Rolling circle amplification (RCA)-based DNA hydrogel

Combination of exciton-plasmon interaction and programmable DNA cyclic amplification for electrochemiluminescence/photoelectrochemical sensing of serotonin

A novel dual-mode electrochemiluminescence (ECL)/photoelectrochemistry (PEC) biosensor was developed for sensitive serotonin detection. In this system, the PEC signal was produced by CdS quantum dots (QDs), while the ECL signal originated from L-Au NPs (luminol decorated Au nanoparticles), thereby avoiding the external interference and signal fluctuations that typically arose from using the same materials for both signals. The presence of target serotonin initiated the non-enzymatic toehold-mediated strand displacement reaction (TSDR) on magnetic bead (MB), which was followed by catalytic hairpin assembly (CHA) on the sensing interface, leading to the aggregation of many L-Au NPs. The strong exciton-plasmon interactions (EPI) induced the energy transfer between CdS QDs and Au NPs, causing the significant suppression of the photocurrent. In addition, this design assured that the ECL and PEC respond in opposing manners and that no background ECL signal was detected, thereby greatly improving the sensitivity of the biosensor. Ultimately, the biosensor demonstrated a broad linear range from 5 pM to 1 μM with a detection limit of 1.6 pM, and also could be used for the assay of serum and urine samples with satisfactory results. With the advantages of high sensitivity, selectivity, accuracy and signal stability, this sensing strategy was helpful for disease diagnosis and the fundamental research of neurotransmitters.

DNA Nanostructures-Based In Situ Cancer Vaccines: Mechanisms and Applications

Current tumor vaccines suffer from inadequate immune responsive due to the insufficient release of tumor antigens, low tumor infiltration, and immunosuppressive microenvironment. DNA nanostructures with their ability to precisely engineer, controlled release, biocompatibility, and the capability to augment the immunogenicity of tumor microenvironment, have gained significant attention for their potential to revolutionize vaccine designing. This review summarizes various applications of DNA nanostructures in the construction of in situ cancer vaccines, which can generate tumor-associated antigens directly from damaged tumors for cancer immune-stimulation. The mechanisms and components of cancer vaccines are listed, the specific strategies for constructing in situ vaccines using DNA nanostructures are explored and their underlying mechanisms of action are elucidated. The immunogenic cell death (ICD) induced by chemotherapeutic agents, photothermal therapy (PTT), photodynamic therapy (PDT), and radiation therapy (RT) and the related cancer vaccines building strategies are systematically summarized. The applications of different DNA nanostructures in various cancer immunotherapy are elaborated, which exerts precise, long-lasting, and robust immune responses. The current challenges and future prospectives are proposed. This review provides a holistic understanding of the evolving role of DNA nanostructures for in situ vaccine development.

Circular Single-Stranded DNA-Based Artificial Nanoviruses Mitigate Colorectal Cancer Development

Colorectal cancer (CRC) remains a significant global health challenge, underscoring the need for innovative therapeutic strategies. Oncogenic miRNAs (oncomiRs) play a significant biological role in the initiation and progression of colorectal cancer. Inspired by the cooperative mechanisms of plant nanovirus, which employ multiple circular single-stranded DNA (CssDNA) genomes, it is hypothesized that the development and delivery of CssDNA to target oncomiRs would achieve therapeutic benefits in CRC. In this study, a multi-omics approach is utilized to identify key tumor suppressor genes (TSGs) and their related oncomiRs implicated in CRC, followed by the development of CssDNA, each of which is loaded with multiple miRNA binding sites targeting one oncomiR. When transfected into the cells, these CssDNA can effectively target and sequester the corresponding oncomiRs to restore the expression of TSGs, leading to a marked reduction in CRC development both in vitro and in vivo. The findings highlight the therapeutic potential of nanovirus-inspired CssDNA in modulating the miRNA-mediated regulatory network in CRC. This study lays the groundwork for the development of non-coding DNA-based therapies with broad implications for the treatment of colorectal cancer and potentially other malignancies.

A straightforward process manipulates the dramatic morphological changes of DNA rolling circle amplification products

Rolling circle amplification (RCA) is a widely used method for the synthesis of DNA nanoparticles and macro-hydrogels. Several strategies, including oscillation-promoted entanglement of DNA chains, multi-round chain amplification, hybridization between DNA chains, and hybridization with functional moieties, were applied to synthesize DNA macro-hydrogels; alternatively, flower-like nanoparticles were also produced. Here we report a straightforward yet effective method to manipulate the morphology of RCA products from nanoparticles to 3D hydrogels using an additional cold treatment step of the circular DNA template prior to elongation using phi29 DNA polymerase. This process induces a minor aggregation of the circular DNA template, significantly enhancing the entanglement of DNA chains in subsequent steps. Compared to contemporary synthesis methods for RCA-based macro-hydrogels, our technique provides milder reaction conditions, shorter reaction time, and a more straightforward system. Notably, our method eliminates the need for oscillation during amplification and requires only a single round of RCA with a single type of circular DNA, thereby simplifying the synthesis process.

Engineering a DNA polymerase for modifying large RNA at specific positions

The synthesis of large RNA with precise modifications at specific positions is in high demand for both basic research and therapeutic applications, but efficient methods are limited. Engineered DNA polymerases have recently emerged as attractive tools for RNA labelling, offering distinct advantages over conventional RNA polymerases. Here, through semi-rational designs, we engineered a DNA polymerase variant and used it to precisely incorporate a diverse range of modifications, including base modifications, 2'-ribose modifications and backbone modifications, into desired positions within RNA. We achieved efficiencies exceeding 85% in the majority of modification cases, demonstrating success in introducing 2'-O-methyl, phosphorothioate, N4-acetylcytidine and a fluorophore to specific sites in eGFP and Firefly luciferase messenger RNA. Our mRNA products with N4-acetylcytidine, 2'-O-methyl and/or phosphorothioate have demonstrated the ability to enhance stability and affect protein production. This method presents a promising tool for the comprehensive functionalization of RNA, enabling the introduction of plentiful modifications irrespective of RNA lengths and sequences.

Multifunctional DNA-Metal Nanohybrids Derived From DNA-MgPPi Microhybrids by Rolling Circle Amplification

Rolling circle amplification (RCA)-derived ultra-long DNA is highly attractive and versatile because of its diverse functionalities conferred by repeated DNA nanostructures. However, magnesium pyrophosphate (MgPPi) crystals, as byproducts of RCA, electrostatically interact with the DNA to form DNA microhybrids and hamper its broad bioapplications, as its large size is unfavorable for cellular uptake and decreases the density of functional DNA nanostructures. In this study, finely tuned synthesis strategies are developed to condense the microhybrids and replace non-functional MgPPi crystals with various functional metal nanostructures by reducing metal ions. By applying this condensation and reduction process to DNA templated by microhybrids, the particle size of organic-inorganic DNA-MgPPi microhybrids is gradually reconfigured into DNA-Au nanohybrids (≈15 fold difference). The effects of the ion concentration and metal ion type on the reduction process are systematically explored through morphological, structural, and compositional analyses. Upon formation of the nanohybrids, the preservation of Au nanostructures and polymerized DNA nanostructure-driven functions are evaluated. The nanohybrids demonstrated not only metal nanoparticle-based near-infrared absorbance but also DNA aptamer-mediated targeted intracellular delivery, indicating successful hybridization of functional organic-inorganic molecules. This synthesis method for RCA-originated ultra-long DNA-metal nanohybrids shows potential for a variety of biological applications.

