Carbon-nanotube reinforcement of DNA-silica nanocomposites yields programmable and cell-instructive biocoatings

Systematic Selection of High-Affinity ssDNA Sequences to Carbon Nanotubes

Single-walled carbon nanotubes (SWCNTs) have gained significant interest for their potential in biomedicine and nanoelectronics. The functionalization of SWCNTs with single-stranded DNA (ssDNA) enables the precise control of SWCNT alignment and the development of optical and electronic biosensors. This study addresses the current gaps in the field by employing high-throughput systematic selection, enriching high-affinity ssDNA sequences from a vast random library. Specific base compositions and patterns are identified that govern the binding affinity between ssDNA and SWCNTs. Molecular dynamics simulations validate the stability of ssDNA conformations on SWCNTs and reveal the pivotal role of hydrogen bonds in this interaction. Additionally, it is demonstrated that machine learning could accurately distinguish high-affinity ssDNA sequences, providing an accessible model on a dedicated webpage (http://service.k-medai.com/ssdna4cnt). These findings open new avenues for high-affinity ssDNA-SWCNT constructs for stable and sensitive molecular detection across diverse scientific disciplines.

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.

Preparation Strategies, Functional Regulation, and Applications of Multifunctional Nanomaterials-Based DNA Hydrogels

With the extensive attention of DNA hydrogels in biomedicine, biomaterial, and other research fields, more and more functional DNA hydrogels have emerged to match the various needs. Incorporating nanomaterials into the hydrogel network is an emerging strategy for functional DNA hydrogel construction. Surprisingly, nanomaterials-based DNA hydrogels can be engineered to possess favorable properties, such as dynamic mechanical properties, excellent optical properties, particular electrical properties, perfect encapsulation properties, improved magnetic properties, and enhanced antibacterial properties. Herein, the preparation strategies of nanomaterials-based DNA hydrogels are first highlighted and then different nanomaterial designs are used to demonstrate the functional regulation of DNA hydrogels to achieve specific properties. Subsequently, representative applications in biosensing, drug delivery, cell culture, and environmental protection are introduced with some selected examples. Finally, the current challenges and prospects are elaborated. The study envisions that this review will provide an insightful perspective for the further development of functional DNA hydrogels.

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.

Functional Carbon from Nature: Biomass-Derived Carbon Materials and the Recent Progress of Their Applications

Biomass is considered as a promising source to fabricate functional carbon materials for its sustainability, low cost, and high carbon content. Biomass-derived-carbon materials (BCMs) have been a thriving research field. Novel structures, diverse synthesis methods, and versatile applications of BCMs have been reported. However, there has been no recent review of the numerous studies of different aspects of BCMs-related research. Therefore, this paper presents a comprehensive review that summarizes the progress of BCMs related research. Herein, typical types of biomass used to prepare BCMs are introduced. Variable structures of BCMs are summarized as the performance and properties of BCMs are closely related to their structures. Representative synthesis strategies, including both their merits and drawbacks are reviewed comprehensively. Moreover, the influence of synthetic conditions on the structure of as-prepared carbon products is discussed, providing important information for the rational design of the fabrication process of BCMs. Recent progress in versatile applications of BCMs based on their morphologies and physicochemical properties is reported. Finally, the remaining challenges of BCMs, are highlighted. Overall, this review provides a valuable overview of current knowledge and recent progress of BCMs, and it outlines directions for future research development of BCMs.

Crystallinity-tuned ultrasoft polymeric DNA networks for controlled release of anticancer drugs

Despite the vast interest in utilizing rolling circle amplification (RCA)-based DNA networks for bioapplications, precise control of the mechanical and physicochemical properties is highly challenging. To address this concern, we aimed to develop ultrasoft self-supporting polymerized DNA networks (pDNets) of variable crystallinities to manipulate sequence-mediated drug release efficiency. A controlled ratio of the inorganic magnesium pyrophosphate (MgPPi) crystal to the organic polymeric DNA resulted in the synthesis of pDNets of various nanoporosities. The number of crystal microstructures influencing drug localization and release pattern and the tunable mechanical properties influencing injectability and structural stability under physiological conditions were investigated. The pDNets exhibited ultrasoft properties with Young's moduli of 0.06-0.54 Pa; approximately 9-fold differences in mechanical properties were obtained by varying the degree of crystallinity. With functional DNA sequences, the developed platforms showed pH stimuli-responsive drug release profiles of the dynamic DNA structures and aptamer-specific cell target adhesion efficiency. Analyses of controlled delivery of anticancer therapeutics in vitro and in vivo revealed crystallinity-dependent antitumor efficacy without side effects. This strategy provides an effective one-pot enzymatic polymerization methodology and a favorable microenvironment for a three-dimensional DNA network based on demand-localized drug delivery.

