View source for DNA nanotechnology

{{Short description|The design and manufacture of artificial nucleic acid structures for technological uses}}
{{Featured article}}
{{Molecular self-assembly subfields}}
[[File:DNA tetrahedron white.png|thumb|DNA nanotechnology involves forming artificial, [[Nucleic acid design|designed]] nanostructures out of [[nucleic acid]]s, such as this [[DNA]] tetrahedron.<ref name="Goodman05" /> Each edge of the tetrahedron is a 20 [[base pair]] DNA [[Nucleic acid double helix|double helix]], and each vertex is a three-arm junction. The 4 DNA strands that form the 4 tetrahedral faces are color-coded.|300px]]

'''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 [[Cell (biology)|cells]]. Researchers in the field have created static structures such as two- and three-dimensional [[Crystal structure|crystal lattices]], [[nanotube]]s, [[Polyhedron|polyhedra]], and arbitrary shapes, and functional devices such as [[molecular machine]]s and [[DNA computing|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 [[X-ray crystallography]] and [[nuclear magnetic resonance spectroscopy of proteins]] to determine structures. 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 pair]]ing rules, which cause only portions of strands with [[Complementarity (molecular biology)|complementary]] [[Nucleic acid sequence|base sequences]] to bind together to form strong, rigid [[Nucleic acid double helix|double helix]] structures. This allows for the [[Nucleic acid design|rational design of base sequences]] that will selectively assemble to form complex target structures with precisely controlled  [[Nanoscopic scale|nanoscale]] features. Several 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 methods. The field's name specifically references [[DNA]], but 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''.

==History==

The conceptual foundation for DNA nanotechnology was first laid out by [[Nadrian Seeman]] in the early 1980s.<!--
--><ref name="Pelesko">History: {{cite book | vauthors = Pelesko JA |title=Self-assembly: the science of things that put themselves together |year=2007 |publisher=Chapman & Hall/CRC |location=New York |isbn=978-1-58488-687-7 |pages=201, 242, 259}}</ref> Seeman's original motivation was to create a three-dimensional DNA lattice for orienting other large molecules, which would simplify their [[crystallography|crystallographic study]] by eliminating the difficult process of obtaining pure crystals.  This idea had reportedly come to him in late 1980, after realizing the similarity between the woodcut ''Depth'' by [[M. C. Escher]] and an array of DNA six-arm junctions.<!--
--><ref name="Seeman-sciam">Overview: {{cite journal | vauthors = Seeman NC | title = Nanotechnology and the double helix | journal = Scientific American | volume = 290 | issue = 6 | pages = 64–75 | date = June 2004 | pmid = 15195395 | doi = 10.1038/scientificamerican0604-64 | bibcode = 2004SciAm.290f..64S }}</ref><!--
--><ref>History: See {{Cite web |url=http://seemanlab4.chem.nyu.edu/nano-pro.html |title=Current crystallization protocol |publisher=Nadrian Seeman Lab}} for a statement of the problem, and {{Cite web |url=http://seemanlab4.chem.nyu.edu/nano-cage.html |title=DNA cages containing oriented guests |publisher=Nadrian Seeman Laboratory}} for the proposed solution.</ref>  Several natural branched DNA structures were known at the time, including the DNA [[replication fork]] and the mobile [[Holliday junction]], but Seeman's insight was that immobile nucleic acid junctions could be created by properly designing the strand sequences to remove symmetry in the assembled molecule, and that these immobile junctions could in principle be combined into rigid crystalline lattices.  The first theoretical paper proposing this scheme was published in 1982, and the first experimental demonstration of an immobile DNA junction was published the following year.<ref name="Seeman2010">Overview: {{cite journal | vauthors = Seeman NC | title = Nanomaterials based on DNA | journal = Annual Review of Biochemistry | volume = 79 | pages = 65–87 | year = 2010 | pmid = 20222824 | pmc = 3454582 | doi = 10.1146/annurev-biochem-060308-102244 }}</ref><ref name="ShihYanChallenges" />
[[File:Escher Depth.jpg|thumb|left|The woodcut ''Depth'' (pictured) by [[M. C. Escher]] reportedly inspired Nadrian Seeman to consider using three-dimensional lattices of DNA to orient hard-to-crystallize molecules. This led to the beginning of the field of DNA nanotechnology.]]

