DNA materials: bridging nanotechnology and biotechnology

Microenvironment-responsive DNA-conjugated albumin nanocarriers for targeted therapy

Drug delivery with accurate targeting and efficient treatment has become an essential strategy for cancer therapy. Two nanocarriers based on bovine serum albumin (BSA) and DNA were synthesized via click chemistry and DNA hybridization reactions (DNA-BSA1 and DNA-BSA2). One of the hybridized oligonucleotides, Linker1, in DNA-BSA1 included a pH-sensitive i-motif sequence and a cancer cell-targeted guanine-quadruplex-structured AS1411 aptamer sequence, and the other, Linker2, in DNA-BSA2 had only the same pH-sensitive i-motif sequence. Doxorubicin (DOX) molecules could be quickly and preferentially intercalated into double-stranded DNA via non-covalent interactions, and the encapsulation efficiency of DNA-BSA1 and DNA-BSA2 was almost 100% and 87.5%, respectively. As a mimic of the cancer cell microenvironment, a pH-trigger and a deoxyribonuclease I (DNase I)-trigger release mechanism was individually proposed to explain the dynamic release of the DNA-BSA@DOX under acidic conditions and the presence of DNase I in vitro. Intracellular uptake and cytotoxicity experiments confirmed that the nanocarrier DNA-BSA1@DOX had accurate targeting and efficient treatment towards cancer cells due to the high affinity and specificity of AS1411 to nucleolin, which is overexpressed in cancer cells. Furthermore, in vivo studies showed that the nanocarrier system could efficiently inhibit tumor growth. Therefore, the entire bio-based nanocarrier DNA-BSA is a promising candidate for the loading and release of anti-cancer drugs for accurate delivery and efficient treatment.

The biological applications of DNA nanomaterials: current challenges and future directions

DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.

Controlled CRISPR-Cas9 Ribonucleoprotein Delivery for Sensitized Photothermal Therapy

Manipulation of CRISPR delivery for stimuli-responsive gene editing is crucial for cancer therapeutics through maximizing efficacy and minimizing side-effects. However, realizing controlled gene editing for synergistic combination therapy remains a key challenge. Here, a near-infrared (NIR) light-triggered thermo-responsive copper sulfide (CuS) multifunctional nanotherapeutic platform is constructed to achieve controlled release of CRISPR-Cas9 ribonucleoprotein (RNP) and doxorubicin for tumor synergistic combination therapy involving in gene therapy, mild-photothermal therapy (PTT), and chemotherapy. The semiconductor CuS serves as a "photothermal converter" and can stably convert NIR light (808 nm) into local thermal effect to provide photothermal stimulation. The double-strand formed between CuS nanoparticle-linked DNA fragments and single-guide RNA is employed as a controlled element in response to photothermal stimulation for controlled gene editing and drug release. Hsp90α, one subunit of heat shock protein 90 (Hsp90), is targeted by Cas9 RNP to reduce tumor heat tolerance for enhanced mild-PTT effects (≈43 °C). Significant synergistic therapy efficacy can be observed by twice NIR light irradiation both in vitro and in vivo, compared to PTT alone. Overall, this exogenously controlled method provides a versatile strategy for controlled gene editing and drug release with potentially synergistic combination therapy.

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.

Aptamer-Programmed DNA Nanodevices for Advanced, Targeted Cancer Theranostics

DNA has been demonstrated to be a versatile material for construction at the nanoscale. DNA nanodevices are highly programmable and allow functionalization with multiple entities such as imaging modalities (fluorophores), targeting entities (aptamers), drug conjugation (chemical linkers), and triggered release (photoresponsive molecules). These features enhance the use of DNA nanodevices in biological applications, catalyzing the rapid growth of this domain of research. In this review, we focus on recent progress in the development and use of aptamer-functionalized DNA nanodevices as theranostic agents, their characterization, applications as delivery platforms, and advantages. We provide a brief background on the development of aptamers and DNA nanodevices in biomedical applications, and we present specific applications of these entities in cancer diagnosis and therapeutics. We conclude with a perspective on the challenges and possible solutions for the clinical translation of aptamer-functionalized DNA nanodevices in the domain of cancer therapeutics.

