Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds

Expanding DNA Origami Design Freedom with De Novo Synthesized Scaffolds

The construction of DNA origami nanostructures is heavily dependent on the folding of the scaffold strand, which is typically a single-stranded DNA genome extracted from a bacteriophage (M13). Custom scaffolds can be prepared in a number of methods, but they are not widely accessible to a broad user base in the DNA nanotechnology community. Here, we explored new design and construction possibilities with custom scaffolds prepared in our cost- and time-efficient production pipeline. According to the pipeline, we de novo produced a variety of scaffolds of specified local and global sequence characteristics and consequent origami constructs of modular arrangement in morphologies and functionalities. Taking advantage of this strategy of template-free scaffold production, we also designed and produced three-letter-coded scaffolds that can fold into designated morphologies rapidly at room temperature. The expanded design and construction freedom immediately brings in many new research opportunities and invites many more on the horizon.

Enzymatic Assembly of Small Synthetic Genes with Repetitive Elements

Gene synthesis efficiency has greatly improved in recent years but is limited when it comes to repetitive sequences, which results in synthesis failure or delays by DNA synthesis vendors. This represents a major obstacle for the development of synthetic biology since repetitive elements are increasingly being used in the design of genetic circuits and design of biomolecular nanostructures. Here, we describe a method for the assembly of small synthetic genes with repetitive elements: First, a gene of interest is split in silico into small synthons of up to 80 base pairs flanked by Golden-Gate-compatible overhangs. Then, synthons are made by oligo extension and finally assembled into a synthetic gene by Golden Gate Assembly. We demonstrate the method by constructing eight challenging genes with repetitive elements, e.g., multiple repeats of RNA aptamers and RNA origami scaffolds with multiple identical aptamers. The genes range in size from 133 to 456 base pairs and are assembled with fidelities of up to 87.5%. The method was developed to facilitate our own specific research but may be of general use for constructing challenging and repetitive genes and, thus, a valuable addition to the molecular cloning toolbox.

Minimalist Design of Wireframe DNA Nanotubes: Tunable Geometry, Size, Chirality, and Dynamics

DNA nanotubes (NTs) have attracted extensive interest as artificial cytoskeletons for biomedical, synthetic biology, and materials applications. Here, we report the modular design and assembly of a minimalist yet robust DNA wireframe nanotube with tunable cross-sectional geometry, cavity size, chirality, and length, while using only four DNA strands. We introduce an h-motif structure incorporating double-crossover (DX) tile-like DNA edges to achieve structural rigidity and provide efficient self-assembly of h-motif-based DNA nanotube (H-NT) units, thus producing programmable, micrometer-long nanotubes. We demonstrate control of the H-NT nanotube length via short DNA modulators. Finally, we use an enzyme, RNase H, to take these structures out of equilibrium and trigger nanotube assembly at a physiologically relevant temperature, underlining future cellular applications. The minimalist H-NTs can assemble at near-physiological salt conditions and will serve as an easily synthesized, DNA-economical modular template for biosensors, plasmonics, or other functional materials and as cost-efficient drug-delivery vehicles for biomedical applications.

Controllable mitochondrial aggregation and fusion by a programmable DNA binder

DNA nanodevices have been feasibly applied for various chemo-biological applications, but their functions as precise regulators of intracellular organelles are still limited. Here, we report a synthetic DNA binder that can artificially induce mitochondrial aggregation and fusion in living cells. The rationally designed DNA binder consists of a long DNA chain, which is grafted with multiple mitochondria-targeting modules. Our results indicated that the DNA binder-induced in situ self-assembly of mitochondria can be used to successfully repair ROS-stressed neuron cells. Meanwhile, this DNA binder design is highly programmable. Customized molecular switches can be easily implanted to further achieve stimuli-triggered mitochondrial aggregation and fusion inside living cells. We believe this new type of DNA regulator system will become a powerful chemo-biological tool for subcellular manipulation and precision therapy.