In 1991, Seeman's laboratory published a report on the synthesis of a cube made of DNA, the first synthetic three-dimensional nucleic acid nanostructure, for which he received the 1995 [[Foresight Institute Feynman Prize in Nanotechnology|Feynman Prize in Nanotechnology]]. This was followed by a DNA [[truncated octahedron]]. It soon became clear that these structures, polygonal shapes with flexible junctions as their [[Vertex (geometry)|vertices]], were not rigid enough to form extended three-dimensional lattices. Seeman developed the more rigid double-crossover (DX) [[structural motif]], and in 1998, in collaboration with [[Erik Winfree]], published the creation of two-dimensional lattices of DX tiles.<ref name="Seeman-sciam" /><ref name="Pelesko" /><ref name="origamichapter" />  These tile-based structures had the advantage that they provided the ability to implement DNA computing, which was demonstrated by Winfree and [[Paul Rothemund]] in their 2004 paper on the algorithmic self-assembly of a Sierpinski gasket structure, and for which they shared the 2006 Feynman Prize in Nanotechnology. Winfree's key insight was that the DX tiles could be used as [[Wang tile]]s, meaning that their assembly could perform computation.<ref name="Pelesko" />  The synthesis of a three-dimensional lattice was finally published by Seeman in 2009, nearly thirty years after he had set out to achieve it.<ref name="growsup" />

New abilities continued to be discovered for designed DNA structures throughout the 2000s.  The first [[DNA machine|DNA nanomachine]]—a motif that changes its structure in response to an input—was demonstrated in 1999 by Seeman.  An improved system, which was the first nucleic acid device to make use of toehold-mediated strand displacement, was demonstrated by [[Bernard Yurke]] in 2000.<ref>{{Cite journal |last1=Yurke |first1=Bernard |last2=Turberfield |first2=Andrew J. |last3=Mills |first3=Allen P. |last4=Simmel |first4=Friedrich C. |last5=Neumann |first5=Jennifer L. |date=August 2000 |title=A DNA-fuelled molecular machine made of DNA |url=https://www.nature.com/articles/35020524 |journal=Nature |language=en |volume=406 |issue=6796 |pages=605–608 |doi=10.1038/35020524 |bibcode=2000Natur.406..605Y |s2cid=2064216 |issn=1476-4687}}</ref> The next advance was to translate this into mechanical motion, and in 2004 and 2005, several DNA walker systems were demonstrated by the groups of Seeman, [[Niles Pierce]], [[Andrew Turberfield]], and [[Chengde Mao]].<ref name="nanomachines">DNA machines: {{cite journal | vauthors = Bath J, Turberfield AJ | title = DNA nanomachines | journal = Nature Nanotechnology | volume = 2 | issue = 5 | pages = 275–284 | date = May 2007 | pmid = 18654284 | doi = 10.1038/nnano.2007.104 | bibcode = 2007NatNa...2..275B }}</ref>  The idea of using DNA arrays to template the assembly of other molecules such as nanoparticles and proteins, first suggested by Bruche Robinson and Seeman in 1987,<!--
--><ref name="biochip">Nanoarchitecture: {{cite journal | vauthors = Robinson BH, Seeman NC | title = The design of a biochip: a self-assembling molecular-scale memory device | journal = Protein Engineering | volume = 1 | issue = 4 | pages = 295–300 | date = August 1987 | pmid = 3508280 | doi = 10.1093/protein/1.4.295 }}</ref> was demonstrated in 2002 by Seeman, Kiehl et al.<!--
--><ref name="Nanoparticles on DNA">Nanoarchitecture: {{cite journal | vauthors = Xiao S, Liu F, Rosen AE, Hainfeld JF, Seeman NC, Musier-Forsyth K, Kiehl RA |s2cid=2257083 |date=August 2002 |title=Selfassembly of metallic nanoparticle arrays by DNA scaffolding |journal=Journal of Nanoparticle Research |volume=4 |issue=4 |pages=313–317 |doi=10.1023/A:1021145208328|bibcode=2002JNR.....4..313X }}</ref> and subsequently by many other groups.

