wearable nanoprobes

In today's world, the progress of wearable tools has gained increasing momentum. Notably, the demand for stretchable strain sensors has considerably increased owing to various potential and emerging applications like human motion monitoring, soft robotics, prosthetics, and electronic skin. Hydrogels possess excellent biocompatibility, flexibility, and stretchability that render them ideal candidates for flexible/wearable substrates. Among them, enormous efforts were focused on the progress of polyvinyl alcohol (PVA) hydrogels to realize multifunctional wearable sensing through using additives/nanofillers/functional groups to modify the hydrogel network. Herein, this review offers an up-to-date and comprehensive summary of the research progress of PVA hydrogel-based wearable sensors in view of their properties, strain sensory efficiency, and potential applications, followed by specifically highlighting their probes using metallic/non-metallic, liquid metal (LM), 2D materials, bio-nanomaterials, and polymer nanofillers. Indeed, flexible electrodes and strain/pressure sensing performance of designed PVA hydrogels for their effective sensing are described. The representative cases are carefully selected and discussed regarding the construction, merits and demerits, respectively. Finally, the necessity and requirements for future advances of conductive and stretchable hydrogels engaged in the wearable strain sensors are also presented, followed by opportunities and challenges.

Interaction of Nucleic Acids with Metal-Organic Framework Nanosheets by Fluorescence Spectroscopy and Molecular Dynamics Simulations

The integration of nanomaterials and nucleic acids has attracted great attention in various research fields, especially biomedical applications. Designing two-dimensional nanomaterials and studying the mechanism of their interaction with nucleic acids are still attractive tasks. Herein, we designed and prepared a class of ultrathin two-dimensional metal-organic framework (MOF) nanosheets, named Zr-BTB MOF nanosheets, composed of Zr-O clusters and 1,3,5-benzenetribenzoate by a bottom-up synthesis strategy. The Zr-BTB MOF nanosheets possessed inherent excellent performance such as a high specific surface area, porosity, and biocompatibility. In addition, we clarified the interaction difference between the Zr-BTB MOF nanosheets and fluorophore-labeled double-stranded DNA and single-stranded DNA via molecular dynamics simulations and fluorescence measurement. Through molecular dynamics simulations, specific interactions between DNA and nanosheets such as forces, binding energies, and binding modes were deeply analyzed and clearly presented. Based on the affinity difference, the system showed the biosensing potential for target DNA detection with considerable specificity, sensitivity, and linearity. Our research results presented the Zr-BTB MOF nanosheet as a platform for nucleic acid detection, showing the potential for hybridization-based biosensing and related biological applications.

Integrated DNA triangular prism nanomachines for two-stage dynamic recognizing and bio-imaging from surface to the inside of living cells

The identification and detection of biomarkers in cancer cells play an essential role in the early detection of diseases, especially the detection of dual-biomarker. However, one of the most important limiting factors is how to realize the identification and labeling of biomarkers dynamically from the plasma membrane to the cytoplasm in living cells. In this study, integrated DNA triangular prism nanomachines (IDTPNs), a two-stage identification and dynamic bio-imaging strategy, recognize biomarkers from the plasma membrane to the cytoplasm have been designed. DNA triangular prism (DTP) was selected to act as a delivery platform with the aptamer Sgc8c and P53 modified on the side as the recognition molecules. Through the specific recognition of aptamers and the superior internalization of DTP, the IDTPNs realize the dynamic responses to PTK7 and p53 from the membrane to the cytoplasm in living cells. It is proved that the IDTPNs can be used for dynamic dual-biomarker recognition and bio-image from the surface to the inside of tumor cells automatically. Therefore, the strategy we developed provides a reliable platform for tumor diagnosis and biomarker research.

DNA Nanotechnology-Based Supramolecular Assemblies for Targeted Biomedical Applications

DNA is a polyanionic, hydrophilic, and natural biopolymer that offers properties such as biodegradability, biocompatibility, non-toxicity, and non-immunogenicity. These properties of DNA as an ideal biopolymer offer modern-day researchers' reasons to exploit these to form high-order supramolecular assemblies. These structures could range from simple to complex and provide various applications. Among them, supramolecular assemblies like DNA hydrogels (DNA-HG) and DNA dendrimers (DNA-DS) show massive growth potential in the areas of biomedical applications such as cell biology, medical stream, molecular biology, pharmacology, and healthcare product manufacturing. The application of both of these assemblies has seen enormous growth in recent years. In this focused review on DNA-based supramolecular assemblies like hydrogels and dendrimers, we present the principles of synthesis and characterization, key developments with examples and applications, and conclude with a brief perspective on challenges and future outlook for such devices and their subsequent applications.

