Molecular self-assembly manipulating DNA

Nanotechnology Self-assembly and self-organization of nanostructures is an important area which often bridges the divide between organic and inorganic systems. Many self-assembly processes rely on the self-assembling nature of organic molecules, including complex species such as DNA; these methods are termed chemical or molecular self-assembly.
There has been significant and novel successes achieved in the fields of nanotechnology, particularly in the formation of nanostructures using guided molecular self-assembly methods.

The technique of self-assembly is one of the few practical strategies available to arrive at ensembles of nanostructures based on ‘bottom-up’ approach of nanotechnology. The self-assembly process, defined as the autonomous organization of components into structurally well defined aggregates, is characterized by numerous beneficial attributes; it is cost-effective, versatile, facile and the process occurs towards the system’s thermodynamic minima, resulting in stable and robust structures.
As the name suggests, it is a process in which the organization or the assembly into desired structures occurs through nature intended phenomena, either through physical or chemical processes or assisted by biomolecules to promote molecular selectivity and specificity. It is also a process in which defects are rejected energetically, and therefore the degree of perfection is relatively high.
There are numerous different mechanisms by which self-assembly of molecules and nanoclusters can be accomplished such as electrostatic and surface forces, chemical interactions, hydrophobic and hydrophilic interactions, and biomolecule-mediated self assembly techniques.

The fundamental insight that spawned DNA computing by self-assembly was made by Winfree when he noted that DNA annealing by itself was theoretically capable of performing universal computation. He went further and recognized that certain stable DNA structures being developed by Seeman for nanoengineering and crystallography could serve as physical incarnations of a mathematical model known as Wang tiles, which has already been shown to be capable of Turing universal computation.

In Wang tiling, unit tiles are labeled with symbols on each edge such that tiles are allowed to associate only if their edge symbols match. Tile sets have been designed that successfully simulate computing devices known as Turing machines and are therefore capable of universal computation.
The recognition that DNA tiles, exemplified by DX and TX complexes, could represent Wang tiles in a physical system, where edge symbols are encoded in the base sequence of sticky ends, led to proofs that DNA tilings are capable of universal computation. Computation of self-assembly of DNA tiles is a significant advance over biochemical manipulation computing schemes because self-assembly involves a single-step procedure in which the computation occurs during the annealing of carefully designed oligonucleotides.

Nanoarchitectonics, a new interdisciplinary field within the nanosciences, investigates the principles responsible for the formation of higher-ordered functional structures starting from their nanoscopic building blocks like atoms and molecules.
Nature has always worked bottom-up, where the principles of self-assembly lead to crystal growth in the inorganic world, and, via molecular self-assembly, to functional structures in biology.
For instance, the three-dimensional architecture of a nanomachine called the ribosome comprises the natural molecular assembler, which organizes the transition from the DNA informational blueprint into polypeptides and other functional units.
To understand and make technological use of the underlying mechanism of this process is one of the major goals of modern proteomics, where the relation between the DNA base sequence and the respective protein must be mastered. One approach to this question is to simplify the process by transferring it into a two-dimensional scenario, thus reducing the complexity of the three-dimensional architecture to an in-plane problem.
Such a reduced coordination space may also be adequate for a primordial-soup scenario, where the spontaneous self-assembly of abiotically produced organic compounds may be facilitated.

The formation of highly ordered monolayers of the purine and pyrimidine DNA bases through physisorption-mediated molecular self-assembly at a solid-liquid mineral interface and the subsequent stereospecific adsorption of amino acids is an example of the spontaneous creation of nanoscale order.

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