DNA materials: bridging nanotechnology and biotechnology

Determination of nucleobase-pairing free energies from rotamer equilibria of 2-(methylamino)pyrimidines

A fast straightforward method for the determination of free energies of modified nucleobase pairing is proposed. The method is based on the nuclear magnetic resonance (NMR) spectroscopy monitoring of conformational changes of 2-(methylamino)-pyrimidines upon intermolecular binding.

Flexibility and thermal dynamic stability increase of dsDNA induced by Ru(bpy)2dppz2+ based on AFM and HRM technique

Ru(bpy)₂dppz²⁺ has been widely used as a probe for exploring the structure of double-stranded DNA (dsDNA). The flexibility change of DNA helix is important in many of its biological functions but not well understood. Here, flexibility change of dsDNA helix caused by intercalation with Ru(bpy)₂dppz²⁺ was investigated using the atomic force microscopy. At first, the interactions between ruthenium complex and dsDNA helix were characterized and the binding site size (p = 2.87 bp) and binding constant (K_a = 5.9 * 10⁷ M⁻¹) were determined by the relative extension of DNA helix using the equation of McGhee and von Hippel. By measuring intercalator-induced DNA elongation and the mean square of end-to-end distance at different molar ratios of Ru(bpy)₂dppz²⁺ to dsDNA, the changes of persistence length under different ruthenium concentrations were determined by the worm-like chain model. We found that the persistence length of dsDNA decreased with increasing Ru(bpy)₂dppz²⁺ concentration, demonstrating that the flexibility of dsDNA obviously enhanced due to the intercalation. Especially, the persistence length changed greatly from 54 to 34 nm on changing the molar ratio of ruthenium to dsDNA from 0 to 0.2. We speculated that the intercalation of dsDNA with Ru(bpy)₂dppz²⁺ resulted in local deformation or bending of the DNA duplex. In addition, the thermal dynamic stability of DNA helix was measured with high resolution melting method which revealed the increase in thermal dynamic stability of DNA helix due to the ruthenium intercalation.

Poly(adenine)-templated fluorescent Au nanoclusters for the rapid and sensitive detection of melamine

A rapid and label-free fluorescence sensing strategy has been established for the sensitive determination of melamine (MA) on the basis of poly(adenine) (poly (A))-templated Au nanoclusters (AuNCs). The poly(A)-templated AuNCs possessed excellent luminescence and photo-stability. In the presence of Hg²⁺, the luminescence of AuNCs was quenched by Hg²⁺ through the metallophilic interactions between Au⁺ and Hg²⁺. When melamine was introduced, the fluorescence intensity of sensing system could be recovered. There was a greater coordination interaction between Hg²⁺ and melamine, which blocked the Hg²⁺-mediated fluorescence quenching of AuNCs. The assay allowed sensitive determination of melamine with a linear detection range from 50 nM to 100 μM. The limit of detection was as low as 16.6 nM. Furthermore, the label-free strategy was successfully employed for the detection of melamine concentration in real samples.

N4-acyl-2'-deoxycytidine-5'-triphosphates for the enzymatic synthesis of modified DNA

A huge diversity of modified nucleobases is used as a tool for studying DNA and RNA. Due to practical reasons, the most suitable positions for modifications are C5 of pyrimidines and C7 of purines. Unfortunately, by using these two positions only, one cannot expand a repertoire of modified nucleotides to a maximum. Here, we demonstrate the synthesis and enzymatic incorporation of novel N⁴-acylated 2′-deoxycytidine nucleotides (dC^Acyl). We find that a variety of family A and B DNA polymerases efficiently use dC^AcylTPs as substrates. In addition to the formation of complementary C^Acyl•G pair, a strong base-pairing between N⁴-acyl-cytosine and adenine takes place when Taq, Klenow fragment (exo–), Bsm and KOD XL DNA polymerases are used for the primer extension reactions. In contrast, a proofreading phi29 DNA polymerase successfully utilizes dC^AcylTPs but is prone to form C^Acyl•A base pair under the same conditions. Moreover, we show that terminal deoxynucleotidyl transferase is able to incorporate as many as several hundred N⁴-acylated-deoxycytidine nucleotides. These data reveal novel N⁴-acylated deoxycytidine nucleotides as beneficial substrates for the enzymatic synthesis of modified DNA, which can be further applied for specific labelling of DNA fragments, selection of aptamers or photoimmobilization.

