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DNA nanotechnology – Wikipedia, the free encyclopedia

Posted: July 20, 2015 at 7:44 pm

DNA nanotechnology is the design and manufacture of artificial nucleic acid structures for technological uses. In this field, nucleic acids are used as non-biological engineering materials for nanotechnology rather than as the carriers of genetic information in living cells. Researchers in the field have created static structures such as two- and three-dimensional crystal lattices, nanotubes, polyhedra, and arbitrary shapes, as well as functional devices such as molecular machines and DNA computers. The field is beginning to be used as a tool to solve basic science problems in structural biology and biophysics, including applications in crystallography and spectroscopy for protein structure determination. Potential applications in molecular scale electronics and nanomedicine are also being investigated.

The conceptual foundation for DNA nanotechnology was first laid out by Nadrian Seeman in the early 1980s, and the field began to attract widespread interest in the mid-2000s. This use of nucleic acids is enabled by their strict base pairing rules, which cause only portions of strands with complementary base sequences to bind together to form strong, rigid double helix structures. This allows for the rational design of base sequences that will selectively assemble to form complex target structures with precisely controlled nanoscale features. A number of assembly methods are used to make these structures, including tile-based structures that assemble from smaller structures, folding structures using the DNA origami method, and dynamically reconfigurable structures using strand displacement techniques. While the field’s name specifically references DNA, the same principles have been used with other types of nucleic acids as well, leading to the occasional use of the alternative name nucleic acid nanotechnology.

Nanotechnology is often defined as the study of materials and devices with features on a scale below 100 nanometers. DNA nanotechnology, specifically, is an example of bottom-up molecular self-assembly, in which molecular components spontaneously organize into stable structures; the particular form of these structures is induced by the physical and chemical properties of the components selected by the designers.[4] In DNA nanotechnology, the component materials are strands of nucleic acids such as DNA; these strands are often synthetic and are almost always used outside the context of a living cell. DNA is well-suited to nanoscale construction because the binding between two nucleic acid strands depends on simple base pairing rules which are well understood, and form the specific nanoscale structure of the nucleic acid double helix. These qualities make the assembly of nucleic acid structures easy to control through nucleic acid design. This property is absent in other materials used in nanotechnology, including proteins, for which protein design is very difficult, and nanoparticles, which lack the capability for specific assembly on their own.[5]

The structure of a nucleic acid molecule consists of a sequence of nucleotides distinguished by which nucleobase they contain. In DNA, the four bases present are adenine (A), cytosine (C), guanine (G), and thymine (T). Nucleic acids have the property that two molecules will only bind to each other to form a double helix if the two sequences are complementary, meaning that they form matching sequences of base pairs, with A only binding to T, and C only to G.[5][6] Because the formation of correctly matched base pairs is energetically favorable, nucleic acid strands are expected in most cases to bind to each other in the conformation that maximizes the number of correctly paired bases. The sequences of bases in a system of strands thus determine the pattern of binding and the overall structure in an easily controllable way. In DNA nanotechnology, the base sequences of strands are rationally designed by researchers so that the base pairing interactions cause the strands to assemble in the desired conformation.[3][5] While DNA is the dominant material used, structures incorporating other nucleic acids such as RNA and peptide nucleic acid (PNA) have also been constructed.[7][8]

DNA nanotechnology is sometimes divided into two overlapping subfields: structural DNA nanotechnology and dynamic DNA nanotechnology. Structural DNA nanotechnology, sometimes abbreviated as SDN, focuses on synthesizing and characterizing nucleic acid complexes and materials that assemble into a static, equilibrium end state. On the other hand, dynamic DNA nanotechnology focuses on complexes with useful non-equilibrium behavior such as the ability to reconfigure based on a chemical or physical stimulus. Some complexes, such as nucleic acid nanomechanical devices, combine features of both the structural and dynamic subfields.[9][10]

The complexes constructed in structural DNA nanotechnology use topologically branched nucleic acid structures containing junctions. (In contrast, most biological DNA exists as an unbranched double helix.) One of the simplest branched structures is a four-arm junction that consists of four individual DNA strands, portions of which are complementary in a specific pattern. Unlike in natural Holliday junctions, each arm in the artificial immobile four-arm junction has a different base sequence, causing the junction point to be fixed at a certain position. Multiple junctions can be combined in the same complex, such as in the widely used double-crossover (DX) motif, which contains two parallel double helical domains with individual strands crossing between the domains at two crossover points. Each crossover point is itself topologically a four-arm junction, but is constrained to a single orientation, as opposed to the flexible single four-arm junction, providing a rigidity that makes the DX motif suitable as a structural building block for larger DNA complexes.[3][5]

Dynamic DNA nanotechnology uses a mechanism called toehold-mediated strand displacement to allow the nucleic acid complexes to reconfigure in response to the addition of a new nucleic acid strand. In this reaction, the incoming strand binds to a single-stranded toehold region of a double-stranded complex, and then displaces one of the strands bound in the original complex through a branch migration process. The overall effect is that one of the strands in the complex is replaced with another one.[9] In addition, reconfigurable structures and devices can be made using functional nucleic acids such as deoxyribozymes and ribozymes, which are capable of performing chemical reactions, and aptamers, which can bind to specific proteins or small molecules.[11]

Structural DNA nanotechnology, sometimes abbreviated as SDN, focuses on synthesizing and characterizing nucleic acid complexes and materials where the assembly has a static, equilibrium endpoint. The nucleic acid double helix has a robust, defined three-dimensional geometry that makes it possible to predict and design the structures of more complicated nucleic acid complexes. Many such structures have been created, including two- and three-dimensional structures, and periodic, aperiodic, and discrete structures.[10]

Small nucleic acid complexes can be equipped with sticky ends and combined into larger two-dimensional periodic lattices containing a specific tessellated pattern of the individual molecular tiles.[10] The earliest example of this used double-crossover (DX) complexes as the basic tiles, each containing four sticky ends designed with sequences that caused the DX units to combine into periodic two-dimensional flat sheets that are essentially rigid two-dimensional crystals of DNA.[15][16] Two-dimensional arrays have been made from other motifs as well, including the Holliday junction rhombus lattice,[17] and various DX-based arrays making use of a double-cohesion scheme.[18][19] The top two images at right show examples of tile-based periodic lattices.

Two-dimensional arrays can be made to exhibit aperiodic structures whose assembly implements a specific algorithm, exhibiting one form of DNA computing.[20] The DX tiles can have their sticky end sequences chosen so that they act as Wang tiles, allowing them to perform computation. A DX array whose assembly encodes an XOR operation has been demonstrated; this allows the DNA array to implement a cellular automaton that generates a fractal known as the Sierpinski gasket. The third image at right shows this type of array.[14] Another system has the function of a binary counter, displaying a representation of increasing binary numbers as it grows. These results show that computation can be incorporated into the assembly of DNA arrays.[21]

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DNA nanotechnology – Wikipedia, the free encyclopedia

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