Silica nanoparticles: Biomedical applications and toxicity

Silica nanoparticles (SiNPs) are composed of silicon dioxide, the most abundant compound on Earth, and are used widely in many applications including the food industry, synthetic processes, medical diagnosis, and drug delivery due to their controllable particle size, large surface area, and great biocompatibility. Building on basic synthetic methods, convenient and economical strategies have been developed for the synthesis of SiNPs. Numerous studies have assessed the biomedical applications of SiNPs, including the surface and structural modification of SiNPs to target various cancers and diagnose diseases. However, studies on the in vitro and in vivo toxicity of SiNPs remain in the exploratory stage, and the toxicity mechanisms of SiNPs are poorly understood. This review covers recent studies on the biomedical applications of SiNPs, including their uses in drug delivery systems to diagnose and treat various diseases in the human body. SiNP toxicity is discussed in terms of the different systems of the human body and the individual organs in those systems. This comprehensive review includes both fundamental discoveries and exploratory progress in SiNP research that may lead to practical developments in the future.

DNA-Based Daisy Chain Rotaxane Nanocomposite Hydrogels as Dual-Programmable Dynamic Scaffolds for Stem Cell Adhesion

Interlocked DNA nanostructures perform programmable movements in nanoscales such as sliding, contraction, and expansion. However, utilizing nanoscaled interlocked movements to regulate the functions of larger length scaled matrix and developing their applications has not yet been reported. Herein we describe the assembly of DNA-based daisy chain rotaxane nanostructure (DNA-DCR) composed of two hollow DNA nanostructures as macrocycles, two interlocked axles and two triangular prism-shaped DNA structures as stoppers, in which three mechanical states─fixed extended state (FES), sliding state (SS), and fixed contracted state (FCS)─are characterized by using toehold-mediated strand displacement reaction (SDR). The DNA-DCRs are further used as nanocomposites and introduced into hydrogel matrix to produce interlocked hydrogels, which shows modulable stiffness by elongating the interlocked axles to regulate the hydrogel swelling with hybridization chain reaction (HCR) treatment. Then the DCR-hydrogels are employed as dynamic biointerfaces for human mesenchymal stem cells (hMSCs) adhesion studies. First, hMSCs showed lower cell density on bare DCR-hydrogel treated with HCR-initiated swelling for stiffness decreasing. Second, the cell adhesion ligand (RGD) modified DNA-DCRs are constructed for hydrogel functionalization. DCR^(RGD) hydrogel endows the mobility of RGDs by switching the mechanical states of DNA-DCR. HMSCs showed increased cell density on DCR^SS(RGD) hydrogel than on DCR^FCS(RGD) hydrogel. Therefore, our DNA-DCR nanocomposite hydrogel exhibit dual-programmable performances including swelling adjustment and offering sliding for incorporated ligands, which can be both utilized as dynamic scaffolds for regulating the stem cell adhesion. The dual-programmable cross-scale regulation from interlocked DNA nanostructures to hydrogel matrix was achieved, demonstrating a new pathway of DNA-based materials.

Applications of Carbon Nanotubes in the Internet of Things Era

The post-Moore's era has boosted the progress in carbon nanotube-based transistors. Indeed, the 5G communication and cloud computing stimulate the research in applications of carbon nanotubes in electronic devices. In this perspective, we deliver the readers with the latest trends in carbon nanotube research, including high-frequency transistors, biomedical sensors and actuators, brain-machine interfaces, and flexible logic devices and energy storages. Future opportunities are given for calling on scientists and engineers into the emerging topics.