Rationally designed DNA-based nanocarriers

Nanomaterials employed for enhanced drug delivery and therapeutic effects have been extensively investigated in the past decade. The outcome of current anticancer treatments based on conventional nanoparticles is suboptimal, due to the lack of biocompatibility, the deficient tumor targeting, the limited drug accumulation in the diseased region, etc. Alternatively, DNA-based nanocarriers have emerged as a novel and versatile platform to integrate the advantages of nanotechnologies and biological sciences, which shows great promise in addressing the key issues for biomedical studies. Rather than a genetic information carrier, DNA molecules can work as building blocks to fabricate programmable and bio-functional nanostructures based on Watson Crick base-pairing rules. The DNA-based materials have demonstrated unique properties, such as uniform sizes and shapes, pre-designable and programmable nanostructures, site-specific surface functionality and excellent biocompatibility. These intrigue features allow DNA nanostructures to carry functional moieties to realize precise tumor recognition, customized therapeutic functions and stimuli-responsive drug release, making them highly attractive in many aspects of cancer treatment. In this review, we focus on the recent progress in DNA-based self-assembled materials for the biomedical applications, such as molecular imaging, drug delivery for in vitro or in vivo cancer treatments. We introduce the general strategies and essential requirements for fabricating DNA-based nanocarriers. We summarize the advances of DNA-based nanocarriers according to their functionalities and structural properties for cancer diagnosis and therapy. Finally, we discuss the challenges and future perspectives regarding the detailed in vivo parameters of DNA materials and the design of intelligent DNA nanomedicine for individualized cancer therapy.

Branched DNA Architectures Produced by PCR-Based Assembly as Gene Compartments for Cell-Free Gene-Expression Reactions

The physical distance between genes plays important roles in controlling gene expression reactions in vivo. Herein, we report the design and synthesis of a branched gene architecture in which three transcription units are integrated into one framework through assembly based on the polymerase chain reaction (PCR), together with the exploitation of these constructs as "gene compartments" for cell-free gene expression reactions, probing the impact of this physical environment on gene transcription and translation. We find that the branched gene system enhances gene expression yields, in particular at low concentrations of DNA and RNA polymerase (RNAP); furthermore, in a crowded microenvironment that mimics the intracellular microenvironment, gene expression from branched genes maintains a relatively high level. We propose that the branched gene assembly forms a membrane-free gene compartment that resembles the nucleoid of prokaryotes and enables RNAP to shuttle more efficiently between neighboring transcription units, thus enhancing gene expression efficiency. Our branched DNA architecture provides a valuable platform for studying the influence of "cellular" physical environments on biochemical reactions in simplified cell-free systems.

Nucleic Acid-Based Functional Nanomaterials as Advanced Cancer Therapeutics

Nucleic acid-based functional nanomaterials (NAFN) have been widely used as emerging drug delivery nanocarriers for cancer therapeutics. Considerable works have demonstrated that NAFN can effectively load and protect therapeutic agents, and particularly enable targeting delivery to the tumor site and stimuli-responsive release. These outstanding performances are due to NAFN's unique properties including inherent biological functions and sequence programmability as well as biocompatibility and biodegradability. In this Review, the recent progress on NAFN as advanced cancer therapeutics is highlighted. Three main cancer therapy approaches are categorized including chemo-, immuno-, and gene-therapy. Examples are presented to show how NAFN are rationally and exquisitely designed to address problems in cancer therapy. The challenges and future development of NAFN are also discussed toward future more practical biomedical applications.

From DNA Nanotechnology to Material Systems Engineering

In the past 35 years, DNA nanotechnology has grown to a highly innovative and vibrant field of research at the interface of chemistry, materials science, biotechnology, and nanotechnology. Herein, a short summary of the state of research in various subdisciplines of DNA nanotechnology, ranging from pure "structural DNA nanotechnology" over protein-DNA assemblies, nanoparticle-based DNA materials, and DNA polymers to DNA surface technology is given. The survey shows that these subdisciplines are growing ever closer together and suggests that this integration is essential in order to initiate the next phase of development. With the increasing implementation of machine-based approaches in microfluidics, robotics, and data-driven science, DNA-material systems will emerge that could be suitable for applications in sensor technology, photonics, as interfaces between technical systems and living organisms, or for biomimetic fabrication processes.

Dynamic Nanostructures from DNA-Coupled Molecules, Polymers, and Nanoparticles

Dynamic and reconfigurable systems that can sense and react to physical and chemical signals are ubiquitous in nature and are of great interest in diverse areas of science and technology. DNA is a powerful tool for fabricating such smart materials and devices due to its programmable and responsive molecular recognition properties. For the past couple of decades, DNA-based self-assembly is actively explored to fabricate various DNA-organic and DNA-inorganic hybrid nanostructures with high-precision structural control. Building upon past development, researchers have recently begun to design and assemble dynamic nanostructures that can undergo an on-demand transformation in the structure, properties, and motion in response to various external stimuli. In this Review, recent advances in dynamic DNA nanostructures, focusing on hybrid structures fabricated from DNA-conjugated molecules, polymers, and nanoparticles, are introduced, and their potential applications and future perspectives are discussed.

