Here we propose an experimentally feasible model for programmed cycles of molecular interactions that is able to continuously change molecular arrangements. Such passive roles of the motifs, and the assembled structures, seem counterintuitive to the dynamic process of computation where programmed molecular interactions could produce continuous structural changes and re-use of the building motifs. The cooperation between the motifs is guided by sticky ends, and once a molecule appears within a larger structure, it has no further computational interaction with its immediate environment. In many programmed structural self-assembly experiments thus far, as well as in the theoretical Tile Assembly Model, it is assumed that the DNA motifs are predesigned and they follow the programmed design to assemble structures, rarely reacting to environmental input.
Three later walking devices showed a significant robustness such that the directions and the actions of the walker were guided by a sequence of strand displacements incorporated within the walking platform. The same mechanisms were used for structures that can perform simple ‘walking’ on an arranged platform. Such devices were incorporated in two-dimensional DNA arrays as well as in the programmable DNA transducer where simultaneous programmed molecular movements were achieved. įurther, ‘DNA fuel’ strands were used to produce devices that were sequence-dependent. Several new designs for strand displacement computational networks attached on a two-dimensional origami platform have been theoretically proposed. became a base for development of DNA strand displacement networks that have been shown to be able to perform digital and analogue computation. On the other side, ‘DNA fuel’ strands introduced by Yurke et al. Further, transducer simulations with programmed inputs by TX DNA molecules have also been reported.
Several successful experiments have confirmed computation by array-like DNA self-assembly such as binary addition (simulation of XOR) using TX molecules (tiles), Sierpinski triangle assembly, and a binary counter by DX molecules. Winfree introduced the Tile Assembly Model and showed that two-dimensional self-assembled arrays made of DX or TX DNA tiles can simulate the dynamics of a bounded one-dimensional cellular automaton and so are capable of potentially performing computations as a Universal Turing machine. The informational character of DNA makes it a perfect molecule for information processing at the nano level. Further, DNA origami, as templates for large DNA-based tiles, were arranged in a two-dimensional crystalline array. Since its appearance, DNA origami has been used as a seed for arranging DX tiles in an array, nanotube constructions, three-dimensional boxes (with cargos). The construction of approximately 100×100 nm two-dimensional DNA nanostructures was significantly facilitated by Rothemund's DNA origami, where a standard single-stranded vector plasmid is used to outline a shape while short DNA strands connect portions of the plasmid fixing its shape in a rigid form. Techniques have been further developed for a variety of polyhedra, and the first macroscopic self-assembled three-dimensional DNA crystals have been reported. In addition to the two-dimensional arrays, three-dimensional structures such as a cube, a truncated octahedron, tetrahedron and arbitrary graphs have been constructed from DNA duplex and junction molecules. Complex DNA motifs that entail the lateral fusion of DNA double helices, such as DNA double (DX), triple (TX), paranemic cross-over molecules have been used as tiles and building blocks for large nanoscale arrays. DNA-based bottom-up assembly, introduced roughly 35 years ago, has been explored by at least 100 laboratories in recent years. These models are inspired by biological molecular processes and chemical self-assembly and have been shown to advance the nanotechnology needed for new material designs and our understanding of biomolecular processes. In the past two decades, new computing paradigms inspired by natural processes such as biomolecular computing have been developed. As a discipline, computer science, or informatics, aims to advance our lives through new information and computation methodologies, as well as to explain natural processes through our understanding of how information propagates and is being computed in nature.