A pH-triggered, fast-responding DNA hydrogel

Combination of i-motif and G-quadruplex structures within the same strand: formation and application

Peaceful coexistence: A double quadruplex composed of an i-motif and a G-quadruplex was constructed within one oligonucleotide strand (see picture). The defined double-quadruplex structure can serve as a NOTIF logic gate on the basis of the fluorescence of crystal violet.

Switchable catalytic acrylamide hydrogels cross-linked by hemin/G-quadruplexes

Copolymer chains consisting of acrylamide units and guanine (G)-containing oligonucleotide-tethered acrylamide units undergo, in the presence of K(+) ions, cross-linking by G-quadruplexes to yield a hydrogel. The hydrogel is dissociated upon addition of 18-crown-6 ether that traps the K(+) ions. Reversible formation and dissociation of the hydrogel is demonstrated by the cyclic addition of K(+) ions and 18-crown-6 ether, respectively. Formation of the hydrogel in the presence of hemin results in a hemin/G-quadruplex-cross-linked catalytic hydrogel mimicking the function of horseradish peroxidase, reflected by the catalyzed oxidation of 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid), ABTS(2-), by H2O2 to ABTS(·-) and by the catalyzed generation of chemiluminescence in the presence of luminol/H2O2. Cyclic "ON" and "OFF" activation of the catalytic functions of the hydrogel are demonstrated upon the formation of the hydrogel in the presence of K(+) ions and its dissociation by 18-crown-6 ether, respectively. The hydrogel is characterized by rheology measurements, circular dichroism, and probing its chemical and photophysical properties.

Study of pH-induced folding and unfolding kinetics of the DNA i-motif by stopped-flow circular dichroism

Using the stopped-flow circular dichroism (SFCD) technique, we investigate the kinetics of the pH-induced folding and unfolding process of the DNA i-motif. The results show that the molecule can fold or unfold on a time scale of 100 ms when the solution pH is changed. It is also found that the folding and unfolding rates strongly depend on the solution pH. On the basis of quantitative data, we propose theoretical models to decipher the folding and unfolding kinetics. Our models suggest that the cooperativity of protons is crucial for both the folding and unfolding process. In the unfolding process, the cooperative neutralization of two protons (out of the total six protons in the i-motif molecule) is the only rate-limiting step. In the folding process, there exists a critical step in which three protons bind cooperatively to the DNA strand. These results offer an in-depth understanding of the folding and unfolding kinetics of the DNA i-motif and may give precise guidance for constructing novel nanodevices based on the DNA i-motif.

A mechanical metamaterial made from a DNA hydrogel

Metamaterials are artificial substances that are structurally engineered to have properties not typically found in nature. To date, almost all metamaterials have been made from inorganic materials such as silicon and copper, which have unusual electromagnetic or acoustic properties that allow them to be used, for example, as invisible cloaks, superlenses or super absorbers for sound. Here, we show that metamaterials with unusual mechanical properties can be prepared using DNA as a building block. We used a polymerase enzyme to elongate DNA chains and weave them non-covalently into a hydrogel. The resulting material, which we term a meta-hydrogel, has liquid-like properties when taken out of water and solid-like properties when in water. Moreover, upon the addition of water, and after complete deformation, the hydrogel can be made to return to its original shape. The meta-hydrogel has a hierarchical internal structure and, as an example of its potential applications, we use it to create an electric circuit that uses water as a switch.

Construction and assembly of chimeric DNA: oligonucleotide hybrid molecules composed of parallel or antiparallel duplexes and tetrameric i-motifs

Chimeric DNA containing parallel (ps) and antiparallel (aps) duplex elements as well as poly-dC tracts were designed and synthesized. Oligonucleotide duplexes with ps chain orientation containing reverse Watson-Crick dA-dT base pairs and short d(C)2 tails are stabilized under slightly acidic conditions by hemiprotonated dCH+-dC base pairs ("clamp" effect). Corresponding molecules with aps orientation containing Watson-Crick dA-dT base pairs do not show this phenomenon. Chimeric DNA with ps duplex elements and long d(C)5 tails at one or at both ends assemble to tetrameric i-motif structures. Molecules with two terminal d(C)5 tails form multimeric assemblies which have the potential to form nanoscopic scaffolds. A preorganization of the ps duplex chains stabilizes the i-motif assemblies up to almost neutral conditions as evidenced by thermal melting and gel electrophoresis. Although, ps DNA is generally less stable than aps DNA, the aps duplexes contribute less to the stability of the i-motif than ps DNA.