An easy-operation aptasensor for simultaneous detection of multiple tumor-associated exosomal proteins based on multicolor fluorescent DNA nanoassemblies

As a promising liquid biopsy biomarker, exosomes have demonstrated great potential and advantages in the noninvasive tumor diagnosis. However, an accurate and sensitive method for tumors-associated exosomes detection is scarce. Herein, we presented an easy-operation aptasensor which simultaneously detect multiple exosomal proteins by using multicolor fluorescent DNA nanoassemblies (FDNs) and CD63 aptamer-modified magnetic beads (MNPs-AptCD63). In this system, the FDNs were firstly constructed by encapsulating different quantum dots (QDs) into rolling circle amplification (RCA) products that contained different aptamer sequences. Thus, the FDNs could selectively recognize the different exosomal proteins captured by the MNPs-AptCD63, and achieve the multiplex and sensitive detection according to the fluorescence of QDs. Benefiting from the signal amplification capacity and high selectivity of FDNs, this aptasensor not only could detect exosomes as low as 650 particles/μL, but also showed accurate analysis in clinical samples. In addition, we can also achieve point-of-care testing (POCT) due to the simple analysis steps and naked-eye observable fluorescence of QDs under the ultraviolet irradiation. We believe that our aptasensor could provide a promising platform for exosomes-based personalized diagnosis and precise monitoring of human health.

Immuno-Rolling Circle Amplification (Immuno-RCA): Biosensing Strategies, Practical Applications, and Future Perspectives

In the rapidly evolving field of life sciences and biomedicine, detecting low-abundance biomolecules, and ultraweak biosignals presents significant challenges. This has spurred a rapid development of analytical techniques aiming for increased sensitivity and specificity. These advancements, including signal amplification strategies and the integration of biorecognition events, mark a transformative era in bioanalytical precision and accuracy. A prominent method among these innovations is immuno-rolling circle amplification (immuno-RCA) technology, which effectively combines immunoassays with signal amplification via RCA. This process starts when a targeted biomolecule, such as a protein or cell, binds to an immobilized antibody or probe on a substrate. The introduction of a circular DNA template triggers RCA, leading to exponential amplification and significantly enhanced signal intensity, thus the target molecule is detectable and quantifiable even at the single-molecule level. This review provides an overview of the biosensing strategy and extensive practical applications of immuno-RCA in detecting biomarkers. Furthermore, it scrutinizes the limitations inherent to these sensors and sets forth expectations for their future trajectory. This review serves as a valuable reference for advancing immuno-RCA in various domains, such as diagnostics, biomarker discovery, and molecular imaging.

Ultra-sensitive detection of norovirus using a three-in-one CRISPR platform based on a DNA hydrogel and composite functional nanomaterials

The ultrasensitive sensor with three optical response mechanisms was proposed for the determination of trace amounts of norovirus using a 3-in-1 GCSNAs (a gap-containing spherical nucleic acid nanoparticles) probe. A simple and highly sensitive three-mode biosensor with Raman, colorimetric, and fluorescence functions was proposed and implemented using the GCSNAs probe and a DNA hydrogel for norovirus detection. When the virus exists, the trans-cleavage activity of CRISPR-Cas12a was activated by double-stranded dsDNA (dsDNA) generated by reverse transcription and recombinase polymerase isothermal amplification (RT-RPA) to degrade the DNA hydrogel/GCSNA composition and release the three-in-one (3-in-1) probe-GCSNA, realising the triple ultrasensitive detection of norovirus. The colorimetric sensing mode allows for semi-quantitative on-site detection, which is visible to the naked eye and the quantitative detection can be achieved by conducting grayscale analysis using the "Colour Grab" function of a smartphone. This new triple sensor achieved the successful quantification of norovirus at concentrations as low as the femtomolar scale with an excellent selectivity and accuracy. Considering the colorimetric properties of rolling circle amplification (RCA)-based DNA hydrogels and GCSNAs, the proposed method has a broad application prospect in virus on-site detection in food. It should be applicable for virus detection in a wide range of fields such, as environmental analysis, medical diagnosis, and food safety. It is anticipated that this mechanism will open new avenues for the development of multimodal analyses and multifunctional sensing platforms for various applications. We anticipate that this sensing mechanism will open up a new way for the development of food safety detection.

DNA Nanotechnology for Application in Targeted Protein Degradation

DNA is a kind of flexible and versatile biomaterial for constructing nanostructures and nanodevices. Due to high biocompatibility and programmability and easy modification and fabrication, DNA nanotechnology has emerged as a powerful tool for application in intracellular targeted protein degradation. In this review, we summarize the recent advances in the design and mechanism of targeted protein degradation technologies such as protein hydrolysis targeted chimeras, lysosomal targeted chimeras, and autophagy based protein degradation. Subsequently, we introduce the DNA nanotechnologies of DNA cascade circuits, DNA nanostructures, and dynamic machines. Moreover, we present the latest developments in DNA nanotechnologies in targeted protein degradation. Finally, the vision and challenges are discussed.

Recent advances in the construction strategy, functional properties, and biosensing application of self-assembled triangular unit-based DNA nanostructures

Research on self-assembled deoxyribonucleic acid (DNA) nanostructures with different shapes, sizes, and functions has recently made rapid progress owing to its biocompatibility, programmability, and stability. Among these, triangular unit-based DNA nanostructures, which are typically multi-arm DNA tiles, have been widely applied because of their unique structural rigidity, spatial flexibility, and cell permeability. Triangular unit-based DNA nanostructures are folded from multiple single-stranded DNA using the principle of complementary base pairing. Its shape and size can be determined using pre-set scaffold strands, segmented base complementary regions, and sequence lengths. The resulting DNA nanostructures retain the desired sequence length to serve as binding sites for other molecules and obtain satisfactory results in molecular recognition, spatial orientation, and target acquisition. Therefore, extensive research on triangular unit-based DNA nanostructures has shown that they can be used as powerful tools in the biosensing field to improve specificity, sensitivity, and accuracy. Over the past few decades, various design strategies and assembly techniques have been established to improve the stability, complexity, functionality, and practical applications of triangular unit-based DNA nanostructures in biosensing. In this review, we introduce the structural design strategies and principles of typical triangular unit-based DNA nanostructures, including triangular, tetrahedral, star, and net-shaped DNA. We then summarize the functional properties of triangular unit-based DNA nanostructures and their applications in biosensing. Finally, we critically discuss the existing challenges and future trends.