In 2006, Rothemund first demonstrated the [[DNA origami]] method for easily and robustly forming folded DNA structures of arbitrary shape. Rothemund had conceived of this method as being conceptually intermediate between Seeman's DX lattices, which used many short strands, and [[William Shih]]'s DNA octahedron, which consisted mostly of one very long strand. Rothemund's DNA origami contains a long strand which folding is assisted by several short strands. This method allowed forming much larger structures than formerly possible, and which are less technically demanding to design and synthesize.<ref name="origamichapter">DNA origami: {{cite book |doi=10.1007/3-540-30296-4_1 | vauthors = Rothemund PW | veditors = Chen J, Jonoska N, Rozenberg G |title=Nanotechnology: science and computation |series=Natural Computing Series |year=2006 |publisher=Springer |location=New York |isbn=978-3-540-30295-7 |chapter=Scaffolded DNA origami: from generalized multicrossovers to polygonal networks |pages=3–21|citeseerx=10.1.1.144.1380 }}</ref> DNA origami was the cover story of ''[[Nature (journal)|Nature]]'' on March 15, 2006.<ref name="rothemundorigami" />  Rothemund's research demonstrating two-dimensional DNA origami structures was followed by the demonstration of solid three-dimensional DNA origami by Douglas ''et al.'' in 2009,<ref name="origami" /> while the labs of [[Jørgen Kjems]] and Yan demonstrated hollow three-dimensional structures made out of two-dimensional faces.<ref name="growsup">History/applications: {{cite journal | vauthors = Service RF | title = DNA nanotechnology. DNA nanotechnology grows up | journal = Science | volume = 332 | issue = 6034 | pages = 1140–1, 1143 | date = June 2011 | pmid = 21636754 | doi = 10.1126/science.332.6034.1140 | bibcode = 2011Sci...332.1140S }}</ref>

DNA nanotechnology was initially met with some skepticism due to the unusual non-biological use of nucleic acids as materials for building structures and doing computation, and the preponderance of [[proof of principle]] experiments that extended the abilities of the field but were far from actual applications. Seeman's 1991 paper on the synthesis of the DNA cube was rejected by the journal ''[[Science (journal)|Science]]'' after one reviewer praised its originality while another criticized it for its lack of biological relevance.<ref>{{cite journal | vauthors = Service RF | title = DNA nanotechnology. DNA nanotechnology grows up | journal = Science | volume = 332 | issue = 6034 | pages = 1140–1, 1143 | date = June 2011 | pmid = 21636754 | doi = 10.1126/science.332.6034.1140 | bibcode = 2011Sci...332.1140S }}</ref>  By the early 2010s the field was considered to have increased its abilities to the point that applications for basic science research were beginning to be realized, and practical applications in medicine and other fields were beginning to be considered feasible.<ref name="growsup" /><ref>History: {{cite journal| vauthors = Hopkin K |title=Profile: 3-D seer|journal=The Scientist|date=August 2011|url=http://the-scientist.com/2011/08/01/3-d-seer/|access-date=8 August 2011|archive-url=https://web.archive.org/web/20111010085248/http://the-scientist.com/2011/08/01/3-d-seer/|archive-date=10 October 2011|url-status=dead|df=dmy-all}}</ref>  The field had grown from very few active laboratories in 2001 to at least 60 in 2010, which increased the talent pool and thus the number of scientific advances in the field during that decade.<ref name="SeemanGrowing">History: {{cite journal | vauthors = Seeman NC | title = Structural DNA nanotechnology: growing along with Nano Letters | journal = Nano Letters | volume = 10 | issue = 6 | pages = 1971–1978 | date = June 2010 | pmid = 20486672 | pmc = 2901229 | doi = 10.1021/nl101262u | bibcode = 2010NanoL..10.1971S }}</ref>


==Fundamental concepts==
[[File:Неподвижная структура Холлидея (англ.).svg|thumb|These four strands associate into a DNA four-arm junction because this structure maximizes the number of correct [[base pair]]s, with [[Adenine|A]] matched to [[Thymine|T]] and [[Cytosine|C]] matched to [[Guanine|G]].<ref name="Mao04" /><ref name="Seeman-sciam" /> See [[:File:Holliday junction coloured.png|this image]] for a more realistic model of the four-arm junction showing its [[Nucleic acid tertiary structure|tertiary structure]].]]

