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2008sci, 824y, 824, circumferences, ekani, nkodo, kumar, fygenson, 16352, 15600335, ja044319l, 12616344r, 16344, primitives, copying, counting, 2592, 16351220, nl052038l, 2586b, 2586, mathieu, liao, 665, 15826105, 3464188, nl050084f, 661m, 661, bundles, 3419, 17036134, 3491902, b605212f, 3414, visualized, 5443, ja9900398, 5437m, 5437, modifying, 922, ja982824a, 917l, 917, wenzler, 6693, 544, 4385579, 9707114, 28998, 1998natur, 539w, 539, e424, 15583715, 534809, 0020424, triangles, finkelstein, highly, conductive, nanowires, 5641, 1884, 137635908, 14512621, 1089389, 2003sci, 1882y, 1882, e73, 15024422, 368168, 0020073, doye, ouldridge, louis, romano, matek, graining, simulations, 20414, 15324396, 24121860, c3cp53545b, 2013pccp, 1520395d, 1308, 3843, arxiv, 20395, physics, dnazymes, 588, 17056247, 004, 580, 257, 17952671, 3479651, s12033, 007, 0059, 246, guo, 842, 21102465, 3149862, 231, 833g, 833, chworos, severcan, koyfman, weinkam, oroudjev, hansma, jaeger, jigsaw, puzzles, 5704, 2072, 9296608, 15604402, 1104686, 2004sci, 2068c, 2068, 1996, fundamentals, hecht, press, 508467, bioorganic, e431, 15597116, 535573, 0020431, emergence, complexity, lessons, hopkin, scientist, profile, seer, dietz, högberg, graf, 7245, 418, 19458720, 2688462, nature08016, 414d, 414, 7082, 302, 4316391, 16541064, nature04586, 2006natur, 297r, 297, xiao, rosen, hainfeld, musier, forsyth, selfassembly, scaffolding, 317, 2257083, 1023, 1021145208328, 2002jnr, 313x, 313, biochip, assembling, memory, 300, 3508280, allen, friedrich, jennifer, 1476, 4687, generalized, multicrossovers, jonoska, rozenberg, 30295, 30296, 4_1, pinheiro, 772, 22056726, 3334823, 187, 2011natna, 763p, 763, challenges, opportunities, problem, oriented, guests, lab, crystallization, protocol, 201, 242, 259, schaap, tardin, berry, schmidt, chiral, blocks, nanofabrication, 5754, 1665, 13678773, 16339440, 1120367, 2005sci, 1661g, comparison, imaged, tip, interaction, fragile, analyzed, 101

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technology 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 19 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 20 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 21 22 subfields edit 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 23 24 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 structural motif which contains two parallel double helical domains with individual strands crossing between the domains at two crossover points each crossover point is topologically a four arm junction but is constrained to one orientation in contrast 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 23 in addition reconfigurable structures and devices can be made using functional nucleic acids such as deoxyribozymes and ribozymes which can perform chemical reactions and aptamers which can bind to specific proteins or small molecules 25 structural dna nanotechnology edit 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 simulate 26 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 24 extended lattices edit the assembly of a dx array left schematic diagram each bar represents a double helical domain of dna with the shapes representing complementary sticky ends the dx complex at top will combine with other dx complexes into the two dimensional array shown at bottom 18 right an atomic force microscopy image of the assembled array the individual dx tiles are clearly visible within the assembled structure the field is 150 nm across left a model of a dna tile used to make another two dimensional periodic lattice right an atomic force micrograph of the assembled lattice 27 28 an example of an aperiodic two dimensional lattice that assembles into a fractal pattern left the sierpinski gasket fractal right dna arrays that display a representation of the sierpinski gasket on their surfaces 29 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 24 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 30 31 two dimensional arrays have been made from other motifs as well including the holliday junction rhombus lattice 32 and various dx based arrays making use of a double cohesion scheme 33 34 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 17 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 29 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 35 dx arrays have been made to form hollow nanotubes 4 20 nm in diameter essentially two dimensional lattices which curve back upon themselves 36 these dna nanotubes are somewhat similar in size and shape to carbon nanotubes and while they lack the electrical conductance of carbon nanotubes dna nanotubes are more easily modified and connected to other structures one of many schemes for constructing dna nanotubes uses a lattice of curved dx tiles that curls around itself and closes into a tube 37 in an alternative method that allows the circumference to be specified in a simple modular fashion using single stranded tiles the rigidity of the tube is an emergent property 38 forming three dimensional lattices of dna was the earliest goal of dna nanotechnology but this proved to be one of the most difficult to realize success using a motif based on the concept of tensegrity a balance between tension and compression forces was finally reported in 2009 17 39 discrete structures edit researchers have synthesized many three dimensional dna complexes that each have the connectivity of a polyhedron such as a cube or octahedron meaning that the dna duplexes trace the edges of a polyhedron with a dna junction at each vertex 6 the earliest demonstrations of dna polyhedra were very work intensive requiring multiple ligations and solid phase synthesis steps to create catenated polyhedra 40 subsequent work yielded polyhedra whose synthesis was much easier these include a dna octahedron made from a long single strand designed to fold into the correct conformation 41 and