Structural and Functional Stability of DNA Nanopores in Biological Media

DNA nanopores offer a unique nano-scale foothold at the membrane interface that can help advance the life sciences as biophysical research tools or gate-keepers for drug delivery. Biological applications require sufficient physiological stability and membrane activity for viable biological action. In this report, we determine essential parameters for efficient nanopore folding and membrane binding in biocompatible cell media. The parameters are identified for an archetypal DNA nanopore composed of six interwoven strands carrying cholesterol lipid anchors. Using gel electrophoresis and fluorescence spectroscopy, the nanostructures are found to assemble efficiently in cell media, such as LB and DMEM, and remain structurally stable at physiological temperatures. Furthermore, the pores’ oligomerization state is monitored using fluorescence spectroscopy and confocal microscopy. The pores remain predominately water-soluble over 24 h in all buffer systems, and were able to bind to lipid vesicles after 24 h to confirm membrane activity. However, the addition of fetal bovine serum to DMEM causes a significant reduction in nanopore activity. Serum proteins complex rapidly to the pore, most likely via ionic interactions, to reduce the effective nanopore concentration in solution. Our findings outline crucial conditions for maintaining lipidated DNA nanodevices, structurally and functionally intact in cell media, and pave the way for biological studies in the future.

Machine Learning Prediction of DNA Charge Transport

First-principles calculations of charge transfer in DNA molecules are computationally expensive given that conducting charge carriers interact with intra- and intermolecular atomic motion. Screening sequences, for example, to identify excellent electrical conductors, is challenging even when adopting coarse-grained models and effective computational schemes that do not explicitly describe atomic dynamics. We present a machine learning (ML) model that allows the inexpensive prediction of the electrical conductance of millions of long double-stranded DNA (dsDNA) sequences, reducing computational costs by orders of magnitude. The algorithm is trained on short DNA nanojunctions with n = 3-7 base pairs. The electrical conductance of the training set is computed with a quantum scattering method, which captures charge-nuclei scattering processes. We demonstrate that the ML method accurately predicts the electrical conductance of varied dsDNA junctions tracing different transport mechanisms: coherent (short-range) quantum tunneling, on-resonance (ballistic) transport, and incoherent site-to-site hopping. Furthermore, the ML approach supports physical observations that clusters of nucleotides regulate DNA transport behavior. The input features tested in this work could be used in other ML studies of charge transport in complex polymers in the search for promising electronic and thermoelectric materials.

Modular Design of Programmable Mechanofluorescent DNA Hydrogels

Mechanosensing systems are ubiquitous in nature and control many functions from cell spreading to wound healing. Biologic systems typically rely on supramolecular transformations and secondary reporter systems to sense weak forces. By contrast, synthetic mechanosensitive materials often use covalent transformations of chromophores, serving both as force sensor and reporter, which hinders orthogonal engineering of their sensitivity, response and modularity. Here, we introduce FRET-based, rationally tunable DNA tension probes into macroscopic 3D all-DNA hydrogels to prepare mechanofluorescent materials with programmable sacrificial bonds and stress relaxation. This design addresses current limitations of mechanochromic system by offering spatiotemporal resolution, as well as quantitative and modular force sensing in soft hydrogels. The programmable force probe design further grants temporal control over the recovery of the mechanofluorescence during stress relaxation, enabling reversible and irreversible strain sensing. We show proof-of-concept applications to study strain fields in composites and to visualize freezing-induced strain patterns in homogeneous hydrogels.

Structure and stimuli-responsiveness of all-DNA dendrimers: theory and experiment

We present a comprehensive theoretical and experimental study of the solution phase properties of a DNA-based family of nanoparticles - dendrimer-like DNA molecules (DL-DNA). These charged DNA dendrimers are novel macromolecular aggregates, which hold high promise in targeted self-assembly of soft matter systems in the bulk and at interfaces. To describe the behaviour of this family of dendrimers (with generations ranging from G1 to G7), we use a theoretical model in which base-pairs of a single DL-DNA molecule are modeled by charged monomers, whose interactions are chosen to mimic the equilibrium properties of DNA correctly. Experimental results on the sizes and conformations of DL-DNA are based on static and dynamic light scattering; and molecular dynamics simulations are employed to model the equilibrium properties of DL-DNA, which compare favorably to the findings from experiments while at the same time providing a host of additional information and insight into the molecular structure of the nanostructures. We also examine the salt-responsiveness of these macromolecules, finding that despite the strong screening of electrostatic interactions brought about by the added salt, the macromolecules shrink only slightly, their size robustness stemming from the high bending rigidity of the DNA-segments. The study of these charged dendrimer systems is an important field of research in the area of soft matter due to their potential role for various interdisciplinary applications, ranging from molecular cages and carriers for drug delivery in a living organism to the development of dendrimer- and dendron-based ultra-thin films in the area of nanotechnology. These findings are essential to determine if DL-DNA is a viable candidate for the experimental realization of cluster crystals in the bulk, a novel form of solid with multiple site occupancy.