DNA-based delivery vehicles: pH-controlled disassembly and cargo release

Non-Watson-Crick base pairing provides an in situ approach for actuation of DNA nanostructures through responses to solution conditions. Here we demonstrate this concept by using physiologically-relevant changes in pH to regulate DNA pyramid assembly/disassembly and to control the release of protein cargo.

Electrochemical switching of photoelectrochemical processes at CdS QDs and photosystem I-modified electrodes

Photoactive inorganic CdS quantum dots (QDs) or the native photosystem I (PSI) is immobilized onto a pyrroloquinoline quinone (PQQ) monolayer linked to Au electrodes to yield hybrid relay/QDs (or photosystem) assemblies. By the electrochemical biasing of the electrode potential, the relay units are retained in their oxidized PQQ or reduced PQQH(2) states. The oxidized or reduced states of the relay units dictate the direction of the photocurrent (anodic or cathodic). By the cyclic biasing of the electrode potential between the values E ≥ -0.05 V and E ≤ -0.3 V vs Ag quasi-reference electrode (Ag QRE), retaining the relay units in the oxidized PQQ or reduced PQQH(2) states, the photocurrents are respectively switched between anodic and cathodic values. Different configurations of electrically switchable photoelectrochemical systems are described: (i) the PQQ/CdS QDs/(triethanolamine, TEOA) or PQQ/PSI/(ascorbic acid/dichlorophenolindophenol, DCPIP) systems, leading to anodic photocurrents; (ii) the PQQ/CdS QDs (or PSI)/(flavin adenine dinucleotide) systems, leading to cathodic photocurrents; (iii) the PQQ/CdS QDs (or PSI)/(O(2)) switchable systems, leading to cyclic anodic/cathodic switching of the photocurrents.

pH Sensitive DNA Devices

The physicochemical properties of small molecules as well as macromolecules are modulated by solution pH, and DNA is no exception. Special sequences of DNA can adopt unusual conformations e.g., triplex, i-motif and A-motif, depending on solution pH. The specific range of pH for these unusual structures is dictated by the pKa of protonation of the relevant nucleobase involved in the resultant non-canonical base pairing that is required to stabilise the structure. The biological significance of these pH-dependent structures is not yet clear. However, these non-B-DNA structures have been used to design different devices to direct chemical reactions, generate mechanical force, sense pH, etc. The performance of these devices can be monitored by a photonic signal. They are autonomous and their ‘waste free’ operation cycles makes them highly processive. Applications of these devices help to increase understanding of the structural polymorphism of the motifs themselves. The design of these devices has continuously evolved to improve their performance efficiency in different contexts. In some examples, these devices have been shown to perform inside complex living systems with similar efficiencies, to report on the chemical environment there. The robust performance of these devices opens up exciting possibilities for pH-sensitive DNA devices in the study of various pH-regulated biological events.

Aptamer-functionalized hydrogel microparticles for fast visual detection of mercury(II) and adenosine

With a low optical background, high loading capacity, and good biocompatibility, hydrogels are ideal materials for immobilization of biopolymers to develop optical biosensors. We recently immobilized mercury and lead binding DNAs within a monolithic gel and demonstrated ultrasensitive visual detection of these heavy metals. The high sensitivity was attributed to the enrichment of the analytes into the gels. The signaling kinetics was slow, however, taking about 1 h to obtain a stable optical signal because of a long diffusion distance. In this work, we aim to understand the analyte enrichment process and improve the signaling kinetics by preparing hydrogel microparticles. DNA-functionalized gel beads were synthesized using an emulsion polymerization technique and most of the beads were between 10 and 50 μm. Acrydite-modified DNA was incorporated by copolymerization. Visual detection of 10 nM Hg(2+) was still achieved and a stable signal was obtained in just 2 min. The gel beads could be spotted to form a microarray and dried for storage. A new visual sensor for adenosine was designed and immobilized within the gel beads. The adenosine aptamer binds its target about 1000-fold less tightly compared to the mercury binding DNA, allowing a comparison to be made on analyte enrichment by aptamer-functionalized hydrogels.

DNA pillars constructed from an i-motif stem and duplex branches

At an acidic pH, cytosine-rich DNA strands can form i-motif tetramers. Pillar-like DNA structures are self-assembled with such i-motifs as the central stems. The central stem has some overhanging structures that can enable hybridization with complementary units by Watson-Crick pairing and, thus, multiple i-motifs can join to form the pillar.