a tetrahedron that can be produced from four dna strands in one step pictured at the top of this article 1 nanostructures of arbitrary non regular shapes are usually made using the dna origami method these structures consist of a long natural virus strand as a scaffold which is made to fold into the desired shape by computationally designed short staple strands this method has the advantages of being easy to design as the base sequence is predetermined by the scaffold strand sequence and not requiring high strand purity and accurate stoichiometry as most other dna nanotechnology methods do dna origami was first demonstrated for two dimensional shapes such as a smiley face a coarse map of the western hemisphere and the mona lisa painting 6 13 42 solid three dimensional structures can be made by using parallel dna helices arranged in a honeycomb pattern 14 and structures with two dimensional faces can be made to fold into a hollow overall three dimensional shape akin to a cardboard box these can be programmed to open and reveal or release a molecular cargo in response to a stimulus making them potentially useful as programmable molecular cages 43 44 templated assembly edit nucleic acid structures can be made to incorporate molecules other than nucleic acids sometimes called heteroelements including proteins metallic nanoparticles quantum dots amines 45 and fullerenes this allows the construction of materials and devices with a range of functionalities much greater than is possible with nucleic acids alone the goal is to use the self assembly of the nucleic acid structures to template the assembly of the nanoparticles hosted on them controlling their position and in some cases orientation 6 46 many of these schemes use a covalent attachment scheme using oligonucleotides with amide or thiol functional groups as a chemical handle to bind the heteroelements this covalent binding scheme has been used to arrange gold nanoparticles on a dx based array 47 and to arrange streptavidin protein molecules into specific patterns on a dx array 48 a non covalent hosting scheme using dervan polyamides on a dx array was used to arrange streptavidin proteins in a specific pattern on a dx array 49 carbon nanotubes have been hosted on dna arrays in a pattern allowing the assembly to act as a molecular electronic device a carbon nanotube field effect transistor 50 in addition there are nucleic acid metallization methods in which the nucleic acid is replaced by a metal which assumes the general shape of the original nucleic acid structure 51 and schemes for using nucleic acid nanostructures as lithography masks transferring their pattern into a solid surface 52 dynamic dna nanotechnology edit dynamic dna nanotechnology often makes use of toehold mediated strand displacement reactions in this example the red strand binds to the single stranded toehold region on the green strand region 1 and then in a branch migration process across region 2 the blue strand is displaced and freed from the complex reactions like these are used to dynamically reconfigure or assemble nucleic acid nanostructures in addition the red and blue strands can be used as signals in a molecular logic gate dynamic dna nanotechnology focuses on forming nucleic acid systems with designed dynamic functionalities related to their overall structures such as computation and mechanical motion there is some overlap between structural and dynamic dna nanotechnology as structures can be formed through annealing and then reconfigured dynamically or can be made to form dynamically in the first place 6 10 nanomechanical devices edit main article dna machine dna complexes have been made that change their conformation upon some stimulus making them one form of nanorobotics these structures are initially formed in the same way as the static structures made in structural dna nanotechnology but are designed so that dynamic reconfiguration is possible after the initial assembly 23 10 the earliest such device made use of the transition between the b dna and z dna forms to respond to a change in buffer conditions by undergoing a twisting motion 53 this reliance on buffer conditions caused all devices to change state at the same time subsequent systems could change states based upon the presence of control strands allowing multiple devices to be independently operated in solution some examples of such systems are a molecular tweezers design that has an open and a closed state 54 a device that could switch from a paranemic crossover px conformation to a jx2 conformation with two non junction juxtapositions of the dna backbone undergoing rotational motion in the process 55 and a two dimensional array that could dynamically expand and contract in response to control strands 56 structures have also been made that dynamically open or close potentially acting as a molecular cage to release or reveal a functional cargo upon opening 43 57 58 in another example a dna origami nanostructure was coupled to t7 rna polymerase and could thus be operated as a chemical energy driven motor that can be coupled to a passive follower which it then drives 59 photoresponsive dna assemblies have also been used to control micron scale condensate motion in 2025 udono nomura and takinoue reported azobenzene modified dna condensates whose binding state and fluidity could be switched by ultraviolet and visible light producing reversible and directional motions 60 dna walkers are a class of nucleic acid nanomachines that exhibit directional motion along a linear track a large number of schemes have been demonstrated 10 one strategy is to control the motion of the walker along the track using control strands that need to be manually added in sequence 61 62 it is also possible to control individual steps of a dna walker by irradiation with light of different wavelengths 63 another approach is to make use of restriction enzymes or deoxyribozymes to cle...