Fabricating an intelligent cell-like nano-prodrug via hierarchical self-assembly based on the DNA skeleton for suppressing lung metastasis of breast cancer

A new intelligent cell-like nanostructure is designed for suppressing lung metastasis of breast cancer.

Stimuli-Responsive DNA-Switchable Biointerfaces

Switchable interfaces, also known as smart interfaces, can alter their macroscopic properties in response to external stimuli. Compared to an artificial switchable interface, DNA-based switchable biointerfaces have high diversity, uniformity, reproducibility, and functionality and are easily designed and developed with atomic precision because the sequence of the DNA strand strictly governs the structural and active properties of its assembly. Moreover, various structures such as double strands based on the Watson-Crick base-pairing rule, G-quadruplexes, i-Motifs, triplexes, and parallel-stranded duplexes exist between or among DNA strands to enrich the structures of DNA biointerfaces. In this article, the design, stimulus responses, and applications of switchable DNA biointerfaces were discussed in terms of single-switch, dual-response, and sequential operation. The applications related to sensing, imaging, delivery, logic gates, and nanomechines were introduced in terms of the design and construction of DNA biointerfaces. Future directions and challenges were also outlined for this rapidly emerging field.

DNA Templated Metal Nanoclusters: From Emergent Properties to Unique Applications

Metal nanoclusters containing a few to several hundred atoms with sizes ranging from sub-nanometer to ∼2 nm occupy an intermediate size regime that bridges larger plasmonic nanoparticles and smaller metal complexes. With strong quantum confinement, metal nanoclusters exhibit molecule-like properties. This Account focuses on noble metal nanoclusters that are synthesized within a single stranded DNA template. Compared to other ligand protected metal nanoclusters, DNA-templated metal nanoclusters manifest intriguing physical and chemical properties that are heavily influenced by the design of DNA templates. For example, DNA-templated silver nanoclusters can show bright fluorescence, tunable emission colors, and enhanced stability by tuning the sequence of the encapsulating DNA template. DNA-templated gold nanoclusters can also serve as excellent cocatalysts, which are integratable with other biocatalysts such as enzymes. In this Account, DNA-templated silver and gold nanoclusters are selected as paradigm systems to showcase their emergent properties and unique applications. We first discuss the DNA-templated silver nanoclusters with a focus on the creation of a complementary palette of emission colors, which has potential applications for multiplex assays. The importance of the DNA template toward enhanced stability of silver nanoclusters is also demonstrated. We then introduce a special class of activable fluorescence probes that are based on the fluorescence turn-on phenomena of DNA-templated silver nanoclusters, which are named nanocluster beacons (NCBs). NCBs have distinct advantages over molecular beacons for nucleic acid detection, and their emission mechanisms are also discussed in detail. We then discuss a universal method of creating novel DNA-silver nanocluster aptamers for protein detection with high specificity. The remainder of the Account is devoted to the DNA-templated gold nanoclusters. We demonstrate that DNA-gold nanoclusters can serve as enhancers for enzymatic reduction of oxygen, which is one of the most important reactions in biofuel cells. Although DNA-templated metal nanoclusters are still in their infancy, we anticipate they will emerge as a new type of functional nanomaterial with wide applications in biology and energy science. Future research will focus on the synthesis of size selected DNA-metal nanoclusters with atomic monodispersity, structural determination of different sized DNA-metal nanoclusters, and establishment of structure-property correlations. Some long-standing mysteries, such as the origin of fluorescence and mechanism for emission color tunability, constitute the central questions regarding the photophysical properties of DNA-metal nanoclusters. On the application side, more studies are required to understand the interaction between nanocluster and biological systems. In the foreseeable future, one can expect that new biosensors, catalysts, and functional devices will be invented based on the intriguing properties of well-designed DNA-metal nanoclusters and their composites. Overall, DNA-metal nanoclusters can add additional spotlights into the highly vibrant field of ligand protected, quantum sized metal nanoclusters.

A RNA producing DNA hydrogel as a platform for a high performance RNA interference system

RNA interference (RNAi) is a mechanism in which small interfering RNA (siRNA) silences a target gene. Herein, we describe a DNA hydrogel capable of producing siRNA and interfering with protein expression. This RNAi-exhibiting gel (termed I-gel for interfering gel) consists of a plasmid carrying the gene transcribing siRNA against the target mRNA as part of the gel scaffold. The RNAi efficiency of the I-gel has been confirmed by green fluorescent protein (GFP) expression assay and RNA production quantification. The plasmid stability in the I-gel results in an 8-times higher transcription efficiency than that of the free plasmid. We further applied the I-gel to live cells and confirmed its effect in interfering with the GFP expression. The I-gel shows higher RNAi effect than plasmids in free form or complexed with Lipofectamine. This nanoscale hydrogel, which is able to produce RNA in a cell, provides a platform technology for efficient RNAi system.