Programming rigidity into size-defined wireframe DNA nanotubes

Nanotubes built from DNA hold promise for several biological and materials applications, due to their high aspect ratio and encapsulation potential. A particularly appealing goal is to control the size, shape, and dynamic behaviour of DNA nanotubes with minimal design alteration, as nanostructures of varying morphologies and lengths have been shown to exhibit distinct cellular uptake, encapsulation behaviour, and in vivo biodistribution. Herein, we report a systematic investigation, combining experimental and computational design, to modulate the length, flexibility, and longitudinal patterns of wireframe DNA nanotubes. Subtle design changes govern the structure and properties of our nanotubes, which are built from a custom-made, long, and size-defined template strand to which DNA rungs and linkers are attached. Unlike DNA origami, these custom-made strands possess regions with repeating sequences at strategic locations, thereby reducing the number of strands necessary for assembly. Through strand displacement, the nanotubes can be reversibly altered between extended and collapsed morphologies. These design concepts enable fine-tuning of the nanotube stiffness and may pave the way for the development of designer nanotubes for a variety of applications, including the study of cellular internalization, biodistribution, and uptake mechanisms for structures of varied shapes and sizes.

Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: concatemers and self-limited complexes

The development of approaches to the design of two- and three-dimensional self-assembled DNA-based nanostructures with a controlled shape and size is an essential task for applied nanotechnology, therapy, biosensing, and bioimaging.

Asymmetric patterning drives the folding of a tripodal DNA nanotweezer

DNA tweezers have emerged as powerful devices for a wide range of biochemical and sensing applications; however, most DNA tweezers consist of single units activated by DNA recognition, limiting their range of motion and ability to respond to complex stimuli. Herein, we present an extended, tripodal DNA nanotweezer with a small molecule junction. Simultaneous, asymmetric elongation of our molecular core is achieved using polymerase chain reaction (PCR) to produce length- and sequence-specific DNA arms with repeating DNA regions. When rigidified, our DNA tweezer can be addressed with streptavidin-binding ligands. Full control over the number, separation, and location of these ligands enables site-specific streptavidin recognition; all three arms of the DNA nanotweezer wrap around multiple streptavidin units simultaneously. Our approach combines the simplicity of DNA tile arrays with the size regime normally provided by DNA origami, offering an integrated platform for the use of branched DNA scaffolds as structural building blocks, protein sensors, and dynamic, stimuli-responsive materials.

A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail

DNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to its high programmability based on canonical Watson-Crick base pairing, with crystal assembly in all three dimensions facilitated by immobile Holliday junctions and sticky end cohesion. Despite the promise of these systems, only a handful of unique crystal scaffolds have been reported. Herein, we describe a new crystal system with a repeating sequence that mediates the assembly of a 3D scaffold via a series of Holliday junctions linked together with complementary sticky ends. By using an optimized junction sequence, we could determine a high-resolution (2.7 Å) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 Å) using a modified sticky-end sequence. The immobile Holliday junction sequence allowed us to produce crystals that provided unprecedented atomic detail. In addition, we expanded the crystal cavities by 50 % by adding an additional helical turn between junctions, and we solved the structure to 4.5 Å resolution by molecular replacement.

A Simple Blocking PCR-Based Method for the Synthesis of High-Copy dsDNA Tandem Repeats

DNA tandem repeats are frequently found in eukaryotic genomes. High-copy DNA repeats can serve as building blocks of complex DNA structures, but the in vitro synthesis of DNA repeats has been challenging due to complicated procedures and the high cost. Here, a new, simple method is developed using the strategy of blocking polymerase chain reaction for highly efficient DNA repeat expansion (BPRE). With BPRE, dsDNA fragments composed of more than 40 copies of the repeat sequence can be quickly produced, while the cost is reduced by at least 90%. As a typical application, reannealing of the dsDNA repeats generates elastic hydrogels, which shows a high capacity for doxycycline absorption and prolonged release.

ATP-Responsive and ATP-Fueled Self-Assembling Systems and Materials

Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-to-cell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATP-triggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to non-equilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring synthetic ATP-dependent systems closer to living systems.

Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies

DNA origami nanocarriers have emerged as a promising tool for many biomedical applications, such as biosensing, targeted drug delivery, and cancer immunotherapy. These highly programmable nanoarchitectures are assembled into any shape or size with nanoscale precision by folding a single-stranded DNA scaffold with short complementary oligonucleotides. The standard scaffold strand used to fold DNA origami nanocarriers is usually the M13mp18 bacteriophage’s circular single-stranded DNA genome with limited design flexibility in terms of the sequence and size of the final objects. However, with the recent progress in automated DNA origami design—allowing for increasing structural complexity—and the growing number of applications, the need for scalable methods to produce custom scaffolds has become crucial to overcome the limitations of traditional methods for scaffold production. Improved scaffold synthesis strategies will help to broaden the use of DNA origami for more biomedical applications. To this end, several techniques have been developed in recent years for the scalable synthesis of single stranded DNA scaffolds with custom lengths and sequences. This review focuses on these methods and the progress that has been made to address the challenges confronting custom scaffold production for large-scale DNA origami assembly.

Three-Dimensional Patterning of Nanoparticles by Molecular Stamping

Directing the formation of nanoscale architectures from nanoparticles is one of the key challenges in designing nanomaterials with prescribed functions. Atomic systems, given their ability to form molecules and crystals via directional chemical bonds, provide an inspiration for establishing approaches where nanoparticles with designed anisotropic binding modalities can be assembled into nanoscale architectures. However, fabricating such nanoparticles has been challenging due to their small dimensions and limited ways for site-specific control of their surface. To this end, we present a molecular stamping (MOST) approach to pattern DNA-coated nanoparticles with molecules at the predefined positions on a nanoparticle surface. This patterning is realized by use of a rigid and coordinative DNA frame as a molecular stamping apparatus (MOST App). The MOST App transfers multiple types of molecular "inks", DNA sequences, onto a nanoparticle surface and fixes these molecular inks into place to form a designed pattern. After a nanoparticle is released the from MOST App, it possesses single-molecule patches that can provide anisotropic bonds with distinctive affinities. We further use these stamped nanoparticles to assemble prescribed clusters, whose structure is determined by the locations of patches. Using electron microscopy and tomographic methods, we investigate the efficiency of cluster formation and the resulting spatial arrangements of nanoparticles. The presented approach provides a single-molecule and spatially determined control over nanoparticle functionalization for creating nanoparticles with designed placement of different molecules and for realizing a rational fabrication of nanomaterial architectures.

Controlling the DNA Hybridization Chain Reaction

A novel method for controlling the oligomerization of metastable DNA hairpins using the hybridization chain reaction (HCR) is reported. Control was achieved through the introduction of a base-pair mismatch in the duplex of the hairpins. The mismatch modification allows one to kinetically differentiate initiation versus propagation events, leading to DNA oligomers up to 10 monomers long and improving dispersities from 2.5 to 1.3-1.6. Importantly, even after two consecutive chain extensions, dispersity remained unaffected, showing that well-defined block co-oligomers can be achieved. As a proof-of-concept, this technique was then applied to hairpin monomers functionalized with a mutant green fluorescent protein to prepare protein oligomers. Taken together, this work introduces an effective method for controlling living macromolecular HCR oligomerization in a manner analogous to the controlled polymerization of small molecules.

Sequence-Defined Macrocycles for Understanding and Controlling the Build-up of Hierarchical Order in Self-Assembled 2D Arrays

Anfinsen's dogma that sequence dictates structure is fundamental to understanding the activity and assembly of proteins. This idea has been applied to all manner of oligomers but not to the behavior of cyclic oligomers, aka macrocycles. We do this here by providing the first proofs that sequence controls the hierarchical assembly of nonbiological macrocycles, in this case, at graphite surfaces. To design macrocycles with one (AAA), two (AAB), or three (ABC) different carbazole units, we needed to subvert the synthetic preferences for one-pot macrocyclizations. We developed a new stepwise synthesis with sequence-defined targets made in 11, 17, and 22 steps with 25, 10, and 5% yields, respectively. The linear build up of primary sequence (1°) also enabled a thermal Huisgen cycloaddition to proceed regioselectively for the first time using geometric control. The resulting macrocycles are planar (2° structure) and form H-bonded dimers (3°) at surfaces. Primary sequences encoded into the suite of tricarb macrocycles were shown by scanning-tunneling microscopy (STM) to impact the next levels of supramolecular ordering (4°) and 2D crystalline polymorphs (5°) at solution-graphite interfaces. STM imaging of an AAB macrocycle revealed the formation of a new gap phase that was inaccessible using only C3-symmetric macrocycles. STM imaging of two additional sequence-controlled macrocycles (AAD, ABE) allowed us to identify the factors driving the formation of this new polymorph. This demonstration of how sequence controls the hierarchical patterning of macrocycles raises the importance of stepwise syntheses relative to one-pot macrocyclizations to offer new approaches for greater understanding and control of hierarchical assembly.