Colorimetric logic gates based on aptamer-crosslinked hydrogels

We have developed a novel molecular logic gate system based on the incorporation of aptamer-crosslinked hydrogels. Modified gold nanoparticles are used as the output signal, which is visible to the naked eye. This system is designed for AND and OR operations using two chemicals as stimulus inputs.

Stimuli-responsive releasing of gold nanoparticles and liposomes from aptamer-functionalized hydrogels

Controlled release of therapeutic agents is important for improving drug efficacy and reducing toxicity. Recently, hydrogels have been used for controlled release applications. While the majority of the previous work focused on releasing the cargo in response to physical stimuli such as temperature, light, electric field, and pH, we aim to trigger cargo release in the presence of small metabolites. In our system a DNA aptamer that can bind to adenosine, AMP, and ATP was used as a linker to attach either DNA-functionalized gold nanoparticles or liposomes to DNA-functionalized hydrogels. In the presence of the metabolite, both the nanoparticle and liposome cargos were released. The effect of salt, temperature, target concentration, and drying has been systematically studied. Interestingly, we found that the gel can be completely dried while retaining the DNA linkages and adenosine induced release was still achieved after rehydration. Our work demonstrates that aptamers can be used to control the release of drugs and other materials attached to hydrogels.

Aptamer-incorporated hydrogels for visual detection, controlled drug release, and targeted cancer therapy

Hydrogels are water-retainable materials, made from cross-linked polymers, that can be tailored to applications in bioanalysis and biomedicine. As technology advances, an increasing number of molecules have been used as the components of hydrogel systems. However, the shortcomings of these systems have prompted researchers to find new materials that can be incorporated into them. Among all of these emerging materials, aptamers have recently attracted substantial attention because of their unique properties, for example biocompatibility, selective binding, and molecular recognition, all of which make them promising candidates for target-responsive hydrogel engineering. In this work, we will review how aptamers have been incorporated into hydrogel systems to enable colorimetric detection, controlled drug release, and targeted cancer therapy.

Engineering DNA-based functional materials

While DNA is a genetic material, it is also an inherently polymeric material made from repeating units called nucleotides. Although DNA's biological functions have been studied for decades, the polymeric features of DNA have not been extensively exploited until recently. In this tutorial review, we focus on two aspects of using DNA as a polymeric material: (1) the engineering methods, and (2) the potential real-world applications. More specifically, various strategies for constructing DNA-based building blocks and materials are introduced based on DNA topologies, which include linear, branched/dendritic, and networked. Different applications in nanotechnology, medicine, and biotechnology are further reviewed.

Synthetic, biofunctional nucleic acid-based molecular devices

Structural DNA nanotechnology seeks to create architectures of highly precise dimensions using the physical property that short lengths of DNA behave as rigid rods and the chemical property of Watson-Crick base-pairing that acts as a specific molecular glue with which such rigid rods may be joined. Thus DNA has been used as a molecular scale construction material to make molecular devices that can be broadly classified under two categories (i) rigid scaffolds and (ii) switchable architectures. This review details the growing impact of such synthetic nucleic acid based molecular devices in biology and biotechnology. Notably, a significant trend is emerging that integrates morphology-rich nucleic acid motifs and alternative molecular glues into DNA and RNA architectures to achieve biological functionality.

Molecular-glue-triggered DNA assembly to form a robust and photoresponsive nano-network

A robust and photoresponsive DNA network has been designed and constructed from branched DNA and molecular glue. The molecular glue is photoswitchable and can specifically bind to G-G mismatched double-stranded DNA. The assembly process can be reversibly controlled by manipulating the wavelength of light. The approach is flexible, allowing tuning of the size, morphology as well as the cavity of the network by variation of the molar ratio and the isotropic/anisotropic character of the branched building blocks. The assembled architectures are versatile and heat tolerant. These properties should allow the use of the network in further applications.