Emerging DNA-based multifunctional nano-biomaterials towards electrochemical sensing applications

DNA is known to be ubiquitous in nature as it is the controlling unit for genetic information storage in most living organisms. Lately, there has been a surge in studies relating to the use of DNA as a biomaterial for various biomedical applications such as biosensing, therapeutics, and drug delivery. The role of DNA as a bioreceptor in biosensors has been known for a long time. DNA-based biosensors are gradually evolving into highly sophisticated and sensitive molecular devices. The current realization of DNA-based biosensors embraces the unique structural and functional properties of DNA in the form of a biopolymer. The interesting properties of DNA, such as self-assembly, programmability, catalytic activity, dynamic behavior, and precise molecular recognition, have led to the emergence of innovative DNA assembly based electrochemical biosensors. This review article aims to cover the recent progress in the field of DNA-based electrochemical (EC) biosensors. It commences with an introduction to electrochemical biosensors and elucidates the advantages of integrating DNA-based materials into them. Besides this, we discuss the principles of EC biosensors based on different types of DNA-based materials. The article concludes by highlighting the outlook and importance of this interesting field for biomedical developments.

DNA-polymer conjugates via the graft-through polymerisation of native DNA in water

The direct, graft-through, ring-opening metathesis polymerisation (ROMP) of unprotected DNA macromonomers is reported. By tuning the polymerisation conditions, good control is achieved, enabling the rapid and efficient synthesis of DNA-containing bottlebrush copolymers, without the need for protection of the DNA bases.

DNA Transformations for Diagnosis and Therapy

Due to its unique physical and chemical characteristics, DNA, which is known only as genetic information, has been identified and utilized as a new material at an astonishing rate. The role of DNA has increased dramatically with the advent of various DNA derivatives such as DNA-RNA, DNA-metal hybrids, and PNA, which can be organized into 2D or 3D structures by exploiting their complementary recognition. Due to its intrinsic biocompatibility, self-assembly, tunable immunogenicity, structural programmability, long stability, and electron-rich nature, DNA has generated major interest in electronic and catalytic applications. Based on its advantages, DNA and its derivatives are utilized in several fields where the traditional methodologies are ineffective. Here, the present challenges and opportunities of DNA transformations are demonstrated, especially in biomedical applications that include diagnosis and therapy. Natural DNAs previously utilized and transformed into patterns are not found in nature due to lack of multiplexing, resulting in low sensitivity and high error frequency in multi-targeted therapeutics. More recently, new platforms have advanced the diagnostic ability and therapeutic efficacy of DNA in biomedicine. There is confidence that DNA will play a strong role in next-generation clinical technology and can be used in multifaceted applications.

Constructing Large 2D Lattices Out of DNA-Tiles

The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.

The Effects of Temperature on the Assembly of Gold Nanoparticle by Interpolymer Complexation

Using synchrotron-based small-angle X-ray scattering techniques, we demonstrate that poly(ethylene glycol)-functionalized gold nanoparticles (PEG-AuNPs) are assembled into close-packed structures that include short-range order with face-centered cubic structure, where crystalline qualities are varied by controlling the electrolyte concentration, pH, and temperature of the suspensions. We show that interpolymer complexation with poly(acrylic acid) (PAA) is induced by lowering the pH level of the PEG-AuNPs suspensions, and furthermore, increasing the temperature of the suspension strengthens interparticle attraction, leading to improved supercrystal structures. Our results indicate that this strategy creates robust nanoparticle superlattices with high thermal stability. The effects of PAA and PEG chain lengths on the assemblies are also investigated, and their optimal conditions for creating improved superlattices are discussed.

Small molecule-induced DNA hydrogel with encapsulation and release properties

Hydrogels are networks of polymers that can be used for packaging different payload types. They are proven to be versatile materials for various biomedical applications. Implanted hydrogels with encapsulated drugs have been shown to release the therapeutic payloads at disease sites. Hydrogels are usually made through chemical polymerization reactions. Whereas, DNA is a naturally occurring biopolymer which can assemble into highly ordered structures through noncovalent interactions. Here, we have employed a small molecule, cyanuric acid (CA), to assemble polyA-tailed DNA motif into a hydrogel. Encapsulation of a small molecule chemotherapeutic drug, a fluorescent molecule, two proteins and several nanoparticle formulations has been studied. Release of doxorubicin, small fluorescent molecule and fluorescently-labeled antibodies has been demonstrated.