[[File:Mao-DX-schematic-2.svg|thumb|This double-crossover (DX) [[supramolecular complex]] consists of five [[DNA]] single strands that form two [[Double helix|double-helical]] domains, on the top and the bottom in this image. There are two crossover points where the strands cross from one domain into the other.<ref name="Mao04">Overview: {{cite journal | vauthors = Mao C | title = The emergence of complexity: lessons from DNA | journal = PLOS Biology | volume = 2 | issue = 12 | pages = e431 | date = December 2004 | pmid = 15597116 | pmc = 535573 | doi = 10.1371/journal.pbio.0020431 | doi-access = free }}</ref>]]

===Properties of nucleic acids===
[[Nanotechnology]] is often defined as the study of materials and devices with features on a scale below 100 [[nanometer]]s.  DNA nanotechnology, specifically, is an example of [[Top-down and bottom-up design|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.<ref>Background: {{cite book | vauthors = Pelesko JA |title=Self-assembly: the science of things that put themselves together |year=2007 |publisher=Chapman & Hall/CRC |location=New York |isbn=978-1-58488-687-7 |pages=5, 7}}</ref>  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 pair]]ing 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 [[protein]]s, for which [[protein design]] is very difficult, and [[nanoparticle]]s, which lack the capability for specific assembly on their own.<ref name="Seeman2010" />

The [[Nucleic acid structure|structure]] of a nucleic acid molecule consists of a sequence of [[nucleotide]]s 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 [[Complementarity (molecular biology)|complementary]], meaning that they form matching sequences of base pairs, with A only binding to T, and C only to G.<ref name="Seeman2010" /><ref>Background: {{cite book| vauthors = Long EC |chapter=Fundamentals of nucleic acids | veditors = Hecht SM |title=Bioorganic chemistry: nucleic acids|year=1996|publisher=Oxford University Press|location=New York |isbn=978-0-19-508467-2|pages=4–10}}</ref>  Because the formation of correctly matched base pairs is [[Nucleic acid thermodynamics|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.<ref name="Seeman-sciam" /><ref name="Seeman2010" />  While [[DNA]] is the dominant material used, structures incorporating other nucleic acids such as [[RNA]] and [[peptide nucleic acid]] (PNA) have also been constructed.<ref>RNA nanotechnology: {{cite journal | vauthors = Chworos A, Severcan I, Koyfman AY, Weinkam P, Oroudjev E, Hansma HG, Jaeger L | title = Building programmable jigsaw puzzles with RNA | journal = Science | volume = 306 | issue = 5704 | pages = 2068–2072 | date = December 2004 | pmid = 15604402 | doi = 10.1126/science.1104686 | s2cid = 9296608 | bibcode = 2004Sci...306.2068C }}</ref><ref>RNA nanotechnology: {{cite journal | vauthors = Guo P | title = The emerging field of RNA nanotechnology | journal = Nature Nanotechnology | volume = 5 | issue = 12 | pages = 833–842 | date = December 2010 | pmid = 21102465 | pmc = 3149862 | doi = 10.1038/nnano.2010.231 | bibcode = 2010NatNa...5..833G }}</ref>

===Subfields===
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, [[Chemical equilibrium|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.<ref name="DDNreview">Dynamic DNA nanotechnology: {{cite journal | vauthors = Zhang DY, Seelig G | title = Dynamic DNA nanotechnology using strand-displacement reactions | journal = Nature Chemistry | volume = 3 | issue = 2 | pages = 103–113 | date = February 2011 | pmid = 21258382 | doi = 10.1038/nchem.957 | bibcode = 2011NatCh...3..103Z }}</ref><ref name="SDNreview" />

The complexes constructed in structural DNA nanotechnology use topologically branched nucleic acid structures containing junctions. (In contrast, most biological DNA exists as an unbranched [[Nucleic acid double helix|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 junction]]s, each arm in the artificial immobile four-arm junction has a different [[Nucleic acid sequence|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.<ref name="Seeman-sciam" /><ref name="Seeman2010" />