Development of smart nanoparticle-aptamer sensing technology

Quantum dots (QDs) are excellent donors in Förster resonance energy transfer (FRET) based sensors because of their broad absorption and narrow symmetric emission. However, the strict requirement of a short donor-acceptor distance to achieve high FRET (hence sensitivity) has posed a significant challenge for QD-FRET-based sensors due to challenges associated with the preparation of QD conjugates that are both compact and highly stable. Consequently, most robust QD-FRET sensors are often too bulky to produce FRET efficiently, especially at low target-to-QD copy numbers. They have largely relied on increasing the target:QD ratio to achieve high FRET, making them undesirable and inefficient in situations of low target:QD copy numbers. Herein we report our work on the preparation of stable, compact and water-soluble QDs and their subsequent use in making compact, functional QD-DNA-based smart nanoparticle sensors for labelled and label-free DNA and protein detection. We have developed two strategies to prepare QD-DNA sensors: 1) via QD-thiolated DNA self-assembly, and 2) via covalent coupling between DNA and a QD surface ligand functional group. We found that thiolated DNA (fluorophore labelled) can self-assemble onto a 3-mercaptopropionic acid-capped QDs to produce highly efficient FRET (~80%) at a DNA:QD ratio of 1 : 1. However, this system suffers from strong non-specific adsorption and the self-assembled single-stranded (ss) DNA target is unable to hybridise to its complementary probe. More recently, we found that a dihydrolipoic acid-capped QD-ssDNA self-assembled system can hybridise to a labelled complementary probe to produce efficient FRET that can be exploited for labelled DNA probe quantification. Further, incorporating an anti-thrombin DNA aptamer to this system leads to a QD-DNA aptamer sensor that can specifically detect a 10 nM unlabelled protein probe (thrombin). The non-specific adsorption problem can be eliminated by introducing a poly(ethylene glycol) (PEG) linker to the QD capping ligands or by capping the QD with a chelating dendritic ligand. The resulting QD-DNA sensors can specifically detect 1 nM unlabelled or 35 pM labelled DNA probes using QD-sensitised dye FRET signals on a conventional fluorimeter. Extension of the DNA target to other functional DNAs or DNA/RNA aptamers should allow the development of a multi-functional QD-DNA platform suitable for biosensing, disease diagnosis and therapeutic applications.

Electrostatically directed visual fluorescence response of DNA-functionalized monolithic hydrogels for highly sensitive Hg²+ detection

Hydrogels are cross-linked hydrophilic polymer networks with low optical background and high loading capacity for immobilization of biomolecules. Importantly, the property of hydrogel can be precisely controlled by changing the monomer composition. This feature, however, has not been investigated in the rational design of hydrogel-based optical sensors. We herein explore electrostatic interactions between an immobilized mercury binding DNA, a DNA staining dye (SYBR Green I), and the hydrogel backbone. A thymine-rich DNA was covalently functionalized within monolithic hydrogels containing a positive, neutral, or negative backbone. These hydrogels can be used as sensors for mercury detection since the DNA can selectively bind Hg(2+) between thymine bases inducing a hairpin structure. SYBR Green I can then bind to the hairpin to emit green fluorescence. For the neutral or negatively charged gels, addition of the dye in the absence of Hg(2+) resulted in intense yellow background fluorescence, which was attributed to SYBR Green I binding to the unfolded DNA. We found that, by introducing 20% positively charged allylamine monomer, the background fluorescence was significantly reduced. This was attributed to the repulsion between positively charged SYBR Green I by the gel matrix as well as the strong binding between the DNA and the gel backbone. The signal-to-background ratio and detection limit was, respectively, improved by 6- and 9-fold using the cationic gel instead of neutral polyacrylamide gel. This study helps understand the electrostatic interaction within hydrogels, showing that hydrogels can not only serve as a high capacity matrix for sensor immobilization but also can actively influence the interaction between involved molecules.

An electrochemical supersandwich assay for sensitive and selective DNA detection in complex matrices

In a traditional sandwich assay, a DNA target hybridizes to a single copy of the signal probe. Here we employ a modified signal probe containing a methylene blue (a redox moiety) label and a "sticky end." When a DNA target hybridizes this signal probe, the sticky end remains free to hybridize another target leading to the creation of a supersandwich structure containing multiple labels. This leads to large signal amplification upon monitoring by voltammetry.

DNA-SWNT hybrid hydrogel

In this communication, we report the preparation of DNA-SWNT hybrid hydrogel which is pH responsive and strength tunable.