Self-assembled, Programmable DNA Nanodevices for Biological and Biomedical Applications

The broad field of structural DNA nanotechnology has diverged into various areas of applications ranging from computing, photonics, synthetic biology, and biosensing to in-vivo bioimaging and therapeutic delivery, to name but a few. Though the field began to exploit DNA to build various nanoscale architectures, it has now taken a new path to diverge from structural DNA nanotechnology to functional or applied DNA nanotechnology. More recently a third sub-branch has emerged-biologically oriented DNA nanotechnology, which seeks to explore the functionalities of combinatorial DNA devices in various biological systems. In this review, we summarize the key developments in DNA nanotechnology revealing a current trend that merges the functionality of DNA devices with the specificity of biomolecules to access a range of functions in biological systems. This review seeks to provide a perspective on the evolution and biological applications of DNA nanotechnology, where the integration of DNA structures with biomolecules can now uncover phenomena of interest to biologists and biomedical scientists. Finally, we conclude with the challenges, limitations, and perspectives of DNA nanodevices in fundamental and applied research.

Dynamic DNA material with emergent locomotion behavior powered by artificial metabolism

Metabolism is a key process that makes life alive-the combination of anabolism and catabolism sustains life by a continuous flux of matter and energy. In other words, the materials comprising life are synthesized, assembled, dissipated, and decomposed autonomously in a controlled, hierarchical manner using biological processes. Although some biological approaches for creating dynamic materials have been reported, the construction of such materials by mimicking metabolism from scratch based on bioengineering has not yet been achieved. Various chemical approaches, especially dissipative assemblies, allow the construction of dynamic materials in a synthetic fashion, analogous to part of metabolism. Inspired by these approaches, here, we report a bottom-up construction of dynamic biomaterials powered by artificial metabolism, representing a combination of irreversible biosynthesis and dissipative assembly processes. An emergent locomotion behavior resembling a slime mold was programmed with this material by using an abstract design model similar to mechanical systems. Dynamic properties, such as autonomous pattern generation and continuous polarized regeneration, enabled locomotion along the designated tracks against a constant flow. Furthermore, an emergent racing behavior of two locomotive bodies was achieved by expanding the program. Other applications, including pathogen detection and hybrid nanomaterials, illustrated further potential use of this material. Dynamic biomaterials powered by artificial metabolism could provide a previously unexplored route to realize "artificial" biological systems with regenerating and self-sustaining characteristics.

Enzymatical biomineralization of DNA nanoflowers mediated by manganese ions for tumor site activated magnetic resonance imaging

DNA nanoflower has been demonstrated as a promising DNA nanostructure for therapeutics and bioimaging primarily because of the programmable DNA sequence and unique structure. Herein, we report manganese ions mediated enzymatic biomineralization to prepare DNA-Mn hybrid nanoflower (DMNF). Paramagnetic Mn²⁺ was explored as the co-factor of DNA polymerase for the extension of long strand DNA. The biomimetic synthesis of DMNF was performed using the long strand DNA as template via nucleation and growth of Mn₂PPi. The morphology and size of DMNF were controllable by tuning reaction time and Mn²⁺ concentration. The aptamer sequence was encoded into circle template to achieve tumor-targeted DMNF, and cellular uptake assay demonstrated obvious aptamer-mediated internalization. DMNF showed enhanced T₁-weighted magnetic resonance (MR) imaging effect in acid environment for high tumor-specific MR imaging, and high spatial resolution imaging of kidneys and liver. Our work provides a facile enzymatically biomineral strategy to integrate multifunctional modules into one DNA structure and promotes the development of DNA nanostructure for precision medicine.

Structural requirement of G-quadruplex/aptamer-combined DNA macromolecule serving as efficient drug carrier for cancer-targeted drug delivery

Photodynamic therapy (PDT) as a clinical cancer treatment method has been used to treat carcinomas in different organs, and G-quadruplex-based DNA nanocompartments serving as the carriers of cationic porphyrin photosensitizers, especially combined with cell-targeting aptamers, is considered to offer new opportunities for future cancer treatment. However, the structural features of G-quadruplex/aptamer complexes suitable for the capsulation of photosensitizers and target cell recognition is unexplored so far. In this study, unimolecular (UM), bimolecular (BM) and tetramolecular (TM) G-quadruplex structures were used as the drug loading compartments and grafted onto tumor cell-targeting aptamer Sgc8, constructing several targeting drug delivery vehicles (T-GMVs). Besides the binding affinity of resulting DNA architectures for target cells and cell recognition specificity were explored in a comparative fashion, the drug loading capability and cancer therapy efficacy were evaluated using TMPyP4 as the model porphyrin-based drug. The experimental results show that only TM G-quadruplex structure is suitable to combine with Sgc8 for the development of drug delivery vehicle and the as-prepared T-GMV- TMPyP4 complexes display the desirable cancer therapy efficacy, holding the potential application in the future cancer therapy. More importantly, T-GMV- TMPyP4 is expected to lay the scientific groundwork for the successful development of G-quadruplex-based photosensitizer drug delivery carriers for the targeted cancer therapy.