Dynamic DNA nanotechnology uses a mechanism called [[Toehold mediated strand displacement|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 [[Sticky end|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.<ref name="DDNreview" />  In addition, reconfigurable structures and devices can be made using functional nucleic acids such as [[deoxyribozyme]]s and [[ribozyme]]s, which can perform chemical reactions, and [[aptamer]]s, which can bind to specific proteins or small molecules.<ref>Dynamic DNA nanotechnology: {{cite journal | vauthors = Lu Y, Liu J | title = Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers | journal = Current Opinion in Biotechnology | volume = 17 | issue = 6 | pages = 580–588 | date = December 2006 | pmid = 17056247 | doi = 10.1016/j.copbio.2006.10.004 }}</ref>

==Structural DNA nanotechnology==
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,<ref name="Doye2013">Simulation of DNA structures: {{cite journal | vauthors = Doye JP, Ouldridge TE, Louis AA, Romano F, Šulc P, Matek C, Snodin BE, Rovigatti L, Schreck JS, Harrison RM, Smith WP | display-authors = 6 | title = Coarse-graining DNA for simulations of DNA nanotechnology | journal = Physical Chemistry Chemical Physics | volume = 15 | issue = 47 | pages = 20395–20414 | date = December 2013 | pmid = 24121860 | doi = 10.1039/C3CP53545B | arxiv = 1308.3843 | s2cid = 15324396 | bibcode = 2013PCCP...1520395D }}</ref> 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.<ref name="SDNreview">Structural DNA nanotechnology: {{cite journal | vauthors = Seeman NC | title = An overview of structural DNA nanotechnology | journal = Molecular Biotechnology | volume = 37 | issue = 3 | pages = 246–257 | date = November 2007 | pmid = 17952671 | pmc = 3479651 | doi = 10.1007/s12033-007-0059-4 }}</ref>

{{anchor|DNA nanotubes}}

===Extended lattices===
{{multiple image
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| image2 = DX DNA array.png
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| footer = The assembly of a DX array. ''Left'', schematic diagram. Each bar represents a double-helical domain of [[DNA]], with the shapes representing [[Complementarity (molecular biology)|complementary]] [[sticky end]]s. The DX complex at top will combine with other DX complexes into the two-dimensional array shown at bottom.<ref name="Mao04" /> ''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&nbsp;[[Nanometer|nm]] across.
}}

[[File:DNA nanostructures.png|thumb|350px|''Left'', a model of a DNA tile used to make another two-dimensional periodic lattice. ''Right'', an atomic force micrograph of the assembled lattice.<ref>Other arrays: {{cite journal | vauthors = Strong M | title = Protein nanomachines | journal = PLOS Biology | volume = 2 | issue = 3 | pages = E73 | date = March 2004 | pmid = 15024422 | pmc = 368168 | doi = 10.1371/journal.pbio.0020073 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Yan H, Park SH, Finkelstein G, Reif JH, LaBean TH | title = DNA-templated self-assembly of protein arrays and highly conductive nanowires | journal = Science | volume = 301 | issue = 5641 | pages = 1882–1884 | date = September 2003 | pmid = 14512621 | doi = 10.1126/science.1089389 | s2cid = 137635908 | bibcode = 2003Sci...301.1882Y }}</ref>]]

{{multiple image
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| image2 = Rothemund-DNA-SierpinskiGasket.jpg
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| footer = 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<ref name="rothemund04winfree" />
}}