Advances in DNA nanotechnology for chronic wound management: Innovative functional nucleic acid nanostructures for overcoming key challenges

Chronic wound management is affected by three primary challenges: bacterial infection, oxidative stress and inflammation, and impaired regenerative capacity. Conventional treatment methods typically fail to deliver optimal outcomes, thus highlighting the urgency to develop innovative materials that can address these issues and improve efficacy. Recent advances in DNA nanotechnology have garnered significant interest, particularly in the field of functional nucleic acid (FNA) nanomaterials, owing to their exceptional biocompatibility, programmability, and therapeutic potential. Among them, FNAs with unique nanostructures have garnered considerable attention. First, they inherit the biological properties of FNAs, including biocompatibility, reactive oxygen species (ROS)-scavenging capabilities, and modulation of cellular functions. Second, based on a precise design, these nanostructures exhibit superior physical properties, stability, and cellular uptake. Third, by leveraging the programmability of DNA strands, FNA nanostructures can be customized to accommodate therapeutic nucleic acids, peptides, and small-molecule drugs, thereby enabling a stable and controlled drug delivery system. These unique characteristics enable the use of FNA nanostructures to effectively address the major challenges in chronic wound management. This review focuses on various FNA nanostructures, including tetrahedral framework nucleic acids (tFNAs), DNA hydrogels, DNA origami, and rolling-circle amplification (RCA) DNA assembly. Additionally, a summary of recent advancements in their design and application for chronic wound management as well as insights for future research in this field are provided.

CRISPR-Responsive RCA-Based DNA Hydrogel Biosensing Platform with Customizable Signal Output for Rapid and Sensitive Nucleic Acid Detection

Current nucleic acid-responsive DNA hydrogels face significant challenges, such as the requirement for high target concentrations, frequent redesigns, and increased costs, which limit their practical applications in biosensing. To address these issues, we developed a novel biosensing platform integrating a CRISPR/Cas12a system into an RCA-based DNA hydrogel. The hydrogel used in the platform could preencapsulate diverse signal molecules comprising GelRed, methylene blue, and gold nanoparticles, which were released upon Cas12a-mediated cleavage. This design enabled customizable signal output, including fluorescence, electrochemistry, and colorimetry, thereby ensuring the platform's adaptability to various detection scenarios. Our platform was highly specific for methicillin-resistant Staphylococcus aureus, with a mecA gene detection limit of 10 copies/μL, and provided fast and accurate results within 2 h for clinical samples. Hence, based on these advantages, the proposed biosensing platform exhibits promising application prospects in the field of nucleic acid detection.

Co-freezing localized CRISPR-Cas12a system enables rapid and sensitive nucleic acid analysis

Rapid and sensitive nucleic acid detection is vital in disease diagnosis and therapeutic assessment. Herein, we propose a co-freezing localized CRISPR-Cas12a (CL-Cas12a) strategy for sensitive nucleic acid detection. The CL-Cas12a was obtained through a 15-minute co-freezing process, allowing the Cas12a/crRNA complex and hairpin reporter confined on the AuNPs surface with high load efficiency, for rapid sensing of nucleic acid with superior performance to other localized Cas12a strategies. This CL-Cas12a based platform could quantitatively detect targets down to 98 aM in 30 min with excellent specificity. Furthermore, the CL-Cas12a successful applied to detect human papillomavirus infection and human lung cancer-associated single-nucleotide mutations. We also achieved powerful signal amplification for imaging Survivin mRNA in living cells. These findings highlight the potential of CL-Cas12a as an effective tool for nucleic acid diagnostics and disease monitoring.

Oral Hydrogels that Balance Microbiome for Tumor Treatment

Intervening in the microbial environment holds promise for enhancing antitumor efficacy by reshaping the tumor microenvironment, yet few strategies have been reported. In a study led by Zou and coworkers, oral hydrogels are introduced to regulate the microbiota balance in the intestines and tumors, triggering an antitumor immune response. This work presents a microbiota-targeted drug delivery system that demonstrates notable efficacy in colon targeting and colon retention for the treatment of colorectal cancer. This represents a significant clinical advancement in treating colorectal cancer, which is particularly vulnerable to microbial infiltration.

NucleoCraft: The Art of Stimuli-Responsive Precision in DNA and RNA Bioengineering

Recent advancements in DNA and RNA bioengineering have paved the way for developing stimuli-responsive nanostructures with remarkable potential across various applications. These nanostructures, crafted through sophisticated bioengineering techniques, can dynamically and precisely respond to both physiological and physical stimuli, including nucleic acids (DNA/RNA), adenosine triphosphate, proteins, ions, small molecules, pH, light, and temperature. They offer high sensitivity and specificity, making them ideal for applications such as biomarker detection, gene therapy, and controlled targeted drug delivery. In this review, we summarize the bioengineering methods used to assemble versatile stimuli-responsive DNA/RNA nanostructures and discuss their emerging applications in structural biology and biomedicine, including biosensing, targeted drug delivery, and therapeutics. Finally, we highlight the challenges and opportunities in the rational design of these intelligent bioengineered nanostructures.

The type V effectors for CRISPR/Cas-mediated genome engineering in plants

A plethora of CRISPR effectors, such as Cas3, Cas9, and Cas12a, are commonly employed as gene editing tools. Among these, Cas12 effectors developed based on Class II type V proteins exhibit distinct characteristics compared to Class II type VI and type II effectors, such as their ability to generate non-allelic DNA double-strand breaks, their compact structures, and the presence of a single RuvC-like nuclease domain. Capitalizing on these advantages, Cas12 family proteins have been increasingly explored and utilized in recent years. However, the characteristics and applications of different subfamilies within the type V protein family have not been systematically summarized. In this review, we focus on the characteristics of type V effector (CRISPR/Cas12) proteins and the current methods used to discover new effector proteins. We also summarize recent modifications based on engineering of type V effectors. In addition, we introduce the applications of type V effectors for gene editing in animals and plants, including the development of base editors, tools for regulating gene expression, methods for gene targeting, and biosensors. We emphasize the prospects for development and application of CRISPR/Cas12 effectors with the goal of better utilizing toolkits based on this protein family for crop improvement and enhanced agricultural production.

Energy-storing DNA-based hydrogel remodels tumor microenvironments for laser-free photodynamic immunotherapy

Photodynamic therapy (PDT) is a promising modality for cancer treatment. However, limited tissue penetration of external radiation and complicated tumor microenvironments (TMEs) restrict the antitumor efficiency of PDT. Herein, we report an energy-storing DNA-based hydrogel, which enables tumor-selective PDT without external radiation and regulates TMEs to achieve boosted PDT-mediated tumor immunotherapy. The system is constructed with two ultralong single-stranded DNA chains, which programmed partial complementary sequences and repeated G-quadruplex forming AS1411 aptamer for photosensitizer loading via hydrophobic interactions and π-π stacking. Then, energy-storing persistent luminescent nanoparticles are incorporated to sensitize PDT selectively at tumor site without external irradiation, generating tumor antigen to agitate antitumor immune response. The system catalytically generates O2 to alleviate hypoxia and releases inhibitors to reverse the IDO-related immunosuppression, synergistically remodeling the TMEs. In the mouse model of breast cancer, this hydrogel shows a remarkable tumor suppression rate of 78.3 %. Our study represents a new paradigm of photodynamic immunotherapy against cancer by combining laser-free fashion and TMEs remodeling.