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.

Dual-responsive carboxymethyl cellulose/dopamine/cystamine hydrogels driven by dynamic metal-ligand and redox linkages for controllable release of agrochemical

The utilization of agrochemicals in crop production is often inefficient due to lack of appropriate carriers, raising in the significant concerns of ecological environment and public health. To enhance the efficiency of agrochemical delivery, a novel cellulose-based hydrogel was constructed in this work by cross-linking dopamine (DA)-modified carboxymethyl cellulose (CMC) with cystamine (CYS) in the presence of Fe³⁺ ions. The hydrogels displayed reversible sol-gel transitions upon exposure to stimulation of changes in pH and redox, leading to the controllable release of model agrochemical (6-benzyladenine). Compared with single-triggered condition, the hydrogel doubled the cumulative release when co-triggered by pH and redox. The dynamic metal/catechol complexation and disulfide bonding coexist in the hydrogel networks, enabling occurrence of dynamic reaction under a variety of environmental conditions. The finite element method (FEM) was employed to simulate the hydrogel to provide a theoretical insight into the tested drug delivery. Benefitting from the reversibly cross-linked networks and the excellent biodegradability of the hydrogels, we anticipate that this dual-responsive, polysaccharide-based hydrogel will offer diverse applications to reach the full potential in sustainable advancement of crop production.

Gelling without Structuring: A SAXS Study of the Interactions among DNA Nanostars

We evaluate, by means of synchrotron small-angle X-ray scattering, the shape and mutual interactions of DNA tetravalent nanostars as a function of temperature in both the gas-like state and across the gel transition. To this end, we calculate the form factor from coarse-grained molecular dynamics simulations with a novel method that includes hydration effects; we approximate the radial interaction of DNA nanostars as a hard-sphere potential complemented by a repulsive and an attractive Yukawa term; and we predict the structure factors by exploiting the perturbative random phase approximation of the Percus-Yevick equation. Our approach enables us to fit all the data by selecting the particle radius and the width and amplitude of the attractive potential as free parameters. We determine the evolution of the structure factor across gelation and detect subtle changes of the effective interparticle interactions, that we associate to the temperature and concentration dependence of the particle size. Despite the approximations, the approach here adopted offers new detailed insights into the structure and interparticle interactions of this fascinating system.

Super-Soft DNA/Dopamine-Grafted-Dextran Hydrogel as Dynamic Wire for Electric Circuits Switched by a Microbial Metabolism Process

Engineering dynamic systems or materials to respond to biological process is one of the major tasks in synthetic biology and will enable wide promising applications, such as robotics and smart medicine. Herein, a super-soft and dynamic DNA/dopamine-grafted-dextran hydrogel, which shows super-fast volume-responsiveness with high sensitivity upon solvents with different polarities and enables creation of electric circuits in response to microbial metabolism is reported. Synergic permanent and dynamic double networks are integrated in this hydrogel. A serials of dynamic hydrogel-based electric circuits are fabricated: 1) triggered by using water as switch, 2) triggered by using water and petroleum ether as switch pair, 3) a self-healing electric circuit; 4) remarkably, a microbial metabolism process which produces ethanol triggering electric circuit is achieved successfully. It is envisioned that the work provides a new strategy for the construction of dynamic materials, particularly DNA-based biomaterials; and the electric circuits will be highly promising in applications, such as soft robotics and intelligent systems.