Construction of branched DNA-based nanostructures for diagnosis, therapeutics and protein engineering

Branched DNA with multibranch-like anisotropic topology serves as a promising and powerful building block in constructing multifunctional-integrated nanomaterials in a programmable and controllable manner. Recently, a series of branched DNA-based functional nanomaterials were developed by elaborate molecular design. In this review, we focused on the construction of branched DNA-based nanostructures for biological and biomedical applications. First, the molecular design and synthesis method of branched DNA monomer were briefly described. Then, the construction strategies of branched DNA-based nanostructures were categorially discussed, including target-triggered polymerization, enzymatic extension and hybrid assembly. Finally, the biological and biomedical applications including diagnosis, therapeutics and protein engineering were summarized. We envision that the review will contribute to the further development of branched DNA-based nanomaterials with great application potential in the field of biomedicine, thus building a new bridge between material chemistry and biomedicine.

Recent developments in DNA-based mechanical nanodevices

Cellular processes and functions can be regulated by mechanical forces. Nanodevices that can measure and manipulate these forces are critical tools in chemical and cellular biology. Synthetic DNA oligonucleotides have been used to develop a wide range of powerful nanodevices due to their programmable nature and precise and predictable self-assembly. In recent years, various types of DNA-based mechanical nanodevices have been engineered for studying molecular-level forces. With the help of these nanodevices, our understanding of cellular responses to physical forces has been significantly advanced. In this article, we have reviewed some recent developments in DNA-based mechanical sensors and regulators for application in the characterization of cellular biomechanics and the manipulation of cellular morphology, motion and other functions. The design principles discussed in this article can be further used to inspire other types of powerful DNA-based mechanical nanodevices.

An Energy-Storing DNA-Based Nanocomplex for Laser-Free Photodynamic Therapy

Photodynamic therapy (PDT) is a therapeutic strategy that is dependent on external light irradiation that faces a major challenge in cancer treatment due to the poor tissue-penetration depths of light irradiation. Herein, a DNA nanocomplex that integrates persistent-luminescence nanoparticles (PLNPs) is developed, which realizes tumor-site glutathione-activated PDT for breast cancer without exogenous laser excitation. The scaffold of the nanocomplex is AS1411-aptamer-encoded ultralong single-stranded DNA chain with two functions: i) providing sufficient intercalation sites for the photosensitizer, and ii) recognizing nucleolin that specifically overexpresses on the surface of cancer cells. The PLNPs in the nanocomplex are energy-charged to act as a self-illuminant and coated with a shell of MnO₂ for blocking energy degradation. In response to the overexpressed glutathione in cancer cells, the MnO₂ shell decomposes to provide Mn²⁺ to catalytically produce O₂ , which is essential to PDT. Meanwhile, PLNPs are released and act as a self-illuminant to activate the photosensitizer to convert O₂ into cytotoxic ¹ O₂ . Significant tumor inhibition effects are demonstrated in breast tumor xenograft models without exogenous laser excitation. It is envisioned that a laser-excitation-free PDT strategy enabled by the PLNP-DNA nanocomplex promotes the development of PDT and provides a new local therapeutic approach.

Recent Advances in Stimuli-Responsive DNA-Based Hydrogels

Stimuli-responsive DNA-based hydrogels are attracting growing interest because of their smart responsiveness, excellent biocompatibility, regulated biodegradability, and programmable design properties. Integration of reconfigurable DNA architectures and switchable supramolecular moieties (as cross-linkers) in hydrogels by responding to external stimuli provides an ideal approach for the reversible tuning structural and mechanical properties of the hydrogels, which can be exploited in the development of intelligent DNA-based materials. This review highlights recent advances in the design of responsive pure DNA hydrogels, DNA-polymer hybrid hydrogels, and autonomous DNA-based hydrogels with transient behaviors. A variety of chemically and physically triggered DNA-based stimuli-responsive hydrogels and their versatile applications in biosensing, biocatalysis, cell culture and separation, drug delivery, shape memory, self-healing, and robotic actuators are summarized. Finally, we address the key challenges that the field will face in the coming years, and future prospects are identified.

Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective

Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.

