Nanodevices and Molecular Motors Using Meta-DNA Structures and DNA Origami

Meta-DNA Structures

In a recent study, a new type of meta-DNA structure has been created that can open up new horizons in opteoelectronics including information storage, encryption as well as synthetic biology; accordingly, the meta-DNA self-assembly is capable of a complete transformation of the microscopic structure of DNA nanotechnology. It has been widely spoken in the scientific community that DNA can be employed as a versatile building block to design sophisticated nanoscopic structures and devices based on the predictable nature of Watson-Crick base pairing as well as the fundamental features of DNA. Some years ago, there was a groundbreaking finding concerning DNA nanotechnology called DNA origami was introduced in which a single-stranded long DNA confirmations can be folded into a number of designated morphologies in incorporation with hundreds of short DNA staple strands. Nevertheless, this patent remained challenging to put short and single-stranded DNA architectures together in the micron and millimeter-scale as an obstacle in the way to DNA origami. But now, DNA strands in the micron scale and as wide as human hair, nearly 1000 times larger than the nanostructured original DNA.1

Meta-DNA Applications and Functions

Particularly, metal DNA strategy makes it possible for various sub micrometer up to the micrometer size DNA strands to engage in a self-assembly similar to the self-assembly of short DNA strands done in the nanoscale. Furthermore, the nanostructured DNA origami with 6-helix bundles in the sub micrometer scale denoted as meta-DNA can potentially be employed as the magnified analog of a DNA structure with a single strand. A couple of meta-DNAs with complimentary meta-base pairs can form double helices based on helical features and programmed handedness. Taking the advantage of meta-DNA building blocks, it is possible to construct DNA structures in the micrometer and micrometer scales comprising junctions with metal and multi arms, various 2D / 3D lattices and 3D polyhedrons. It has also been demonstrated that a reaction with hierarchical strand displacement nature is carried out on meta-DNA capable of transferring the dynamic features of DNA to the meta-DNA. The calculations and predictions are carried out by a coarse-gained computational model of the DNA to stimulate and predict the double-stranded DNA structure and with determined distinct helices of right-handed and left-handed structures.1

More specifically, it is possible to design a class of micron-scale or sub micrometer-scale structures of DNA with distinct 1, 2 and 3 dimensions with a broad range of geometric morphologies including six types of closely packed lattices, octahedron, double-cross over tiles, meta junctions, prisms and headphones. Based on this technique, it will be possible to rationally design even more complicated circuits, nanodevices and molecular motors using meta-DNA structures with broad range of applications in the areas of biosensing and molecular computation. Moreover, the creation of dynamic micron-scale DNA structures, that are basically reconfigurable after simulation, can significantly be more feasible now. It is also anticipated that the emergence of this method of DNA strategy can transform DNA nanotechnology from the nanoscale to the microscopic scale with a consequence of creating a range of complex dynamic and static structures, the micron and sub-micrometer scales and enable novel application. As an example, these meta-DNA structures can be employed as a scaffold to pattern complex functional components basically more complex and greater compared to previously designed structures. Based on this new finding, it is expected to observe more complex and sophisticated behaviors similar to what is processed in cells or in cellular components in combination with distinct meta-DNA-based hierarchical strand displacement reactions.1

DNA origami

DNA origami has shown to be a perfectly programmable technique to design customized devices and objects in the nanoscale. However, it is possible to enable many potential applications including surface-based biophysical essays and metamaterial construction by scaling up the size of DNA origami. Meta-DNA building blocks are capable of forming various complex structures on the micrometer scale through mimicking the molecular properties and behaviors of strands of DNA and assembly strategies. The construction of a series of DNA structures on micrometer and sub-micrometer scales comes true using meta-DNA building blocks.

At the moment, there are three reports and strategies concerning the micrometer-sized DNA structures designing. According to the first method, the scaffolds or staples are enlarged to be employed as the preliminary starting materials to fabricate the DNA origami. Basically, larger-scale scaffolds are possible to be designed by polymerase chain reaction or large genome extraction from a bacteriophage. Tiles or DNA origami is capable of functioning even as larger is staples to fold to create M13, which is the most common scaffold, into bigger structures. The second method for scaling up DNA origami nanostructures is to utilize blunt-end stacking or sticky-end cohesion to build individual origami structures together. In order to build two-dimensional arrays and 3-dimensional polyhedral structures, hexagonal tiles, v-shaped bricks, two-layered crosses, DNA origami tripods and planner squares are used. Technically, every micrometer-scale DNA structure demands 1 to several unique DNA origami structures with different sizes and morphologies as well as prescribed matching rules. The construction of DNA devices at the micrometer scale will come true by creating a versatile sub micrometer 3D building blocks.1

Mechanism and Structure

To begin with, the 6-helix DNA origami bundle containing several unpaired DNA probes similar to base pairs is created to serve as the meta-DNA unit. This simulated structure is similar to the classic short single-stranded DNA oligonucleotides from three points of view. The first similarity is, the metal DNA can bind to some specific nucleobases with their complementary method DNA. The nucleobases of the metal-DNA are composed of a set of 10-nucleotide long single-stranded DNA overhangs created to broaden specifically from some pre-selected positions on the metal DNA to act selectively. The meta-DNA bases can later be programmed with as many as 410 different sequences allowing the structure to have adequate orthogonal instructions between the complementary metal base pairs. Second, similar to classic short single-stranded DNA oligonucleotides, meta-DNA is somehow rigid with the persistent length of 2 micrometers therefore, it is possible to tune local flexibility by removing some of the staple strands from some selected positions. The flexibility and the rigidity makes meta-DNA possess various geometric morphologies. Third, meta-DNA is basically an object with three dimensions and a three-dimensional arrangement of meta bases available for hybridization with the subsequent assembly of them into 1, 2 and 3D structures.

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