Colorimetric nanoplatform for visual determination of cancer cells via target-catalyzed hairpin assembly actuated aggregation of gold nanoparticles

According to aptamer-mediated hairpin DNA cascade amplifier and gold nanoparticles aggregation, an optical platform for cancer cells determination has been proposed. High-affinity chimeric aptamers were used for cancer cell detection and also as an initiator for beginning hairpin assembly to construct three-way junction (3WJ) nanostructures. These three hairpins were modified at 3' ends with biotin. In the presence of target cell, chimeric aptamer binds to its ligand on cell surface and initiates 3WJ nanostructures formation. These 3WJ nanostructures interact with streptavidin-modified gold nanoparticles (AuNPs) via non-covalent biotin-streptavidin interactions and create a crossover lattice of nanoparticles. This event leads to AuNPs aggregation and red-shifting. The results were confirmed by gel electrophoresis and UV-visible spectrophotometry. The dynamic range of this assay is 25 to 10⁷ cells with a detection limit of 10 cells which is respectively 9 and 4 times more significant than the sensitivity of AuNP-based approaches without amplification and enzyme-mediated signal amplification. Graphical abstract.

Segregation of Dispersed Silica Nanoparticles in Microfluidic Water-in-Oil Droplets: A Kinetic Study

Dispersed negatively charged silica nanoparticles segregate inside microfluidic water-in-oil (W/O) droplets that are coated with a positively charged lipid shell. We report a methodology for the quantitative analysis of this self-assembly process. By using real-time fluorescence microscopy and automated analysis of the recorded images, kinetic data are obtained that characterize the electrostatically-driven self-assembly. We demonstrate that the segregation rates can be controlled by the installment of functional moieties on the nanoparticle's surface, such as nucleic acid and protein molecules. We anticipate that our method enables the quantitative and systematic investigation of the segregation of (bio)functionalized nanoparticles in microfluidic droplets. This could lead to complex supramolecular architectures on the inner surface of micrometer-sized hollow spheres, which might be used, for example, as cell containers for applications in the life sciences.

Aptamer-tethered self-assembled FRET-flares for microRNA imaging in living cancer cells

We report an aptamer-tethered, self-assembled DNA nanowire as a multivalent vehicle for the intracellular delivery of FRET flares. The FRET flares are bound to the nanowire and fluorescently labeled donors and acceptors at two ends, respectively. In the absence of targets, the flares are captured by binding with the nanowires, separating the donor and acceptor (low FRET). However, in the presence of target miRNAs, the flares are displaced from the nanowire, subsequently forming hairpin structures that bring the donor and acceptor into close proximity (high FRET).

A DNA and Self-Doped Conjugated Polyelectrolyte Assembled for Organic Optoelectronics and Bioelectronics

Deoxyribonucleic acid (DNA) and a self-doped conjugated polyelectrolyte, poly(4-(2,3-dihydrothieno[3,4-b]-[1,4]dioxin-2-yl-methoxy)-1-butanesulfonic acid (PEDOT-S), are assembled for organic optoelectronics and bioelectronics. The DNA's helix-coil phase transition in water is studied as a function of composition by thermo-optical analysis. DNA and PEDOT-S are functionalized by using a surfactant, cetyltrimethylammonium chloride (CTMA), and DNA:CTMA, PEDOT-S:CTMA, and DNA:CTMA:PEDOT-S:CTMA complexes were characterized regarding thermal, optical, morphological, and structural properties. Finally, DNA and DNA:PEDOT-S mixtures are processed in water for fabricating organized films through brushing. The electrical properties of these films are characterized using an interdigitated electrode. The films show an electronic conductivity of ∼10^-6-10^-5 S/cm in a range of semiconductors.

Supramolecular DNA Three-Way Junction Motifs With a Bridging Metal Center

Various nano-sized supramolecular architectures have been constructed from DNA molecules via sequence-dependent self-assembly. A DNA three-way junction (3WJ), consisting of three oligonucleotides that are partially complementary to each other, is one of the simplest DNA supramolecular structures. This minireview covers studies on DNA 3WJ motifs bridged by an interstrand metal complex with some related works. The incorporation of interstrand metal complexes into DNA has attracted increasing attention because it potentially allows for metal-dependent regulation of the thermal stability and the structure of DNA supramolecules. Metal-bridged DNA 3WJs were synthesized from three DNA strands containing a bipyridine (bpy)-modified nucleotide in the presence of appropriate metal ions. The bpy-modified DNA strands were crosslinked by an interstrand 3:1 metal complex [Ni^II(bpy)₃ etc.] at the junction core. As a result, the thermal stability of the 3WJs was significantly enhanced upon metal complexation. Furthermore, metal-mediated structural transformation between DNA duplexes and 3WJs was demonstrated by using the same bpy-modified DNA strands. A mixture of bpy-modified strands and their natural complementary strands were self-assembled exclusively into duplexes in the absence of any transition metal ions. In contrast, addition of Ni^II ions induced the formation of 3WJs through the formation of an interstrand Ni^II(bpy)₃ complex, which served as a template for the 3WJ assembly. Because DNA 3WJ structures are essential structural motifs for DNA-based nanoarchitectures, the metal-mediated stabilization and structural induction of metal-locked 3WJs would lead to many potential applications to artificial DNA architectures.