Construction of rolling circle amplification-based DNA nanostructures for biomedical applications

DNA-based materials exhibit great potential in biomedical applications due to the excellent sequence programmability and unique functional designability. Rolling circle amplification (RCA) is an efficient isothermal enzymatic amplification strategy to...

T Lymphocyte-Captured DNA Network for Localized Immunotherapy

The efficient isolation of immune cells with high purity and low cell damage is important for immunotherapy and remains highly challenging. We herein report a cell capture DNA network containing polyvalent multimodules for the specific isolation and in situ incubation of T lymphocytes (T-cells). Two ultralong DNA chains synthesized by an enzymatic amplification process were rationally designed to include functional multimodules as cell anchors and immune adjuvants. Mutually complementary sequences facilitated the formation of a DNA network and encapsulation of T-cells, as well as offering cutting sites of a restriction enzyme for the responsive release of T-cells and immune adjuvants. The purity of captured tumor-infiltrating T-cells reached 98%, and the viability of T-cells maintained ∼90%. The T-cells-containing DNA network was further administrated to a tumor lesion for localized immunotherapy. Our work provides a robust nanobiotechnology for efficient isolation of immune cells and other biological particles.

Sustainable Bioplastic Made from Biomass DNA and Ionomers

Plastics play important roles in modern life and currently the development of plastic recycling is highly demanding and challenging. To relieve this dilemma, one option is to develop new sustainable bioplastics that are compatible with the environment over the whole material life cycle. We report a sustainable bioplastic made from natural DNA and biomass-derived ionomers, termed as DNA plastics. The sustainability involves all aspects of the production, use, and end-of-life options of DNA plastics: (1) the raw materials are derived from biorenewable resources; (2) the water-processable strategy is environmentally friendly, not involving high-energy consumption, the use of organic solvents, and the production of byproducts; (3) recyclable and nondestructive use is achieved to significantly prolong the service lifetime of the plastics; and (4) the disposal of waste plastics follows two green routes including the recycling of waste plastics and enzyme-triggered controllable degradation under mild conditions. Besides, DNA plastics can be "aqua-welded" to form arbitrary designed products such as a plastic cup. This work provides a solution to transform biobased hydrogel to bioplastic and demonstrates the closed-loop recycling of DNA plastics, which will advance the development of sustainable materials.

Rolling circle amplification (RCA)-based DNA hydrogel

DNA hydrogels have unique properties, including sequence programmability, precise molecular recognition, stimuli-responsiveness, biocompatibility and biodegradability, that have enabled their use in diverse applications ranging from material science to biomedicine. Here, we describe a rolling circle amplification (RCA)-based synthesis of 3D DNA hydrogels with rationally programmed sequences and tunable physical, chemical and biological properties. RCA is a simple and highly efficient isothermal enzymatic amplification strategy to synthesize ultralong single-stranded DNA that benefits from mild reaction conditions, and stability and efficiency in complex biological environments. Other available methods for synthesis of DNA hydrogels include hybridization chain reactions, which need a large amount of hairpin strands to produce DNA chains, and PCR, which requires temperature cycling. In contrast, the RCA process is conducted at a constant temperature and requires a small amount of circular DNA template. In this protocol, the polymerase phi29 catalyzes the elongation and displacement of DNA chains to amplify DNA, which subsequently forms a 3D hydrogel network via various cross-linking strategies, including entanglement of DNA chains, multi-primed chain amplification, hybridization between DNA chains, and hybridization with functional moieties. We also describe how to use the protocol for isolation of bone marrow mesenchymal stem cells and cell delivery. The whole protocol takes ~2 d to complete, including hydrogel synthesis and applications in cell isolation and cell delivery.

Self-Assembly of Dendritic DNA into a Hydrogel: Application in Three-Dimensional Cell Culture

With inherent biocompatibility, biodegradability, and unique programmability, hydrogels with a DNA framework show great potential in three-dimensional (3D) cell culture. Here, a DNA hydrogel was assembled by a dendritic DNA with four branches. The hydrogel showed tunable mechanical strength and reversible thixotropy even under a nanomolar DNA concentration. The cell culture medium can be converted into the hydrogel isothermally at physiological temperature. This DNA hydrogel allows both cancer and somatic cells to be seeded in situ and to achieve high proliferation and viability. The bis-entity of dendritic branches enabled the specific loading of bioactive clues to regulate cell behaviors. Thus, the dendritic DNA-assembled hydrogel could serve as a highly biocompatible, readily functionalizing, and easy-casting gel platform for 3D cell culture.