Formulation of DNA Nanocomposites: Towards Functional Materials for Protein Expression

DNA hydrogels are an emerging class of materials that hold great promise for numerous biotechnological applications, ranging from tissue engineering to targeted drug delivery and cell-free protein synthesis (CFPS). In addition to the molecular programmability of DNA that can be used to instruct biological systems, the formulation of DNA materials, e.g., as bulk hydrogels or microgels, is also relevant for specific applications. To advance the state of knowledge in this research area, the present work explores the scope of a recently developed class of complex DNA nanocomposites, synthesized by RCA polymerization of DNA-functionalized silica nanoparticles (SiNPs) and carbon nanotubes (CNTs). SiNP/CNT-DNA composites were produced as bulk materials and microgels which contained a plasmid with transcribable genetic information for a fluorescent marker protein. Using confocal microscopy and flow cytometry, we found that the materials are very efficiently taken up by various eukaryotic cell lines, which were able to continue dividing while the ingested material was evenly distributed to the daughter cells. However, no expression of the encoded protein occurred within the cells. While the microgels did not induce production of the marker protein even in a CFPS procedure with eukaryotic cell lysate, the bulk composites proved to be efficient templates for CFPS. This work contributes to the understanding of the molecular interactions between DNA composites and the functional cellular machinery. Implications for the use of such materials for CFPS procedures are discussed.

Smart and Functionalized Development of Nucleic Acid-Based Hydrogels: Assembly Strategies, Recent Advances, and Challenges

Nucleic acid-based hydrogels that integrate intrinsic biological properties of nucleic acids and mechanical behavior of their advanced assemblies are appealing bioanalysis and biomedical studies for the development of new-generation smart biomaterials. It is inseparable from development and incorporation of novel structural and functional units. This review highlights different functional units of nucleic acids, polymers, and novel nanomaterials in the order of structures, properties, and functions, and their assembly strategies for the fabrication of nucleic acid-based hydrogels. Also, recent advances in the design of multifunctional and stimuli-responsive nucleic acid-based hydrogels in bioanalysis and biomedical science are discussed, focusing on the applications of customized hydrogels for emerging directions, including 3D cell cultivation and 3D bioprinting. Finally, the key challenge and future perspectives are outlined.

Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications

The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.

Preservation of DNA for data storage

The preservation of DNA has attracted significant interest of scientists in diverse research fields from ancient biological remains to the information field. In light of the different DNA safekeeping requirements (e.g., storage time, storage conditions) in these disparate fields, scientists have proposed distinct methods to maintain the DNA integrity. Specifically, DNA data storage is an emerging research, which means that the binary digital information is converted to the sequences of nucleotides leading to dense and durable data storage in the form of synthesized DNA. The intact preservation of DNA plays a significant role because it is closely related to data integrity. This review discusses DNA preservation methods, aiming to confirm an appropriate one for synthetic oligonucleotides in DNA data storage. First, we analyze the impact factors of the DNA long-term storage, including the intrinsic stability of DNA, environmental factors, and storage methods. Then, the benefits and disadvantages of diverse conservation approaches (e.g., encapsulation-free, chemical encapsulation) are discussed. Finally, we provide advice for storing non-genetic information in DNA in vitro. We expect these preservation suggestions to promote further research that may extend the DNA storage time.

The bibliography includes 99 references.

Insights into the Formation of DNA-Magnetic Nanoparticle Hybrid Structures: Correlations between Morphological Characterization and Output from Magnetic Biosensor Measurements

Understanding the binding mechanism between probe-functionalized magnetic nanoparticles (MNPs) and DNA targets or amplification products thereof is essential in the optimization of magnetic biosensors for the detection of DNA. Herein, the molecular interaction forming hybrid structures upon hybridization between DNA-functionalized magnetic nanoparticles, exhibiting Brownian relaxation, and rolling circle amplification products (DNA-coils) is investigated by the use of atomic force microscopy in a liquid environment and magnetic biosensors measuring the frequency-dependent magnetic response and the frequency-dependent modulation of light transmission. This approach reveals the qualitative and quantitative correlations between the morphological features of the hybrid structures with their magnetic response. The suppression of the high-frequency peak in the magnetic response and the appearance of a new peak at lower frequencies match the formation of larger sized assemblies upon increasing the concentration of DNA-coils. Furthermore, an increase of the DNA-coil concentration induces an increase in the number of MNPs per hybrid structure. This study provides new insights into the DNA–MNP binding mechanism, and its versatility is of considerable importance for the mechanistic characterization of other DNA-nanoparticle biosensor systems.