Polymer Stereocomplexation as a Scalable Platform for Nanoparticle Assembly

DNA-mediated assembly of inorganic particles has demonstrated to be a powerful approach for preparing nanomaterials with a range of interesting optical and electrical properties. Building on this inspiration, we describe a generalizable gram-scale method to assemble nanoparticles through the formation of poly(methyl methacrylate) (PMMA) triple-helices. In this work, alkene-terminated syndiotactic (st-) and isotactic (it-) PMMA polymers were prepared and subsequently functionalized to afford nanoparticle ligands. Nanoparticles with complementary st- and it-PMMA ligands could then be spontaneously assembled upon mixing at room temperature. This process was robust and fully reversible through multiple heating and cooling cycles. The versatility of PMMA stereocomplexation was highlighted by assembling hybrid structures composed of nanoparticles of different compositions (e.g., Au and quantum dots) and shapes (e.g., spheres and rods). These initial demonstrations of nanoparticle self-assembly from inexpensive PMMA-based materials present an attractive alternative to DNA-based nanomaterials.

Double Rolling Circle Amplification Generates Physically Cross-Linked DNA Network for Stem Cell Fishing

Stem cells have been widely studied in cell biology and utilized in cell-based therapies, and fishing stem cells from marrow is highly challenging due to the ultralow content. Herein, a physically cross-linked DNA network-based cell fishing strategy is reported, achieving efficient capture, 3D envelop, and enzyme-triggered release of bone marrow mesenchymal stem cells (BMSCs). DNA network is constructed via a double rolling circle amplification method and through the intertwining and self-assembly of two strands of ultralong DNA chains. DNA-chain-1 containing aptamer sequences ensures specific anchor with BMSCs from marrow. Hybridization between DNA-chain-1 and DNA-chain-2 enables the cross-link of cell-anchored DNA chains to form a 3D network, thus realizing cell envelop and separation. DNA network creates a favorable microenvironment for 3D cell culture, and remarkably the physically cross-linked DNA network shows no damage to cells. DNA network is digested by nuclease, realizing the deconstruction from DNA network to fragments, and achieving enzyme-triggered cell release; after release, the activity of cells is well maintained. The strategy provides a powerful and effective method for fishing stem cells from tens of thousands of nontarget cells.

Functional DNA-based hydrogel intelligent materials for biomedical applications

Multifunctional intelligent DNA hydrogels have been reviewed for many biomedical applications.

Super-Soft and Super-Elastic DNA Robot with Magnetically Driven Navigational Locomotion for Cell Delivery in Confined Space

Soft organisms such as earthworms can access confined, narrow spaces, inspiring scientists to fabricate soft robots for in vivo manipulation of cells or tissues and minimally invasive surgery. We report a super-soft and super-elastic magnetic DNA hydrogel-based soft robot (DNA robot), which presents a shape-adaptive property and enables magnetically driven navigational locomotion in confined and unstructured space. The DNA hydrogel is designed with a combinational dynamic and permanent crosslinking network through chain entanglement and DNA hybridization, resulting in shear-thinning and cyclic strain properties. DNA robot completes a series of complex magnetically driven navigational locomotion such as passing through narrow channels and pipes, entering grooves and itinerating in a maze by adapting and recovering its shape. DNA robot successfully works as a vehicle to deliver cells in confined space by virtue of the 3D porous networked structure and great biocompatibility.

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

Biomedical applications require substrata that allow for the grafting, colonization and control of eukaryotic cells. Currently available materials are often limited by insufficient possibilities for the integration of biological functions and means for tuning the mechanical properties. We report on tailorable nanocomposite materials in which silica nanoparticles are interwoven with carbon nanotubes by DNA polymerization. The modular, well controllable and scalable synthesis yields materials whose composition can be gradually adjusted to produce synergistic, non-linear mechanical stiffness and viscosity properties. The materials were exploited as substrata that outperform conventional culture surfaces in the ability to control cellular adhesion, proliferation and transmigration through the hydrogel matrix. The composite materials also enable the construction of layered cell architectures, the expansion of embryonic stem cells by simplified cultivation methods and the on-demand release of uniformly sized stem cell spheroids.

