Scientists have long been eager to use self-assembly to construct artificial objects to achieve the size and complexity of cells or organelles to build synthetic cell machines for research, engineering, and medical applications.
iNature: The self-assembly process exists in nature in a variety of forms, from molecular folding at the molecular level and formation of lipid bilayers to the entire biological system that builds the Earth. Scientists have long been eager to use self-assembly to construct artificial objects to achieve the size and complexity of cells or organelles to build synthetic cell machines for research, engineering, and medical applications. On this issue, Nature's four papers address this goal by reporting ways to expand DNA self-assembly and design nanostructure size and production.
Biopolymers such as DNA, RNA and proteins are used as building blocks for nanoscale structures to regulate the function of organisms. DNA is the most useful nanoscale building block because it has several advantages - especially its programmability - derived from predictable and stable pairing structures formed between the bases of complementary DNA strands. In addition, the DNA structure is stable, the geometry of the double helix is ​​well studied, and it is compatible with other biomolecules, which allows the construction of complex "heterogeneous biomaterials". Various DNA self-assembly methods have been developed for constructing synthetic structures that exhibit large geometric complexity and nanoscale precision.
Fractal assembly of micrometre-scale DNA
One of the milestones in DNA nanotechnology is the invention of DNA nanopore materials. In this technique, long single-stranded DNA is folded into a target shape with the help of hundreds of short DNA strands called "staples". Short chains are designed to complement specific regions of long DNA to guide the folding process. Various 2D and 3D nano-objects have been fabricated using this technique. Many of them are fully positionable; that is, they can be modified at selected locations to meet future application needs. However, the size of individual DNA origami nanostructures is limited by the length of the scaffold DNA they construct. For example, a widely used scaffold is genomic DNA of approximately 7,200 nucleotides in length that can be folded into an origami structure having a diameter of no more than 100 nanometers.
Another important design strategy for DNA nanotechnology is single-stranded tile (SST) assembly, in which SSTs - nanoscale two-dimensional rectangles or three-dimensional bricks formed from single-stranded DNA are interlocked with each other at their interfaces by forming DNA duplexes. The collection of SSTs is used to form 2D drawings or 3D tiles, which can be selectively "engraved" to create different patterns and shapes by simply including or omitting a particular SST. However, the size of the DNA structure produced by this method is usually comparable to the size of origami nanostructures; larger structures are already prepared, but the synthesis efficiency is low. The papers reported on this issue are based on SST and origami strategies to create micron-sized structures and expand the number of products that can be produced.
Gigadalton-scale shape-programmable
Tikhomirov et al. used a square DNA origami composed of a surface pattern (formed by a DNA strand extending from an origami surface) as a building unit to create a two-dimensional DNA origami array having a diameter of about half a micrometer (Fig. 1a). Square origami are joined together by forming short DNA duplexes at their interface. In order to program the interaction between square origami, the authors developed a fractal method in which local assembly rules are used recursively to assemble a multi-step process of increasing number of square origami arrays. Tikhomirov and colleagues also created a design software called FracTile Compiler, which will be able to design DNA sequences and experimental programs to make large DNA patterns. The authors used this to create several DNA "pictures", including Mona Lisa, a cock and a chess game mode to validate this automated design process.
Fig. 1 Method of manufacturing micron-sized DNA objects
Wagenbauer et al. used another layered self-assembly method (Fig. 1b) to make a 3D DNA origami structure up to the micron size. They use a V-shaped DNA origami object as the basic component, where the angle of V can be changed. High-order components can be constructed by controlling the geometric relationships and interactions between the components. The authors demonstrated the ability of the method by constructing a stack of planar rings up to 350 nm in diameter and three polyhedrons up to 450 nm in diameter to construct microscale long tubes (similar to the size of some bacteria).
Ong et al. reported a method for 3D SST DNA construction on the micron scale (Fig. 1c). By extending the principles of the first-generation SST system, the authors designed a brick-like DNA building block consisting of 52 nucleotides containing four 13-nucleotide binding domains. These areas enable bricks to be assembled into larger structures. The longer binding domains of DNA bricks provide better yield and stability for larger assembled structures than first generation bricks (containing four binding domains, each consisting of eight nucleotides). The author developed a software called Nanobricks to design the brickchain needed to make a target 3D object and use it to plan a synthesis of a different set of complex architectures.
Programmable self-assembly of three-dimensional nanostructures
The biotechnology reported by Praetorius et al. will greatly reduce the cost of the hundreds of backbones typically used to make DNA origami. They use a virus called a phage to generate single-stranded precursor DNA containing hundreds of short-chain sequences. These sequences are separated by the "DNAzyme" sequence that cleaves itself; the cleavage products then self-assemble into the designated DNA origami shape. It is worth noting that the author's method reduces the cost of folded DNA origami structures from about $200 per milligram to about 20 cents. This strategy will enable scalable and efficient mass production of DNA origami and SST structures for large-scale applications such as treatment, drug delivery systems and nanoelectronics.
Biotechnological mass production
These papers also provide solutions to the long-term challenges of biomolecular engineering, providing a low-cost method for manufacturing self-assembled structures from smaller building blocks that can be sized to use complementary "top-down" techniques (those in bulk) Material engraving structure). Furthermore, the reported DNA structure is large enough to enable the production of devices for therapeutic applications with cells, or to manufacture complex molecular machines and assembly lines for the manufacture of synthetic polymers or programmed cell-cell interactions. Such self-assembled structures can even be used in systems that synthesize organelles to monitor and regulate biological processes in living cells.
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