Small nucleic acid complexes can be equipped with [[sticky end]]s and combined into larger two-dimensional periodic lattices containing a specific [[Tessellation|tessellated]] pattern of the individual molecular tiles.<ref name="SDNreview" />  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.<!--
--><ref>DX arrays: {{cite journal | vauthors = Winfree E, Liu F, Wenzler LA, Seeman NC | title = Design and self-assembly of two-dimensional DNA crystals | journal = Nature | volume = 394 | issue = 6693 | pages = 539–544 | date = August 1998 | pmid = 9707114 | doi = 10.1038/28998 | s2cid = 4385579 | bibcode = 1998Natur.394..539W }}</ref><!--
--><ref>DX arrays: {{cite journal | vauthors = Liu F, Sha R, Seeman NC |date=10 February 1999 |title=Modifying the surface features of two-dimensional DNA crystals |journal=Journal of the American Chemical Society |volume=121 |issue=5 |pages=917–922 |doi=10.1021/ja982824a}}</ref>  Two-dimensional arrays have been made from other motifs as well, including the [[Holliday junction]] [[rhombus]] lattice,<!--
--><ref>Other arrays: {{cite journal | vauthors = Mao C, Sun W, Seeman NC |date=16 June 1999 |title=Designed two-dimensional DNA Holliday junction arrays visualized by atomic force microscopy |journal=Journal of the American Chemical Society |volume=121 |issue=23 |pages=5437–5443|doi=10.1021/ja9900398}}</ref> and various DX-based arrays making use of a double-cohesion scheme.<!--
--><ref>Other arrays: {{cite journal | vauthors = Constantinou PE, Wang T, Kopatsch J, Israel LB, Zhang X, Ding B, Sherman WB, Wang X, Zheng J, Sha R, Seeman NC | display-authors = 6 | title = Double cohesion in structural DNA nanotechnology | journal = Organic & Biomolecular Chemistry | volume = 4 | issue = 18 | pages = 3414–3419 | date = September 2006 | pmid = 17036134 | pmc = 3491902 | doi = 10.1039/b605212f }}</ref><!--
--><ref>Other arrays: {{cite journal | vauthors = Mathieu F, Liao S, Kopatsch J, Wang T, Mao C, Seeman NC | title = Six-helix bundles designed from DNA | journal = Nano Letters | volume = 5 | issue = 4 | pages = 661–665 | date = April 2005 | pmid = 15826105 | pmc = 3464188 | doi = 10.1021/nl050084f | bibcode = 2005NanoL...5..661M }}</ref>  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.<ref name="SeemanGrowing" /> The DX tiles can have their sticky end sequences chosen so that they act as [[Wang tile]]s, allowing them to perform computation. A DX array whose assembly encodes an [[Exclusive or|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.<!--
--><ref name="rothemund04winfree">Algorithmic self-assembly: {{cite journal | vauthors = Rothemund PW, Papadakis N, Winfree E | title = Algorithmic self-assembly of DNA Sierpinski triangles | journal = PLOS Biology | volume = 2 | issue = 12 | pages = e424 | date = December 2004 | pmid = 15583715 | pmc = 534809 | doi = 10.1371/journal.pbio.0020424 | doi-access = free }}</ref> Another system has the function of a binary [[Counter (digital)|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.<ref>Algorithmic self-assembly: {{cite journal | vauthors = Barish RD, Rothemund PW, Winfree E | title = Two computational primitives for algorithmic self-assembly: copying and counting | journal = Nano Letters | volume = 5 | issue = 12 | pages = 2586–2592 | date = December 2005 | pmid = 16351220 | doi = 10.1021/nl052038l | citeseerx = 10.1.1.155.676 | bibcode = 2005NanoL...5.2586B }}</ref>

DX arrays have been made to form hollow nanotubes 4–20&nbsp;[[Nanometer|nm]] in diameter, essentially two-dimensional lattices which curve back upon themselves.<ref name="Feldkamp" /> These DNA nanotubes are somewhat similar in size and shape to [[carbon nanotube]]s, 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.<ref>DNA nanotubes: {{cite journal | vauthors = Rothemund PW, Ekani-Nkodo A, Papadakis N, Kumar A, Fygenson DK, Winfree E | title = Design and characterization of programmable DNA nanotubes | journal = Journal of the American Chemical Society | volume = 126 | issue = 50 | pages = 16344–16352 | date = December 2004 | pmid = 15600335 | doi = 10.1021/ja044319l | url = https://resolver.caltech.edu/CaltechAUTHORS:20110309-104202496 }}</ref> 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]].<ref>DNA nanotubes: {{cite journal | vauthors = Yin P, Hariadi RF, Sahu S, Choi HM, Park SH, Labean TH, Reif JH | title = Programming DNA tube circumferences | journal = Science | volume = 321 | issue = 5890 | pages = 824–826 | date = August 2008 | pmid = 18687961 | doi = 10.1126/science.1157312 | s2cid = 12100380 | bibcode = 2008Sci...321..824Y | url = https://resolver.caltech.edu/CaltechAUTHORS:20111020-104503059 }}</ref>

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.<ref name="SeemanGrowing" /><!--
--><ref name="3Darrays">Three-dimensional arrays: {{cite journal | vauthors = Zheng J, Birktoft JJ, Chen Y, Wang T, Sha R, Constantinou PE, Ginell SL, Mao C, Seeman NC | display-authors = 6 | title = From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal | journal = Nature | volume = 461 | issue = 7260 | pages = 74–77 | date = September 2009 | pmid = 19727196 | pmc = 2764300 | doi = 10.1038/nature08274 | bibcode = 2009Natur.461...74Z }}</ref>