Postsynthetic Functionalization of DNA-Nanocomposites with Proteins Yields Bioinstructive Matrices for Cell Culture Applications

We report on the directed postsynthetic functionalization of soft DNA nanocomposite materials with proteins. Using the example of the functionalization of silica nanoparticle-modified DNA polymer materials with agonists or antagonists of the epidermal growth factor receptor EGFR cell membrane receptor, we demonstrate that hierarchically structured interfaces to living cells can be established. Owing to the modular design principle, even complex DNA nanostructures can be integrated into the materials, thereby enabling the high-precision arrangement of ligands on the lower nanometer length scale. We believe that such complex biohybrid material systems can be used for new applications in biotechnology.

Carbon Nanotubes under Scrutiny: Their Toxicity and Utility in Mesothelioma Research

Research on the toxicity of engineered carbon nanotubes (CNT) was initiated by Belgian academic chemists and toxicologists more than 15 years ago. It is now undisputed that some of these attractive nanomaterials induce serious illness such as fibrosis and cancer. The physico-chemical determinants of CNT-induced adverse effects are now elucidated and include shape, nanoscale diameter, and structural defects. Generated in vitro and in vivo data on their inflammogenic and fibrogenic activities were combined and translated in AOP (adverse outcome pathways) available for risk assessment and regulatory policies. The asbestos-like carcinogenic effect of CNT, notably their capacity to induce malignant mesothelioma (MM), remain, however, a cause of concern for public health and strongly curb the craze for CNT in industries. MM still represents a real challenge for clinicians and a highly refractory cancer to existing therapeutic strategies. By comparing mesotheliomagenic CNT (needle-like CNT-N) to non mesotheliomagenic CNT (tangled-like CNT-T), our group generated a relevant animal model that highlights immune pathways specifically associated to the carcinogenic process. Evidence indicates that only CNT-N possess the intrinsic capacity to induce a preferential, rapid, and sustained accumulation of host immunosuppressive cells that subvert immune surveillance and suppress anti-mesothelioma immunity. This new concept offers novel horizons for the clinical management of mesothelioma and represents an additional tool for predicting the mesotheliomagenic activity of newly elaborated CNT or nanoparticles.

Cultivation of Exoelectrogenic Bacteria in Conductive DNA Nanocomposite Hydrogels Yields a Programmable Biohybrid Materials System

The use of living microorganisms integrated within electrochemical devices is an expanding field of research, with applications in microbial fuel cells, microbial biosensors or bioreactors. We describe the use of porous nanocomposite materials prepared by DNA polymerization of carbon nanotubes (CNTs) and silica nanoparticles (SiNPs) for the construction of a programmable biohybrid system containing the exoelectrogenic bacterium Shewanella oneidensis. We initially demonstrate the electrical conductivity of the CNT-containing DNA composite by employment of chronopotentiometry, electrochemical impedance spectroscopy, and cyclic voltammetry. Cultivation of Shewanella oneidensis in the conductive materials shows that the exoelectrogenic bacteria populate the matrix of the conductive composite, while nonexoelectrogenic Escherichia coli remain on its surface. Moreover, the ability to use extracellular electron transfer pathways is positively correlated with the number of cells within the conductive synthetic biofilm matrix. The Shewanella-containing composite remains stable for several days and shows electrochemical activity, indicating that the conductive backbone is capable of extracting the metabolic electrons produced by the bacteria under strictly anoxic conditions and conducting them to the anode. Programmability of this biohybrid material system is demonstrated by on-demand release and degradation induced by a short-term enzymatic stimulus. We believe that the application possibilities of such biohybrid materials could even go beyond microbial biosensors, bioreactors, and fuel cell systems.

Designer DNA-silica/carbon nanotube nanocomposites for traceable and targeted drug delivery

Due to their unique properties like porosity, high water content, softness and biocompatibility, hydrogels are of great interest for biomedical applications such as tissue engineering and drug delivery. We describe a programmable drug delivery system that is based on highly biocompatible SiNP/CNT-DNA nanocomposites, which can be synthesized in a highly modular fashion from DNA-functionalized carbon nanotubes and silica nanoparticles via enzymatic rolling circle amplification. Specific molecular recognition properties were implemented into the materials by DNA sequence design, as demonstrated by incorporation of GC/CG-rich stem loop and aptamer motifs that enable selective binding of intercalating drugs and cell surface receptors, respectively. In a proof-of-concept study we demonstrate the utility of this approach by targeting nanocomposites loaded with the anthracycline drug doxorubicin to HeLa cancer cells. Our observation that these designer materials work more efficiently than the pure drug alone suggests that further developments of the concept might be useful to selectively trigger more complex cellular pathways.