A minimalist's approach for DNA nanoconstructions

Structural DNA nanotechnology takes DNA, a biopolymer, far beyond being the molecule that stores and transmits genetic information in biological systems. DNA has been employed as building blocks for the assembly of designed, nanoscaled, supramolecular DNA architectures for applications in biophysics, structure determination, synthetic biology, diagnostics, and drug delivery. Herein, we review a symmetric approach of tile-based DNA self-assembly. This approach allows the construction of DNA nanostructures from minimal numbers of different types of DNA strands based on sequence and structural symmetries. Some examples of the applications of this approach in siRNA delivery are discussed as well.

Chemistries for DNA Nanotechnology

The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.

Single-stranded templates as railroad tracks for hierarchical assembly of DNA origami

DNA origami is one of the most effective tools for bottom-up construction of novel objects and devices at the nanometer-scale. However, many applications require larger structures than can be obtained with the conventional single-stranded scaffold, typically 7249 nucleotides. Here, we address this limitation by developing custom-made single-stranded scaffolds that bind pre-assembled origami tiles and induce their one-dimensional organization in high yields. Our synthetic method allows the conversion of multiple repetitive and unique sequences into correctly assembled, large backbones, and to finely tune the position and frequency of each building block. Granted with these regions, three and five origami tiles were successfully arranged in 1-D with the aid of one or two scaffolds, forming a nano-"railroad track". This new method increases length scale in DNA origami without increasing cost and complexity, and is anticipated to increase the yield of other approaches aiming to assemble large origami structures.

Recent advances in DNA nanotechnology

DNA is a powerful guiding molecule to achieve the precise construction of arbitrary structures and high-resolution organization of functional materials. The combination of sequence programmability, rigidity and highly specific molecular recognition in this molecule has resulted in a wide range of exquisitely designed DNA frameworks. To date, the impressive potential of DNA nanomaterials has been demonstrated from fundamental research to technological advancements in materials science and biomedicine. This review presents a summary of some of the most recent developments in structural DNA nanotechnology regarding new assembly approaches and efforts in translating DNA nanomaterials into practical use. Recent work on incorporating blunt-end stacking and hydrophobic interactions as orthogonal instruction rules in DNA assembly, and several emerging applications of DNA nanomaterials will also be highlighted.

Fluorescence Resonance Energy Transfer-Based DNA Nanoprism with a Split Aptamer for Adenosine Triphosphate Sensing in Living Cells

We have developed a DNA nanoprobe for adenosine triphosphate (ATP) sensing in living cells, based on the split aptamer and the DNA triangular prism (TP). In which nucleic acid aptamer was split into two fragments, the stem of the split aptamer was respectively labeled donor and acceptor fluorophores that underwent a fluorescence resonance energy transfer if two ATP molecules were bound as target molecule to the recognition module. Hence, ATP as a target induced the self-assembly of split aptamer fragments and thereby brought the dual fluorophores into close proximity for high fluorescence resonance energy transfer (FRET) efficiency. In the in vitro assay, an almost 5-fold increase in F_A/F_D signal was observed, the fluorescence emission ratio was found to be linear with the concentration of ATP in the range of 0.03-2 mM, and the nanoprobe was highly selective toward ATP. For the strong protecting capability to nucleic acids from enzymatic cleavage and the excellent biocompatibility of the TP, the DNA TP nanoprobe exhibited high cellular permeability, fast response, and successfully realized "FRET-off" to "FRET-on" sensing of ATP in living cells. Moreover, the intracellular imaging experiments indicated that the DNA TP nanoprobe could effectively detect ATP and distinguish among changes of ATP levels in living cells. More importantly, using of the split aptamer and the FRET-off to FRET-on sensing mechanism could efficiently avoid false-positive signals. This design provided a strategy to develop biosensors based on the DNA nanostructures for intracellular molecules analysis.