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.

A non-enzymatic, isothermal amplification sensor for quantifying the relative abundance of Akkermansia muciniphila

Herein, we have developed a non-enzymatic, isothermal amplification assay (NIA sensor) based on a catalytic hairpin assembly (CHA) reaction for quantifying the relative abundance of Akkermansia muciniphila. Through detection of the MUC-1437 gene (limit of detection: 8.3 fM) in a dynamic range from 10 fM to 1 nM, the NIA sensor shows high sensitivity and selectivity in preclinical models of mice fed a normal or high-fat diet (HFD), and treated with antibiotics (ATB). The NIA sensor, which operates without the use of any enzymes, leading to simplicity and cost-effectiveness, has great potential for biosensing research and clinical diagnostic applications.

Self-Assembled DNA Microflowers for Platelet-Derived Extracellular Vesicle Isolation and Infected Wound Healing

Platelet-derived extracellular vesicles (PEVs) showing great potential in wound healing have attracted increasing attention recently. Nondestructive isolation and effective utilization strategies are highly conducive for PEVs developing into recognized therapeutic entities. Here, we present an efficient strategy for PEV isolation and bacterial infected wound healing based on self-assembled DNA microflowers. First, DNA microflowers are prepared using rolling circle amplification. Then, the hydrophobic interaction between cholesteryl modified on DNA microflowers and the phospholipid bilayer membrane of PEVs leads to the formation of a network structure with improved mechanical strength and the separation of PEVs from biological samples. Finally, controlled release of PEVs is achieved through bacterial-induced hydrogel degradation. In vitro experiments demonstrate the obtained DNA hydrogel with good cytocompatibility and therapeutic potential. Taken together, the DNA microflower-based hydrogels with bioadhesive, self-healing, tunable mechanical properties and bacteria-responsive behavior offer substantial potential for EV isolation and wound healing.

DNA-functionalized cryogel based colorimetric biosensor for sensitive on-site detection of aflatoxin B1 in food samples

Hydrogel biosensors present numerous advantages in food safety analysis owing to their remarkable biocompatibility, cargo-loading capabilities and optical properties. However, the current drawbacks (slow target responsiveness and poor mechanical strength) restricted their further utilization at on-site detection of targets. To address these challenges, a DNA-functionalized cryogel with hierarchical pore structures is constructed to improve the reaction rate and the robustness of hydrogel biosensor. During cryogel preparation, ice crystals serve as templates, shaping interconnected hierarchical microporous structures to enhance mass transfer for faster responses. Meanwhile, in the non-freezing zone, concentrated monomers create a dense cross-linked network, strengthening cryogel matrix strength. Accordingly, a colorimetric biosensor based on DNA cryogel has been developed as a proof of concept for rapid detection of aflatoxin B1 (AFB1) in food samples, and an excellent analytical performance was obtained under the optimized conditions with a low detection limit (1 nM), broad detection range (5-100 nM), satisfactory accuracy and precision (recoveries, 81.2-112.6 %; CV, 2.75-5.53 %). Furthermore, by integrating with a smartphone sensing platform, a portable device was created for rapid on-site measurement of target within 45 min, which provided some insight for hydrogel biosensors design.

Neutrophil extracellular traps-inspired DNA hydrogel for wound hemostatic adjuvant

Severe traumatic bleeding may lead to extremely high mortality rates, and early intervention to stop bleeding plays as a critical role in saving lives. However, rapid hemostasis in deep non-compressible trauma using a highly water-absorbent hydrogel, combined with strong tissue adhesion and bionic procoagulant mechanism, remains a challenge. In this study, a DNA hydrogel (DNAgel) network composed of natural nucleic acids with rapid water absorption, high swelling and instant tissue adhesion is reported, like a band-aid to physically stop bleeding. The excellent swelling behavior and robust mechanical performance, meanwhile, enable the DNAgel band-aid to fill the defect cavity and exert pressure on the bleeding vessels, thereby achieving compression hemostasis for deep tissue bleeding sites. The neutrophil extracellular traps (NETs)-inspired DNAgel network also acts as an artificial DNA scaffold for erythrocytes to adhere and aggregate, and activates platelets, promoting coagulation cascade in a bionic way. The DNAgel achieves lower blood loss than commercial gelatin sponge (GS) in male rat trauma models. In vivo evaluation in a full-thickness skin incision model also demonstrates the ability of DNAgel for promoting wound healing. Overall, the DNAgel band-aid with great hemostatic capacity is a promising candidate for rapid hemostasis and wound healing.

Engineering of a DNAzyme-Based dimeric G-quadruplex rolling circle amplification for robust analysis of lead ion

Detecting heavy metal pollution, particularly lead ion (Pb2⁺) contamination, is imperative for safeguarding public health. In this study, we introduced an innovative approach by integrating DNAzyme with rolling circle amplification (RCA) to propose an amplification sensing method termed DNAzyme-based dimeric-G-quadruplex (dimer-G4) RCA. This sensing approach allows for precise and high-fidelity Pb2⁺ detection. Strategically, in the presence of Pb2⁺, the DNAzyme undergoes substrate strand (S-DNA) cleavage, liberating its enzyme strand (E-DNA) to prime isothermal amplification. This initiates the RCA process, producing numerous dimer-G-Quadruplexes (dimer-G4) as the signal reporting transducers. Compared to conventional strategies using monomeric G-quadruplex (mono-G4) as the reporting transducers, these dimer-G4 structures exhibit significantly enhanced fluorescence when bound with Thioflavin T (ThT), offering superior target signaling ability for even detection of Pb2⁺ at low concentration. Conversely, in the absence of Pb2⁺, the DNAzyme structure remains intact so that no primers can be produced to cause the RCA initiation. This nucleic acid amplification-based Pb2⁺ detection method combing with the high specificity of DNAzymes for Pb2⁺ recognition ensures highly sensitive detection of Pb2+ with a detection limit of 0.058 nM, providing a robust tool for food safety analysis and environmental monitoring.

A DNA/Poly-(L-lysine) Hydrogel with Long Shelf-Time for 3D Cell Culture

Deoxyribonucleic acid (DNA)-based hydrogels are emerging as promising functional materials for biomedical applications. However, the shelf-time of DNA hydrogels in biological media is severely shortened by nucleases, which limit the application of DNA hydrogels. Herein, a DNA hydrogel with long shelf-time is reported for 3D cell culture. Poly-(L-lysine) (PLL) is introduced as both a cross-linker and a protectant. The electrostatic interaction between PLL and DNA drove the formation of hydrogel. PLL coating on DNA increased the steric hindrance between DNA and nucleases, thus weakening the digestion of nucleases toward phosphodiester bond. As a result, the shelf-time of DNA/PLL hydrogel for 3D cell culture is extended from generally 1 day to longer than 15 days, which has not been achieved previously. Notably, poly-AS1411-aptamers are integrated to DNA/PLL hydrogels for anchoring U87 cells, and the cell encapsulation efficiency of the DNA/PLL hydrogels with aptamer is 4-time higher than that of the hydrogels without aptamer. DNA/PLL hydrogel provided a favorable microenvironment to support the proliferation of cells, which formed cell spheroid in 15 days. This protective coating strategy solves the long-standing problem on the shelf-time of DNA hydrogel, and is envisioned to promote the development of DNA hydrogel in more biomedical applications.