Ultrasensitive Detection of Serum MicroRNA Using Branched DNA-Based SERS Platform Combining Simultaneous Detection of α-Fetoprotein for Early Diagnosis of Liver Cancer

We provided an ultrasensitive sensing strategy for microRNA detection by first employing branched DNA. With the aid of microcontact printing, we realized the multiplex sensing of different kinds of liver cancer biomarkers: microRNA and protein simultaneously. Delicately designed branched DNA included multiple complementary sticky ends as probe to microRNA capture and the double-stranded rigid branched core to increase the active sticky-ends distance and expose more DNA probes for sensitivity. The branched DNA enables 2 orders of magnitude increase in sensitivity for microRNA detection over single-stranded DNA. The limit of detection reaches as low as 10 attomolar (S/N = 3) for miR-223 and 10^-12 M for α-fetoprotein. In addition, this system shows high selectivity and appropriate reproducibility (the relative standard deviation is less than 20%) in physiological media. Serum samples are tested and the results of α-fetoprotein are in good agreement with the current gold-standard method, electrochemiluminescence immunoassay analyzer. The results suggest the reliability of this approach in physiological media and show high potential in the sensing of low abundant microRNA in serum, especially for early diagnosis of primary liver cancers.

Shape-memory and self-healing functions of DNA-based carboxymethyl cellulose hydrogels driven by chemical or light triggers

Photoresponsive nucleic acid-based carboxymethyl cellulose (CMC) hydrogels are synthesized, and their application as shape-memory and self-healing functional matrices are discussed. One system involves the preparation of a carboxymethyl cellulose hydrogel crosslinked by self-complementary nucleic acid duplexes and by photoresponsive trans-azobenzene/β-cyclodextrin (β-CD) supramolecular complexes. Photoisomerization of the trans-azobenzene to the cis-azobenzene results in a hydrogel exhibiting lower stiffness due to the separation of the azobenzene/β-CD bridging units. The hydrogel is switched between high and low stiffness states by the cyclic and reversible light-induced isomerization of the azobenzene units between the trans and cis states. The light-controlled stiffness properties of the hydrogel are used to develop a shape-memory hydrogel, where the duplex bridging units act as permanent memory in the quasi-liquid shapeless state of the hydrogel. A second system in the study is a carboxymethyl cellulose hydrogel crosslinked by the K+-stabilized G-quadruplex bridging units and by trans-azobenzene/β-CD complexes. The resulting hydrogel includes dual-trigger functionalities, where the trans-azobenzene/β-CD complexes can be reversibly formed and dissociated through the trans and cis photoisomerization of the azobenzene units, and the K+-stabilized G-quadruplexes can be reversibly dissociated and reformed in the presence of 18-crown-6-ether/K+-ions. The signal-responsive crosslinked hydrogel reveals controlled stiffness properties, where the hydrogel crosslinked by the trans-azobenzene/β-CD and K+-ion-stabilized G-quadruplex reveals high stiffness and the hydrogel crosslinked only by the K+-ion-stabilized G-quadruplexes or only by the trans-azobenzene/β-CD complexes reveals low stiffness properties. The controlled stiffness properties of the hydrogel are used to develop shape-memory hydrogels, where the trans-azobenzene/β-CD complexes or the K+-ion-stabilized G-quadruplexes act as permanent memories in the shapeless and quasi-liquid states of the hydrogels. In addition, the hydrogel that includes two types of stimuli-responsive crosslinking units is used as a self-healing matrix, where each of the triggers guides the self-healing processes.

Programmable and Multifunctional DNA-Based Materials for Biomedical Applications

DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg²⁺ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.

DNA Directed Self-Assembly of Single Walled Carbon Nanotubes into Three-Way Junction Nanostructures

Utilization of a self-assembled two-dimensional DNA nanostructure to arrange single-walled carbon nanotubes (SWNTs) into predetermined structures at controllable angles is presented. A specially designed DNA three-way junction (3WJ) composed of three double-stranded DNA arms containing single-stranded overhang sequences was prepared by annealing of partially complementary ssDNA sequences and ultrasonicated with SWNTs, resulting in DNA-3WJ/SWNT hybrid nanostructures. Utilization of DNA-3WJ not only allowed the precise dispersion of SWNTs but also acted as a rigid template for the self-assembly of SWNTs into three-armed junctions at an angle of approximately 120° to each other as visualized by scanning electron microscopy and atomic force microscopy. Prepared DNA-3WJ/SWNT nanostructures were also demonstrated to have the appropriate binding sites for fluorophores, providing a simple method for the fluorescent labeling of SWNTs. When ssDNA sequences forming the DNA-3WJ are ultrasonicated with SWNTs, followed by annealing of resulting ssDNA wrapped SWNTs, instead of hybrid junctions composed of three SWNT molecules, a web-like structure composed of interconnected SWNT junctions was obtained. The design approaches demonstrated here provide simple methods for the arrangement of SWNTs into desired nanostructures utilizing pre-assembled DNA nanostructures as linkers in aqueous solution through noncovalent interactions which can greatly contribute to efforts along the controlled assembly of SWNTs.