Bottom-Up Assembly of DNA-Silica Nanocomposites into Micrometer-Sized Hollow Spheres

Although DNA nanotechnology has developed into a highly innovative and lively field of research at the interface between chemistry, materials science, and biotechnology, there is still a great need for methodological approaches for bridging the size regime of DNA nanostructures with that of micrometer- and millimeter-sized units for practical applications. We report on novel hierarchically structured composite materials from silica nanoparticles and DNA polymers that can be obtained by self-assembly through the clamped hybridization chain reaction. The nanocomposite materials can be assembled into thin layers within microfluidically generated water-in-oil droplets to produce mechanically stabilized hollow spheres with uniform size distributions at high throughput rates. The fact that cells can be encapsulated in these microcontainers suggests that our concept not only contributes to the further development of supramolecular bottom-up manufacturing, but can also be exploited for applications in the life sciences.

Interaction of single- and double-stranded DNA with multilayer MXene by fluorescence spectroscopy and molecular dynamics simulations

The integration of nucleic acids with nanomaterials has attracted great attention from various research communities in search of new nanoscale tools for a range of applications, from electronics to biomedical uses. MXenes are a new class of multielement 2D materials baring exciting properties mostly directed to energy-related fields. These advanced materials are now beginning to enter the biomedical field given their biocompatibility, hydrophilicity and near-infrared absorption. Herein, we elucidate the interaction of MXene Ti3C2T x with fluorophore-tagged DNA by fluorescence measurements and molecular dynamics simulations. The system showed potential for biosensing with unequivocal detection at picomole levels and single-base discrimination. We found that this material possesses a kinetically unique entrapment/release behavior, with potential implications in time-controlled biomolecule delivery. Our findings present MXenes as platforms for binding nucleic acids, contributing to their potential for hybridization-based biosensing and related bio-applications.

Gene Circuit Compartment on Nanointerface Facilitatating Cascade Gene Expression

Cellular genes that are functionally related to each other are usually confined in specialized subcellular compartments for efficient biochemical reactions. Construction of spatially controlled biosynthetic systems will facilitate the study of biological design principles. Herein, we fabricated a gene circuit compartment by coanchoring two function-related genes on surface of gold nanoparticles and investigated the compartment effect on cascade gene expression in a cell-free system. The gene circuit consisted of a T7 RNA polymerase (T7 RNAP) expression cassette as regulatory gene and a fluorescent protein expression cassette as regulated reporter gene. Both the expression cassettes were attached on a Y-shaped DNA nanostructure whose other two branches were mercapto-modified in order to steadily anchor the gene expression cassettes on the surface of gold nanoparticles. Experimental results demonstrated that both the yield and initial expression rate of the fluorescent reporter protein in the gene circuit compartment system were enhanced compared with those in free gene circuit system. Mechanism investigation revealed that the gene circuit compartment on nanoparticle made the regulatory gene and regulated reporter gene spatially proximal at nanoscale, thus effectively improving the transfer efficiency of the regulatory proteins (T7 RNAP) from regulatory genes to the regulated reporter genes in the compartments, and consequently, the biochemical reaction efficiency was significantly increased. This work not only provided a simplified model for rational molecular programming of genes circuit compartments on nanointerface but also presented implications for the cellular structure-function relationship.

Electrostatically PEGylated DNA enables salt-free hybridization in water

Chemically modified nucleic acids have long served as a very important class of bio-hybrid structures. In particular, the modification with PEG has advanced the scope and performance of oligonucleotides in materials science, catalysis and therapeutics. Most of the applications involving pristine or modified DNA rely on the potential of DNA to form a double-stranded structure. However, a substantial requirement for metal-cations to achieve hybridization has restricted the range of applications. To extend the applicability of DNA in salt-free or low ionic strength aqueous medium, we introduce noncovalent DNA-PEG constructs that allow canonical base-pairing between individually PEGylated complementary strands resulting in a double-stranded structure in salt-free aqueous medium. This method relies on grafting of amino-terminated PEG polymers electrostatically onto the backbone of DNA, which results in the formation of a PEG-envelope. The specific charge interaction of PEG molecules with DNA, absolute absence of metal ions within the PEGylated DNA molecules and formation of a double helix that is significantly more stable than the duplex in an ionic buffer have been unequivocally demonstrated using multiple independent characterization techniques.