A New SPQC Biosensor for the Detection of a New Target of Escherichia/Shigella Genera Based on a Novel Method of Synthesizing Long-Range DNA

The rapid and sensitive detection of Escherichia/Shigella genera is crucial for human disease and health. This study introduces a novel series of piezoelectric quartz crystal (SPQC) sensors for detecting Escherichia/Shigella genera. In this innovative biosensor, we propose a new target and novel method for synthesizing long-range DNA. The method relies on the amplification of two DNA probes, referred to as H and P amplification (HPA), resulting in the products of long-range DNA named Sn. The new target was screened from the 16S rRNA gene and utilized as a biomarker. The SPQC sensor operates as follows: the Capture probe is modified on the electrodes. In the presence of a Displace probe and target, the Capture can form a complex with the Displace probe. The resulting complex hybridizes with Sn, bridging the gap between the electrodes. Finally, silver wires are deposited between the electrodes using Sn as a template. This process results in a sensitive response from the SPQC. The detection limit of the SPQC sensor is 1 CFU/mL, and the detection time is within 2 h. This sensor would be of great benefit for food safety monitoring and clinical diagnosis.

Two-layer cascaded catalytic hairpin assemblies based on locked nucleic acids for one-step and highly sensitive ctDNA detection

Enzyme-free signal amplification of catalytic hairpin assembly (CHA) has enabled sensitive detection of circulating tumor DNA (ctDNA) in early clinical diagnosis. Conventional CHA strategies are restrained by the limited amplification efficiency of the single-stage system, and signal leakage from "breathing" influence and nuclease degradation. Here, we introduced two-layer cascaded locked nucleic acid (LNA)-assisted CHA circuits with the intelligent incorporation of LNA in the hairpins and reporter for the highly sensitive one-step detection of scarce ctDNA. The target-triggered upstream CHA reaction continuously generates hybrid products to catalyze the downstream CHA reaction for transducing the primary sensing event, and the released target and the produced hybrid product trigger the next catalytic reaction round at the same time and finally cascade to amplify the target ctDNA fluorescence output signal. Meanwhile, the stronger binding affinity of the LNA-DNA duplex endows the two-layer LNA-assisted CHA system with thermodynamic stability and nuclease resistance, and thus our designed system exhibits an excellent detection performance for target ctDNA in the range from 2 pM to 5 nM with a low detection limit of 0.6 pM. Significantly, the two-layer LNA-assisted CHA circuits have been successfully implemented for the feasible analysis of clinical samples. This two-layer cascaded LNA-assisted CHA strategy provides a promising high sensitivity tool for one-step detection of scarce ctDNA from complex clinical samples and would facilitate the reconfiguration of DNA circuit-based DNA nanotechnology for the precise analysis of other biomarkers in clinical research fields.

DNA Polymerase-Endonuclease Efficiently Synthesizes DNA to Prepare DNA Materials and Develop Novel Signal Amplification System

DNA biosynthesis, a focus of fundamental and applied research, typically involves DNA polymerases by using templates, primers, and dNTPs. Some polymerases can polymerize dNTPs for DNA de novo synthesis, although this is generally to occur randomly. This novel synthesis method has garnered our attention and practical use. Herein, we observed that the addition of endonuclease significantly enhances the efficiency of the de novo synthesis reaction catalyzed by the DNA polymerase. We further investigated the reaction conditions that influence this efficiency. Building on the optimal reaction conditions, we developed a rapid and efficient strategy for preparing DNA hydrogel. Further, coupled with the CRISPR-Cas system, we developed a nucleic acid signal amplification system characterized by versatility, sensitivity, specificity, and no risk of aerosol contamination. We successfully detected viral nucleic acids in clinical samples. In summary, our study demonstrates the significant potential of DNA polymerase- and endonuclease-catalyzed DNA de novo synthesis in diverse applications.

Hydrogel-integrated sensors for food safety and quality monitoring: Fabrication strategies and emerging applications

Food safety is a global issue in public hygiene. The accurate, sensitive, and on-site detection of various food contaminants performs significant implications. However, traditional methods suffer from the time-consuming and professional operation, restricting their on-site application. Hydrogels with the merits of highly porous structure, high biocompatibility, good shape-adaptability, and stimuli-responsiveness offer a promising biomaterial to design sensors for ensuring food safety. This review describes the emerging applications of hydrogel-based sensors in food safety inspection in recent years. In particular, this study elaborates on their fabrication strategies and unique sensing mechanisms depending on whether the hydrogel is stimuli-responsive or not. Stimuli-responsive hydrogels can be integrated with various functional ligands for sensitive and convenient detection via signal amplification and transduction; while non-stimuli-responsive hydrogels are mainly used as solid-state encapsulating carriers for signal probe, nanomaterial, or cell and as conductive media. In addition, their existing challenges, future perspectives, and application prospects are discussed. These practices greatly enrich the application scenarios and improve the detection performance of hydrogel-based sensors in food safety detection.

DNA Hydrogels with Programmable Condensation, Expansion, and Degradation for Molecular Carriers

Molecular carriers are necessary for the controlled release of drugs and genes to achieve the desired therapeutic outcomes. DNA hydrogels can be a promising candidate in this application with their distinctive sequence-dependent programmability, which allows precise encapsulation of specific cargo molecules and stimuli-responsive release of them at the target. However, DNA hydrogels are inherently susceptible to the degradation of nucleases, making them vulnerable in a physiological environment. To be an effective molecular carrier, DNA hydrogels should be able to protect encapsulated cargo molecules until they reach the target and release them once they are reached. Here, we develop a simple way of controlling the enzyme resistance of DNA hydrogels for cargo protection and release by using cation-mediated condensation and expansion. We found that DNA hydrogels condensed by spermine are highly resistant to enzymatic degradation. They become degradable again if expanded back to their original, uncondensed state by sodium ions interfering with the interaction between spermine and DNA. These controllable condensation, expansion, and degradation of DNA hydrogels pave the way for the development of DNA hydrogels as an effective molecular carrier.

Sample-to-answer salivary miRNA testing: New frontiers in point-of-care diagnostic technologies

MicroRNA (miRNA), crucial non-coding RNAs, have emerged as key biomarkers in molecular diagnostics, prognosis, and personalized medicine due to their significant role in gene expression regulation. Salivary miRNA, in particular, stands out for its non-invasive collection method and ease of accessibility, offering promising avenues for the development of point-of-care diagnostics for a spectrum of diseases, including cancer, neurodegenerative disorders, and infectious diseases. Such development promises rapid and precise diagnosis, enabling timely treatment. Despite significant advancements in salivary miRNA-based testing, challenges persist in the quantification, multiplexing, sensitivity, and specificity, particularly for miRNA at low concentrations in complex biological mixtures. This work delves into these challenges, focusing on the development and application of salivary miRNA tests for point-of-care use. We explore the biogenesis of salivary miRNA and analyze their quantitative expression and their disease relevance in cancer, infection, and neurodegenerative disorders. We also examined recent progress in miRNA extraction, amplification, and multiplexed detection methods. This study offers a comprehensive view of the development of salivary miRNA-based point-of-care testing (POCT). Its successful advancement could revolutionize the early detection, monitoring, and management of various conditions, enhancing healthcare outcomes. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.