Synthesis of Branched DNA Scaffolded Super-Nanoclusters with Enhanced Antibacterial Performance

Metal nanoclusters (NCs) possess unique optical properties, and exhibit a wide variety of potential applications. DNA with robust molecular programmability is demonstrated as an ideal scaffold to regulate the formation of NCs, offering a rational approach to precisely tune the spatial structures of NCs. Herein, the first use of branched DNA as scaffold to regulate the formation of silver nanoclusters (super-AgNC) is reported, in which the spatial structures are precisely designed and constructed. Super-AgNC with tunable shapes and arm-lengths including Y-, X-, and (Y-X)- shaped super-AgNC is achieved. The molecular structures and optical properties of super-AgNCs are systemically studied. As a proof of application, remarkably, super-AgNCs exhibit superior antibacterial performance. In addition, super-AgNCs show excellent biocompatibility with three types of tissue cells including 293T (human embryonic kidney cells), SMCs (vascular smooth muscle cells), and GLC-82 (lung adenocarcinoma cells). These performances enable the super-AgNCs adaptable in a variety of applications such as biosensing, bioimaging, and antibacterial agents.

Liposome Crosslinked Polyacrylamide/DNA Hydrogel: a Smart Controlled-Release System for Small Molecular Payloads

A novel stimuli-responsive hydrogel system with liposomes serving as both noncovalent crosslinkers and functional small molecules carriers for controlled-release is developed. Liposomes can crosslink polyacrylamide copolymers functionalized with cholesterol-modified DNA motifs to yield a DNA hydrogel system, due to the hydrophobic interaction between cholesteryl groups and the lipid bilayer of liposomes. Functional information encoded DNA motifs on the polymer backbones endow the hydrogel with programmable smart responsive properties. In a model system, the hydrogel exhibits stimuli-responsive gel-to-sol transformation triggered by the opening of DNA motifs upon the presence of a restriction endonuclease enzyme, EcoR I, or temperature change, realizing the controlled-release of liposomes which are highly efficient carriers of active small molecules payloads. Two active molecules, 1,1-dioctadecyl-3,3,3,3-tetramethylindodicarbocyanine perchlorate (DiIC18(5)) and calcein, are chosen as the hydrophobic and hydrophilic model payloads, respectively, to address the feasibility of the releasing strategy. Moreover, the hydrogel exhibits injectable property as well as self-recovery behaviors.

A Fluorescent Biofunctional DNA Hydrogel Prepared by Enzymatic Polymerization

DNA has arisen as a promising building material for the construction of hydrogels owing to its unique properties such as designability and biocompatibility. All-DNA hydrogels with only DNA molecules may have limited applications; hence a composite DNA hydrogel with multifunctional moieties is highly desired to cater for specific applications. Herein, a multifunctional DNA hydrogel is created by incorporating DNA with silver nanoclusters (AgNCs), in which AgNCs render the hydrogel simultaneously with fluorescent and antibacterial functions. A circular DNA is rationally designed, which allows for the elongation of DNA chain via an enzymatic polymerization as well as the formation of AgNCs onto DNA scaffolds. The resultant hybrid DNA hydrogel not only shows distinctive morphology and mechanical properties, but also exhibits fluorescent and antibacterial functions. These characteristics, along with its biocompatibility, will allow the hydrogel to be suitable for a variety of potential biomedical applications such as tissue engineering, wound dressing, biosensing, and bioimaging.

Hierarchical Design of Tissue Regenerative Constructs

The worldwide shortage of organs fosters significant advancements in regenerative therapies. Tissue engineering and regeneration aim to supply or repair organs or tissues by combining material scaffolds, biochemical signals, and cells. The greatest challenge entails the creation of a suitable implantable or injectable 3D macroenvironment and microenvironment to allow for ex vivo or in vivo cell-induced tissue formation. This review gives an overview of the essential components of tissue regenerating scaffolds, ranging from the molecular to the macroscopic scale in a hierarchical manner. Further, this review elaborates about recent pivotal technologies, such as photopatterning, electrospinning, 3D bioprinting, or the assembly of micrometer-scale building blocks, which enable the incorporation of local heterogeneities, similar to most native extracellular matrices. These methods are applied to mimic a vast number of different tissues, including cartilage, bone, nerves, muscle, heart, and blood vessels. Despite the tremendous progress that has been made in the last decade, it remains a hurdle to build biomaterial constructs in vitro or in vivo with a native-like structure and architecture, including spatiotemporal control of biofunctional domains and mechanical properties. New chemistries and assembly methods in water will be crucial to develop therapies that are clinically translatable and can evolve into organized and functional tissues.