DNA-functionalized monolithic hydrogels and gold nanoparticles for colorimetric DNA detection

Highly sensitive and selective DNA detection plays a central role in many fields of research, and various assay platforms have been developed. Compared to homogeneous DNA detection, surface-immobilized probes allow washing steps and signal amplification to give higher sensitivity. Previously research was focused on developing glass or gold-based surfaces for DNA immobilization; we herein report hydrogel-immobilized DNA. Specifically, acrydite-modified DNA was covalently functionalized to the polyacrylamide hydrogel during gel formation. There are several advantages of these DNA-functionalized monolithic hydrogels. First, they can be easily handled in a way similar to that in homogeneous assays. Second, they have a low optical background where, in combination with DNA-functionalized gold nanoparticles, even ∼0.1 nM target DNA can be visually detected. By using the attached gold nanoparticles to catalyze the reduction of Ag+, as low as 1 pM target DNA can be detected. The gels can be regenerated by a simple thermal treatment, and the regenerated gels perform similarly to freshly prepared ones. The amount of gold nanoparticles adsorbed through DNA hybridization decreases with increasing gel percentage. Other parameters including the DNA concentration, DNA sequence, ionic strength of the solution, and temperature have also been systematically characterized in this study.

Novel DNA materials and their applications

The last two decades have witnessed the exponential development of DNA as a generic material instead of just a genetic material. The biological function, nanoscale geometry, biocompatibility, biodegradability, and molecular recognition capacity of DNA make it a promising candidate for the construction of novel functional nanomaterials. As a result, DNA has been recognized as one of the most appealing and versatile nanomaterial building blocks. Scientists have used DNA in this way to construct various amazing nanostructures, such as ordered lattices, origami, supramolecular assemblies, and even three-dimensional objects. In addition, DNA has been utilized as a guide and template to direct the assembly of other nanomaterials including nanowires, free-standing membranes, and crystals. Furthermore, DNA can also be used as structural components to construct bulk materials such as DNA hydrogels, demonstrating its ability to behave as a unique polymer. Overall, these novel DNA materials have found applications in various areas in the biomedical field in general, and nanomedicine in particular. In this review, we summarize the development of DNA assemblies, describe the innovative progress of multifunctional and bulk DNA materials, and highlight some real-world nanomedical applications of these DNA materials. We also show our insights throughout this article for the future direction of DNA materials.

Functional nucleic acid nanostructures and DNA machines

The information encoded in the base sequence of DNA provides instructions for the structural and functional properties of this biopolymer. Structural information includes the formation of duplexes, supramolecular crossover tiles, G-quadruplexes, i-motifs, base-metal-ion complexes, and more. Functional information encoded in the DNA is reflected by specific binding (aptamers) or catalytic properties (DNAzymes). Recent advances in tailoring supramolecular DNA structures for DNA-based machinery and for amplified biosensing are reviewed. Different DNA machines that perform 'tweezer', 'walker' or 'metronome' functions are discussed, and the control of macroscopic surface properties or the motility of micro-objects by molecular DNA devices is introduced. Furthermore, the design of DNA machines for the ultrasensitive detection of DNA, low-molecular-weight substrates, and macromolecules is discussed. Supramolecular aptamer and DNAzyme structures are used as molecular tools for amplified sensing.

DNA-molecular-motor-controlled dendron association

In this letter, we described a new strategy to study the macromolecule interactions rationally controlled by the movements of a DNA molecular motor. Two amphiphilic dendrons are covalently attached to the 3' and 5' ends of a pH-driven DNA motor, a 21-mer single-stranded DNA containing four stretches of cytosine-rich sequences. The resulting DNA-dendron conjugates were purified by polyacrylamide gel electrophoresis (PAGE), and their molecular weights were confirmed by MALDI-TOF. The reversible association-dissociation of the two DNA-attached dendrons controlled by the opening and closing of the DNA motor following pH changes was verified by circular dichroism spectroscopy and DNA stability studies in aqueous solutions. The results suggest that the DNA molecular motor may serve as a new platform for studying nonspecific and specific macromolecular interactions on the molecular level.

An electrochemically actuated reversible DNA switch

In this Letter, we have realized the electrical actuation of a DNA molecular device in a rapid and reliable manner with a microfabricated chip. The three-electrode chip containing Ir, IrO(2), and Ag electrodes deposited in designed shapes and positions on the SiO(2) surface was made by photolithography and magnetron reaction sputter deposition technology. In this design, the negative feedback property enabled the system to rapidly change and maintain the solution pH at arbitrary value by water electrolysis. As a proof-of-concept, we can drive a DNA switch based on the opening and close of an i-motif structure by switching the potential between the working and reference electrodes between -304 and -149 mV. We have demonstrated that DNA can be electrically switched within seconds, without obvious decay of the fluorescence amplitudes for at least 30 cycles, suggesting that this DNA switch is rapid in response and fairly robust. We have also demonstrated that this device could manipulate the DNA switch automatically by using chronoamperometry.