Oligonucleotide based nanogels for cancer therapeutics

Oligonucleotide-based nanogels, as nascent biomaterials, possess several unique functional, structural, and physicochemical features with excellent drug-loading capacity and high potential for cancer gene therapy. Ongoing studies utilizing oligonucleotide-based nanogels hold great promise, as these cutting-edge nanoplatforms can be elegantly developed with predesigned oligonucleotide sequences and complementary strands which are self-assembled or chemically crosslinked leading to the development of nanogels with predictable shape and tunable size with the desired functional properties. Current paper provides a summary of the properties, preparation methods, and applications of oligonucleotide-based nanogels in cancer therapy. The review is focused on both conventional and modified forms of oligonucleotide-based nanogels, including targeted nanogels, smart release nanogels (responsive to stimuli such as pH, temperature, and enzymes), as well as nanogels used for gene delivery. Their application in cancer immunotherapy and vaccination, photodynamic therapy, and diagnostic applications when combined with other nanoparticles is further discussed. Despite emerging designs in the development of oligonucleotide based nanogels, this field of study is still in its infancy, and clinical translation of these versatile nano-vehicles might face challenges. Hence, extensive research must be performed on in vivo behavior of such platforms determining their biodistribution, biological fate, and acute/subacute toxicity.

Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications

The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.

Microfluidic Immunosensing Platform Based on a Rolling Circle Amplification-Assisted DNA Dendrimer Probe for Portable and Sensitive Detection of Allergen-Specific IgE

The robust point-of-care platform for sensitive, multiplexed, and affordable detection of allergen-specific IgE (sIgE) is an urgent demand in component-resolved diagnostics. Here, we developed a microfluidic immunosensing platform based on a rolling circle amplification-assisted DNA dendrimer probe for sensitive detection of multiple sIgEs. The versatile multichannel microfluidic whole blood analytical device integrates cell filtration, recombinant antigen-modified magnetic enrichment, and DNA dendrimer probe-amplified signal transduction for portable on-chip analysis. Three sIgEs against common oyster allergens were simultaneously detected in blood samples by simple smartphone-based imaging without any pretreatment. The quantitative detection of multiple allergen-specific antibodies on the platform was achieved with limits of detection of less than 50 pg/mL, exhibiting superior sensitivity compared to most point-of-care testing. The detection results of 55 serum samples and 4 whole blood samples were 100% consistent with the ELISA results, confirming the accuracy and stability of our platform. Additionally, the reversible combination of hexahistidine6-tag and Ni-IMAC magbead was elegantly utilized on the immunosensing platform for desired reversibility. With the advantages of general applicability, high sensitivity, and reversibility, the DNA dendrimer-based microfluidic immunosensing platform provides great potential for the portable detection of immune proteins as a point-of-care platform in disease diagnostics and biological analysis.

A Smart DNA Hydrogel Enables Synergistic Immunotherapy and Photodynamic Therapy of Melanoma

Immunotherapy faces insufficient immune activation and limited immune effectiveness. Herein, we report a smart DNA hydrogel that enables the release of multivalent functional units at the tumor site to enhance the efficacy of immunotherapy. The smart DNA hydrogel was assembled from two types of ultra-long DNA chains synthesized via rolling circle amplification. One DNA chain contained immune adjuvant CpG oligonucleotides and polyaptamers for loading natural killer cell-derived exosomes; the other chain contained multivalent G-quadruplex for loading photodynamic agents. DNA chains formed DNA hydrogel through base-pairing. HhaI restriction endonuclease sites were designed between functional units. Upon stimuli in the tumor sites, the hydrogel was effectively cleaved by the released HhaI and disassembled into functional units. Natural killer cell-derived exosomes played an anti-tumor role, and the CpG oligonucleotide activated antigen-presenting cells to enhance the immunotherapy. Besides the tumor-killing effect of photodynamic therapy, the generated cellular debris acted as an immune antigen to further enhance the immunotherapeutic effect. In a mouse melanoma orthotopic model, the smart DNA hydrogel as a localized therapeutic agent, achieved a remarkable tumor suppression rate of 91.2 %. The smart DNA hydrogel exhibited enhanced efficacy of synergistic immunotherapy and photodynamic therapy, expanding the application of DNA materials in biomedicine.

Application of extremophile cell factories in industrial biotechnology

Due to the extreme living conditions, extremophiles have unique characteristics in morphology, structure, physiology, biochemistry, molecular evolution mechanism and so on. Extremophiles have superior growth and synthesis capabilities under harsh conditions compared to conventional microorganisms, allowing for unsterilized fermentation processes and thus better performance in low-cost production. In recent years, due to the development and optimization of molecular biology, synthetic biology and fermentation technology, the identification and screening technology of extremophiles has been greatly improved. In this review, we summarize techniques for the identification and screening of extremophiles and review their applications in industrial biotechnology in recent years. In addition, the facts and perspectives gathered in this review suggest that next-generation industrial biotechnology (NGIBs) based on engineered extremophiles holds the promise of simplifying biofuturing processes, establishing open, non-sterilized continuous fermentation production systems, and utilizing low-cost substrates to make NGIBs attractive and cost-effective bioprocessing technologies for sustainable manufacturing.

Recent advances in the synthesis of single-stranded DNA in vitro

Single-stranded DNA (ssDNA) is the foundation of modern biology, with wide applications in gene editing, sequencing, DNA information storage, and materials science. However, synthesizing ssDNA with high efficiency, high throughput, and low error rate in vitro remains a major challenge. Various methods have been developed for ssDNA synthesis, and some significant results have been achieved. In this review, six main methods were introduced, including solid-phase oligonucleotide synthesis, terminal deoxynucleotidyl transferase-based ssDNA synthesis, reverse transcription, primer exchange reaction, asymmetric polymerase chain reaction, and rolling circle amplification. The advantages and limitations of each method were compared, as well as illustrate their representative achievements and applications. Especially, rolling circle amplification has received significant attention, including ssDNA synthesis, assembly, and application based on recent work. Finally, the future challenges and opportunities of ssDNA synthesis were summarized and discussed. Envisioning the development of new methods and significant progress will be made in the near future with the efforts of scientists around the world.