Aptamer-integrated DNA nanoassembly: A simple and sensitive DNA framework to detect cancer cells

The development of powerful techniques to detect cancer cells at early stages plays a notable role in diagnosing and prognosing cancer patients and reducing mortality. This paper reports on a novel functional DNA nanoassembly capable of detecting cancer cells based on structural DNA nanotechnology. DNA nanoassemblies were constructed by the self-assembly of a DNA concatemer to a plenty of sticky-ended three-way junctions. While an aptamer moiety guided the nanoassembly to the target cancer cell, the peroxidase-mimicking DNAzymes embedded in the nanoassemblies were used as the sensing element to produce colorimetric signals. As proof-of-concept, as low as 175 cancer cells were detected by the assay, and color change was clearly distinguished by the naked eyes. The proposed system enjoys potential applications for point-of-care cancer diagnosis, with its excellent sensitivity and selectivity.

DNA decorated Cu9S5 nanoparticles as NIR light responsive drug carriers for tumor chemo–phototherapy

Recently, near-infrared (NIR) light responsive drug delivery systems have attracted much attention for tumor therapy.

DNA Hydrogel with Tunable pH-Responsive Properties Produced by Rolling Circle Amplification

Recently, smart DNA hydrogels, which are generally formed by the self-assembly of oligonucleotides or through the cross-linking of oligonucleotide-polymer hybrids, have attracted tremendous attention. However, the difficulties of fabricating DNA hydrogels limit their practical applications. We report herein a novel method for producing pH-responsive hydrogels by rolling circle amplification (RCA). In this method, pH-sensitive cross-linking sites were introduced into the polymeric DNA chains during DNA synthesis. As the DNA sequence can be precisely defined by its template, the properties of such hydrogels can be finely tuned in a very facile way through template design. We have investigated the process of hydrogel formation and pH-responsiveness to provide rationales for functional hydrogel design based on the RCA reaction.

Enzymatic Synthesis, Amplification, and Application of DNA with a Functionalized Backbone

The ability to amplify DNA along with its unprecedented sequence control has led to its use for different applications, but all are limited by the properties available to natural nucleotides. We previously reported the evolution of polymerase SFM4-3, which better tolerates 2'-modified substrates. To explore the utility of SFM4-3, we now report the characterization of its recognition of substrates with 2'-azido, 2'-chloro, 2'-amino, or arabinose sugars. We find that SFM4-3 can efficiently synthesize polymers composed of these nucleotides, and most interestingly, that SFM4-3 can also PCR amplify these modified oligonucleotides. When combined with post-amplification modification, the latter allows for the exponential amplification of polymers that may be functionalized with desired moieties arrayed in a controlled fashion, the utility of which we demonstrate with extensive small molecule functionalization and the production and initial characterization of a novel DNA hydrogel.

Sequence-Independent DNA Nanogel as a Potential Drug Carrier

DNA nanostructures largely rely on pairing DNA bases; thus, sequence designing is required. Here, this study demonstrates a sequence-independent strategy to fabricate DNA nanogel (NG) inspired by cisplatin, a chemotherapeutic drug that acts as a DNA crosslinker. A simple heating and cooling of the genomic DNA extracts and cisplatin produces DNA NG with a size controlled by the heating time. Furthermore, the drug-loaded NG is formulated by spontaneously mixing DNA segments, cisplatin, and doxorubicin. The in vitro cell studies demonstrate that the doxorubicin-loaded NG alters the drug distribution in cells while its cytotoxic potential is well-maintained. This chemotherapeutic-inspired method provides a facile one-pot and cost-effective strategy to fabricate size-controllable DNA NG that potentially acts as drug carrier.

Multifunctional quantum dot DNA hydrogels

Biotemplated nanomaterials offer versatile functionality for multimodal imaging, biosensing, and drug delivery. There remains an unmet need for traceable and biocompatible nanomaterials that can be synthesized in a precisely controllable manner. Here, we report self-assembled quantum dot DNA hydrogels that exhibit both size and spectral tunability. We successfully incorporate DNA-templated quantum dots with high quantum yield, long-term photostability, and low cytotoxicity into a hydrogel network in a single step. By leveraging DNA-guided interactions, we introduce multifunctionality for a variety of applications, including enzyme-responsive drug delivery and cell-specific targeting. We report that quantum dot DNA hydrogels can be used for delivery of doxorubicin, an anticancer drug, to increase potency 9-fold against cancer cells. This approach also demonstrated high biocompatibility, trackability, and in vivo therapeutic efficacy in mice bearing xenografted breast cancer tumors. This work paves the way for the development of new tunable biotemplated nanomaterials with multiple synergistic functionalities for biomedical applications.