Minimalist Approach to Complexity: Templating the Assembly of DNA Tile Structures with Sequentially Grown Input Strands

Given its highly predictable self-assembly properties, DNA has proven to be an excellent template toward the design of functional materials. Prominent examples include the remarkable complexity provided by DNA origami and single-stranded tile (SST) assemblies, which require hundreds of unique component strands. However, in many cases, the majority of the DNA assembly is purely structural, and only a small "working area" needs to be aperiodic. On the other hand, extended lattices formed by DNA tile motifs require only a few strands; but they suffer from lack of size control and limited periodic patterning. To overcome these limitations, we adopt a templation strategy, where an input strand of DNA dictates the size and patterning of resultant DNA tile structures. To prepare these templating input strands, a sequential growth technique developed in our lab is used, whereby extended DNA strands of defined sequence and length may be generated simply by controlling their order of addition. With these, we demonstrate the periodic patterning of size-controlled double-crossover (DX) and triple-crossover (TX) tile structures, as well as intentionally designed aperiodicity of a DX tile structure. As such, we are able to prepare size-controlled DNA structures featuring aperiodicity only where necessary with exceptional economy and efficiency.

Self-organized architectures from assorted DNA-framed nanoparticles

The science of self-assembly has undergone a radical shift from asking questions about why individual components self-organize into ordered structures, to manipulating the resultant order. However, the quest for far-reaching nanomanufacturing requires addressing an even more challenging question: how to form nanoparticle (NP) structures with designed architectures without explicitly prescribing particle positions. Here we report an assembly concept in which building instructions are embedded into NPs via DNA frames. The integration of NPs and DNA origami frames enables the fabrication of NPs with designed anisotropic and selective interactions. Using a pre-defined set of different DNA-framed NPs, we show it is possible to design diverse planar architectures, which include periodic structures and shaped meso-objects that spontaneously emerge on mixing of the different topological types of NP. Even objects of non-trivial shapes, such as a nanoscale model of Leonardo da Vinci's Vitruvian Man, can be self-assembled successfully.

Dynamic DNA Nanotubes: Reversible Switching between Single and Double-Stranded Forms, and Effect of Base Deletions

DNA nanotubes hold great potential as drug delivery vehicles and as programmable templates for the organization of materials and biomolecules. Existing methods for their construction produce assemblies that are entirely double-stranded and rigid, and thus have limited intrinsic dynamic character, or they rely on chemically modified and ligated DNA structures. Here, we report a simple and efficient synthesis of DNA nanotubes from 11 short unmodified strands, and the study of their dynamic behavior by atomic force microscopy and in situ single molecule fluorescence microscopy. This method allows the programmable introduction of DNA structural changes within the repeat units of the tubes. We generate and study fully double-stranded nanotubes, and convert them to nanotubes with one, two and three single-stranded sides, using strand displacement strategies. The nanotubes can be reversibly switched between these forms without compromising their stability and micron-scale lengths. We then site-specifically introduce DNA strands that shorten two sides of the nanotubes, while keeping the length of the third side. The nanotubes undergo bending with increased length mismatch between their sides, until the distortion is significant enough to shorten them, as measured by AFM and single-molecule fluorescence photobleaching experiments. The method presented here produces dynamic and robust nanotubes that can potentially behave as actuators, and allows their site-specific addressability while using a minimal number of component strands.

Enzyme-Operated DNA-Based Nanodevices

Functional molecular nanodevices and nanomachines have attracted a growing interest for their potential use in life science and nanomedicine. In particular, due to their versatility and modularity DNA-based nanodevices appear extremely promising. However, a limitation of such devices is represented by the limited number of molecular stimuli and cues that can be used to control and regulate their function. Here we demonstrate the possibility to rationally control and regulate DNA-based nanodevices using biocatalytic reactions catalyzed by different enzymes. To demonstrate the versatility of our approach, we have employed three model DNA-based systems and three different enzymes (belonging to several classes, i.e., transferases and hydrolases). The possibility to use enzymes and enzymatic substrates as possible cues to operate DNA-based molecular nanodevices will expand the available toolbox of molecular stimuli to be used in the field of DNA nanotechnology and could open the door to many applications including enzyme-induced drug delivery and enzyme-triggered nanostructures assembly.

Isothermal Amplification of Nucleic Acids

Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.