DNA Adjuvant Hydrogel-Optimized Enzymatic Cascade Reaction for Tumor Chemodynamic-Immunotherapy

Chemodynamic therapy (CDT) shows immense potential in cancer treatment as it not only directly kills tumor cells but also induces anti-tumor immune responses. However, the efficacy of CDT is hampered by challenges in targeting CDT catalysts specifically to tumors using nanomaterials, along with the limitations of low H2 O2 levels and short catalyst duration within the tumor microenvironment. In this study, DNA adjuvant hydrogel to arrange a glucose oxidase-ferrocene cascade for continuously generating reactive oxygen species (ROS) from glucose in situ for tumor CDT combined with immunotherapy is employed. By precisely tuning the catalyst spacing with DNA double helix, ROS production efficiency is elevated by up to nine times compared to free catalysts, resulting in stronger immunogenetic cell death. Upon intratumoral injection, the DNA hydrogel system elicited potent anti-tumor immune responses, thereby effectively inhibiting established tumors and rejecting re-challenged tumors. This work offers a novel platform for integrated CDT and immunotherapy in cancer treatment.

Multi-enzymatic systems synergize new RCA technique amplified super-long dsDNA from DNA circle

BACKGROUND

In the field of DNA amplification, there are great challenges in the effectively amplify of long-chain amplification, especially amplification up to several hundred kb level.

RESULTS

A novel technique for the unbiased whole genome amplification from a thimbleful of DNA circles, such as low as 10 ng/ 10 μL of the circular cpDNA or low as 5 ng/ 10 μL of the plasmid, is developed, which can amplify an abundance of the whole genome sequences. Specifically, the new technique that combines rolling-amplification and triple-enzyme system presents a tightly controlled process of a series of buffers/reactions and optimized procedures, that applies from the primer-template duplexes to the Elution step. The result of this technique provides a new approach for extending RCA capacity, where it can reach 200 kb from the circular cpDNA amplification and 150 kb from the plasmid DNA amplification, that demonstrates superior breadth and evenness of genome coverage, high reproducibility, small amplification bias with the amplification efficiency.

SIGNIFICANCE AND NOVELTY

This new technique will develop into one of the powerful tools for isothermal DNA amplification in vitro, genome sequencing/analysis, phylogenetic analysis, physical mapping, and other molecular biology applications.

Multimode adaptive logic gates based on temperature-responsive DNA strand displacement

Living organisms switch their intrinsic biological states to survive environmental turbulence, in which temperature changes are prevalent in nature. Most artificial temperature-responsive DNA nanosystems work as switch modules that transit between "ON-OFF" states, making it difficult to construct nanosystems with diverse functions. In this study, we present a general strategy to build multimode nanosystems based on a temperature-responsive DNA strand displacement reaction. The temperature-responsive DNA strand displacement was controlled by tuning the sequence of the substrate hairpin strands and the invading strands. The nanosystems were demonstrated as logic gates that performed a set of Boolean logical functions at specific temperatures. In addition, an adaptive logic gate was fabricated that could exhibit different logic functions when placed in different temperatures. Specifically, upon the same input strands, the logic gate worked as an XOR gate at 10 °C, an OR gate at 35 °C, an AND gate at 46 °C, and was reset at 55 °C. The design and fabrication of the multifunctional nanosystems would help construct advanced temperature-responsive systems that may be used for temperature-controlled multi-stage drug delivery and thermally-controlled multi-step assembly of nanostructures.

Rational Design of DNA Hydrogels Based on Molecular Dynamics of Polymers

In recent years, DNA has emerged as a fascinating building material to engineer hydrogel due to its excellent programmability, which has gained considerable attention in biomedical applications. Understanding the structure-property relationship and underlying molecular determinants of DNA hydrogel is essential to precisely tailor its macroscopic properties at molecular level. In this review, the rational design principles of DNA molecular networks based on molecular dynamics of polymers on the temporal scale, which can be engineered via the backbone rigidity and crosslinking kinetics, are highlighted. By elucidating the underlying molecular mechanisms and theories, it is aimed to provide a comprehensive overview of how the tunable DNA backbone rigidity and the crosslinking kinetics lead to desirable macroscopic properties of DNA hydrogels, including mechanical properties, diffusive permeability, swelling behaviors, and dynamic features. Furthermore, it is also discussed how the tunable macroscopic properties make DNA hydrogels promising candidates for biomedical applications, such as cell culture, tissue engineering, bio-sensing, and drug delivery.

Effect of pH on the Poly(acrylic acid)/Poly(vinyl alcohol)/Lysozyme Complexes Formation

The interactions between poly(acrylic acid) (PAA), poly(vinyl alcohol) (PVA), and lysozyme (Lys) in an aqueous environment at pHs of 2, 4, and 7.4 were discussed considering the experimental data obtained by turbidimetry, electrokinetic and rheological measurements, and FTIR analysis. It was found that the increase in PAA amount reduces the coacervation zone by shifting the critical pHcr1to higher values while the critical pHcr2 remains unchanged. The coacervation zone extended from 3.1-4.2 to 2.9-4.7 increasing the Lys concentration from 0.2% to 0.5%. The zeta potential measurements showed that the PAA-PVA-Lys mixture in water is the most stable in the pH range of 4.5-8. Zero shear viscosity exhibited deviations from additivity at both investigated pHs, and a maximum value corresponding to a maximum hydrodynamic volume was revealed at PAA weight fractions of 0.4 and 0.5 for pHs of 4 and 7.4, respectively. The binding affinity to Lys of PAA, established by molecular dynamics simulation, was slightly higher than that of PVA. The more stable complex was PAA-Lys formed in a very acidic environment; for that, a binding affinity of -7.1 kcal/mol was determined.

CRISPR/Cas12a-Responsive Hydrogels for Conjugation-Free and Universal Indicator Release in Colorimetric Detection

Recent advances have demonstrated the significant potential and advantages to repurpose existing point-of-care reactions/devices to realize portable detection of nonoriginal targets, e.g., pathogen genes. However, pursuing this aim usually requires protein indicator-nucleic acid conjugation via a covalent bond, which may bring drawbacks such as high cost, complicated procedure, and annoying component rebuilding. Herein, we developed a conjugation-free, effective, and universal detection platform called CRIs-gel (CRISPR/Cas12a-Responsive Indicators@RCA hydrogels). Various protein indicators are pre-encapsulated into the hydrogels made of effective and high-yield rolling circle amplification (RCA). Upon a targeting sequence binding with its antisense crRNA, CRISPR/Cas12a starts its trans-cleavage activity to crush the hydrogel, which may directly release the indicator for downstream readout. Two proteins, amylase (GA) and human chorionic gonadotropin (hCG), are successfully used as model indicators to trigger the downstream amylum-I2 color change and pregnancy test strip response. After coupling with upstream isothermal nucleic acid amplification, both portable readouts may detect as few as 2 copies/μL genetic sequences of influenza A virus (FluA), human papilloma virus (HPV), SARS-CoV-2, and influenza B virus (FluB). This conjugation-free CRIs-gel platform is thus simple, sensitive, and universal and can provide innovative insights for portable point-of-care testing (POCT) development.