The development of nanomaterials for imaging and drug delivery has been of great interest to the field. Here, the authors synthesized multifunctional enzyme-responsive hydrogels with self-assembling quantum dots for nucleic acid and drug delivery as well as having imaging capability.

Aptamer-integrated DNA nanostructures for biosensing, bioimaging and cancer therapy

The combination of nanostructures with biomolecules leading to the generation of functional nanosystems holds great promise for biotechnological and biomedical applications. As a naturally occurring biomacromolecule, DNA exhibits excellent biocompatibility and programmability. Also, scalable synthesis can be readily realized through automated instruments. Such unique properties, together with Watson-Crick base-pairing interactions, make DNA a particularly promising candidate to be used as a building block material for a wide variety of nanostructures. In the past few decades, various DNA nanostructures have been developed, including one-, two- and three-dimensional nanomaterials. Aptamers are single-stranded DNA or RNA molecules selected by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), with specific recognition abilities to their targets. Therefore, integrating aptamers into DNA nanostructures results in powerful tools for biosensing and bioimaging applications. Furthermore, owing to their high loading capability, aptamer-modified DNA nanostructures have also been altered to play the role of drug nanocarriers for in vivo applications and targeted cancer therapy. In this review, we summarize recent progress in the design of aptamers and related DNA molecule-integrated DNA nanostructures as well as their applications in biosensing, bioimaging and cancer therapy. To begin with, we first introduce the SELEX technology. Subsequently, the methodologies for the preparation of aptamer-integrated DNA nanostructures are presented. Then, we highlight their applications in biosensing and bioimaging for various targets, as well as targeted cancer therapy applications. Finally, we discuss several challenges and further opportunities in this emerging field.

Bioresponsive DNA Hydrogels: Beyond the Conventional Stimuli Responsiveness

Bioresponsive hydrogels can respond to various biological stimuli by a macroscopic change of physical state or by converting biochemical inputs into biological or mechanical outputs. These materials are playing an increasingly important role in a wide variety of applications, especially in the biological and biomedical fields. However, the design and engineering of intriguing bioresponsive materials with adequate biocompatibility and biodegradability have proven to be a great challenge. DNA, on the other hand, possesses many unique and fascinating properties, including its indispensable genetic function, broad biocompatibility, precise molecular recognition capability, tunable multifunctionality, and convenient programmability. Therefore, DNA has provided crucial prerequisites for the exploration of novel bioresponsive hydrogels and has since become an ideal building block for the construction of novel materials. In this Account, we describe our efforts over more than a decade to develop DNA-based materials including bioresponsive hydrogels. These DNA hydrogels were created through either chemical cross-linking or physical entanglement among DNA chains. We further divided them into two categories: pure DNA-based and hybrid DNA-based hydrogels. For the pure DNA-based hydrogels, we developed the first bulk DNA hydrogel entirely from branched DNA by using enzymatic ligation. Certain drugs were encapsulated in such hydrogels in situ and released in a controllable manner under the stimulation of environmental factors such as nucleases and/or changes in ionic strength. Furthermore, we prepared a protein-producing hydrogel (termed a "P-gel") by ligating X-shaped DNA (X-DNA) and linear plasmids. Following the central dogma of molecular biology, this hydrogel responded to enzymes and substrate and converted them into proteins. This was the first example showing that a hydrogel could be employed to produce proteins without the involvement of live cells. This might also be the first attempt to create cell-like hydrogels that will be ultimately bioresponsive. In addition, we also constructed a DNA physical hydrogel via entanglement of DNA chains elongated by a special polymerase: Phi29. This hydrogel (termed a "meta-hydrogel") exhibited a "meta" property: freely reversible change between liquidlike and solidlike states through stimulation by water molecules. Besides these pure DNA-based hydrogels, we also created a hybrid DNA-based hydrogel: a DNA-clay hybrid hydrogel utilizing electrostatic interactions between DNA and clay nanocrystals. We discovered a synergistic responsiveness in biochemical reaction in this hydrogel, suggesting that a DNA-clay hydrogel might be the environment for the origination of life and that DNA and clay might have been coevolving during early evolution. In summary, DNA links the nonbiological world with biological processes by virtue of its bioresponsiveness. We envision that bioresponsive DNA hydrogels will play an irreplaceable part in the development of future evolvable materials such as soft robots and artificial cells.