Chemical and Biological Engineering Strategies to Make and Modify Next-Generation Hydrogel Biomaterials

There is a growing interest in the development of technologies to probe and direct in vitro cellular function for fundamental organoid and stem cell biology, functional tissue and metabolic engineering, and biotherapeutic formulation. Recapitulating many critical aspects of the native cellular niche, hydrogel biomaterials have proven to be a defining platform technology in this space, catapulting biological investigation from traditional two-dimensional (2D) culture into the 3D world. Seeking to better emulate the dynamic heterogeneity characteristic of all living tissues, global efforts over the last several years have centered around upgrading hydrogel design from relatively simple and static architectures into stimuli-responsive and spatiotemporally evolvable niches. Towards this end, advances from traditionally disparate fields including bioorthogonal click chemistry, chemoenzymatic synthesis, and DNA nanotechnology have been co-opted and integrated to construct 4D-tunable systems that undergo preprogrammed functional changes in response to user-defined inputs. In this Review, we highlight how advances in synthetic, semisynthetic, and bio-based chemistries have played a critical role in the triggered creation and customization of next-generation hydrogel biomaterials. We also chart how these advances stand to energize the translational pipeline of hydrogels from bench to market and close with an outlook on outstanding opportunities and challenges that lay ahead.

Biomass RNA for the Controlled Synthesis of Degradable Networks by Radical Polymerization

Nucleic acids extracted from biomass have emerged as sustainable and environmentally friendly building blocks for the fabrication of multifunctional materials. Until recently, the fabrication of biomass nucleic acid-based structures has been facilitated through simple crosslinking of biomass nucleic acids, which limits the possibility of material properties engineering. This study presents an approach to convert biomass RNA into an acrylic crosslinker through acyl imidazole chemistry. The number of acrylic moieties on RNA was engineered by varying the acylation conditions. The resulting RNA crosslinker can undergo radical copolymerization with various acrylic monomers, thereby offering a versatile route for creating materials with tunable properties (e.g., stiffness and hydrophobic characteristics). Further, reversible-deactivation radical polymerization methods, such as atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT), were also explored as additional approaches to engineer the hydrogel properties. The study also demonstrated the metallization of the biomass RNA-based material, thereby offering potential applications in enhancing electrical conductivity. Overall, this research expands the opportunities in biomass-based biomaterial fabrication, which allows tailored properties for diverse applications.

Morphology Dictated Immune Activation with Framework Nucleic Acids

Framework nucleic acids (FNAs) of various morphologies, designed using the precise and programmable Watson-Crick base pairing, serve as carriers for biomolecule delivery in biology and biomedicine. However, the impact of their shape, size, concentration, and the spatial presentation of cytosine-phosphate-guanine oligodeoxynucleotides (CpG ODNs) on immune activation remains incompletely understood. In this study, representative FNAs with varying morphologies are synthesized to explore their immunological responses. Low concentrations (50 nM) of all FNAs elicited no immunostimulation, while high concentrations of elongated DNA nanostrings and tetrahedrons triggered strong activation due to their larger size and increased cellular uptake, indicating that the innate immune responses of FNAs depend on both dose and morphology. Notably, CpG ODNs' immune response can be programmed by FNAs through regulating the spatial distance, with optimal spacing of 7-8 nm eliciting the highest immunostimulation. These findings demonstrate FNAs' potential as a designable tool to study nucleic acid morphology's impact on biological responses and provide a strategy for future CpG-mediated immune activation carrier design.

Advances in antimicrobial hydrogels for dental tissue engineering: regenerative strategies for endodontics and periodontics

Dental tissue infections have been affecting millions of patients globally leading to pain, severe tissue damage, or even tooth loss. Commercial sterilizers may not be adequate to prevent frequent dental infections. Antimicrobial hydrogels have been introduced as an effective therapeutic strategy for endodontics and periodontics since they have the capability of imitating the native extracellular matrix of soft tissues. Hydrogel networks are considered excellent drug delivery platforms due to their high-water retention capacity. In this regard, drugs or nanoparticles can be incorporated into the hydrogels to endow antimicrobial properties as well as to improve their regenerative potential, once biocompatibility criteria are met avoiding high dosages. Herein, novel antimicrobial hydrogel formulations were discussed for the first time in the scope of endodontics and periodontics. Such hydrogels seem outstanding candidates especially when designed not only as simple volume fillers but also as smart biomaterials with condition-specific adaptability within the dynamic microenvironment of the defect site. Multifunctional hydrogels play a pivotal role against infections, inflammation, oxidative stress, etc. along the way of dental regeneration. Modern techniques (e.g., 3D and 4D-printing) hold promise to develop the next generation of antimicrobial hydrogels together with their limitations such as infeasibility of implantation.

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.

Programming Injectable DNA Hydrogels Yields Tumor Microenvironment-Activatable and Immune-Instructive Depots for Augmented Chemo-Immunotherapy

Injectable hydrogels have attracted increasing attention for promoting systemic antitumor immune response through the co-delivery of chemotherapeutics and immunomodulators. However, the biosafety and bioactivity of conventional hydrogel depots are often impaired by insufficient possibilities for post-gelling injection and means for biofunction integration. Here, an unprecedented injectable stimuli-responsive immunomodulatory depot through programming a super-soft DNA hydrogel adjuvant is reported. This hydrogel system encoded with adenosine triphosphate aptamers can be intratumorally injected in a gel formulation and then undergoes significant molecular conformation change to stimulate the distinct release kinetics of co-encapsulated therapeutics. In this scenario, doxorubicin is first released to induce immunogenic cell death that intimately works together with the polymerized cytosine-phosphate-guanine oligodeoxynucleotide (CpG ODN) in gel scaffold for effectively recruiting and activating dendritic cells. The polymerized CpG ODN not only enhances tumor immunogenicity but minimizes free CpG-induced splenomegaly. Furthermore, the subsequently released anti-programmed cell death protein ligand 1 (aPDL1) blocks the corresponding immune inhibitory checkpoint molecule on tumor cells to sensitize antitumor T-cell immunity. This work thus contributes to the first proof-of-concept demonstration of a programmable super-soft DNA hydrogel system that perfectly matches the synergistic therapeutic modalities based on chemotherapeutic toxicity, in situ vaccination, and immune checkpoint blockade.

Application of intelligent responsive DNA self-assembling nanomaterials in drug delivery

Smart nanomaterials are nano-scaled materials that respond in a controllable and reversible way to external physical or chemical stimuli. DNA self-assembly is an effective way to construct smart nanomaterials with precise structure, diverse functions and wide applications. Among them, static structures such as DNA polyhedron, DNA nanocages and DNA hydrogels, as well as dynamic reactions such as catalytic hairpin reaction, hybridization chain reaction and rolling circle amplification, can serve as the basis for building smart nanomaterials. Due to the advantages of DNA, such as good biocompatibility, simple synthesis, rational design, and good stability, these materials have attracted increasing attention in the fields of pharmaceuticals and biology. Based on their specific response design, DNA self-assembled smart nanomaterials can deliver a variety of drugs, including small molecules, nucleic acids, proteins and other drugs; and they play important roles in enhancing cellular uptake, resisting enzymatic degradation, controlling drug release, and so on. This review focuses on different assembly methods of DNA self-assembled smart nanomaterials, therapeutic strategies based on various intelligent responses, and their applications in drug delivery. Finally, the opportunities and challenges of smart nanomaterials based on DNA self-assembly are summarized.