===Discrete structures===
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 [[Edge (geometry)|edges]] of a polyhedron with a DNA junction at each vertex.<ref name="ShihYanChallenges">Overview: {{cite journal | vauthors = Pinheiro AV, Han D, Shih WM, Yan H | title = Challenges and opportunities for structural DNA nanotechnology | journal = Nature Nanotechnology | volume = 6 | issue = 12 | pages = 763–772 | date = November 2011 | pmid = 22056726 | pmc = 3334823 | doi = 10.1038/nnano.2011.187 | bibcode = 2011NatNa...6..763P }}</ref> The earliest demonstrations of DNA polyhedra were very work-intensive, requiring multiple [[DNA ligase|ligations]] and [[solid-phase synthesis]] steps to create [[Catenane|catenated]] polyhedra.<!--
--><ref>DNA polyhedra: {{cite journal | vauthors = Zhang Y, Seeman NC |date=1 March 1994 |title=Construction of a DNA-truncated octahedron |journal=Journal of the American Chemical Society |volume=116 |issue=5 |pages=1661–1669|doi=10.1021/ja00084a006}}</ref> 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,<!--
--><ref>DNA polyhedra: {{cite journal | vauthors = Shih WM, Quispe JD, Joyce GF | title = A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron | journal = Nature | volume = 427 | issue = 6975 | pages = 618–621 | date = February 2004 | pmid = 14961116 | doi = 10.1038/nature02307 | s2cid = 4419579 | bibcode = 2004Natur.427..618S }}</ref> and a tetrahedron that can be produced from four DNA strands in one step, pictured at the top of this article.<!--
--><ref name="Goodman05">DNA polyhedra: {{cite journal | vauthors = Goodman RP, Schaap IA, Tardin CF, Erben CM, Berry RM, Schmidt CF, Turberfield AJ | title = Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication | journal = Science | volume = 310 | issue = 5754 | pages = 1661–1665 | date = December 2005 | pmid = 16339440 | doi = 10.1126/science.1120367 | s2cid = 13678773 | bibcode = 2005Sci...310.1661G }}</ref>

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 [[Nucleic acid sequence|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|smiley face]], a coarse map of the Western Hemisphere, and the Mona Lisa painting.<ref name="ShihYanChallenges" /><ref name="rothemundorigami" /><ref>{{cite journal | vauthors = Tikhomirov G, Petersen P, Qian L | title = Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns | journal = Nature | volume = 552 | issue = 7683 | pages = 67–71 | date = December 2017 | pmid = 29219965 | doi = 10.1038/nature24655 | s2cid = 4455780 | bibcode = 2017Natur.552...67T | url = https://resolver.caltech.edu/CaltechAUTHORS:20171004-131452371 }}</ref> Solid three-dimensional structures can be made by using parallel DNA helices arranged in a honeycomb pattern,<ref name="origami">DNA origami: {{cite journal | vauthors = Douglas SM, Dietz H, Liedl T, Högberg B, Graf F, Shih WM | title = Self-assembly of DNA into nanoscale three-dimensional shapes | journal = Nature | volume = 459 | issue = 7245 | pages = 414–418 | date = May 2009 | pmid = 19458720 | pmc = 2688462 | doi = 10.1038/nature08016 | bibcode = 2009Natur.459..414D }}</ref> 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 encapsulation|molecular cages]].<!--
--><ref name="AndersenBox">DNA boxes: {{cite journal | vauthors = Andersen ES, Dong M, Nielsen MM, Jahn K, Subramani R, Mamdouh W, Golas MM, Sander B, Stark H, Oliveira CL, Pedersen JS, Birkedal V, Besenbacher F, Gothelf KV, Kjems J | display-authors = 6 | title = Self-assembly of a nanoscale DNA box with a controllable lid | journal = Nature | volume = 459 | issue = 7243 | pages = 73–76 | date = May 2009 | pmid = 19424153 | doi = 10.1038/nature07971 | hdl-access = free | s2cid = 4430815 | bibcode = 2009Natur.459...73A | hdl = 11858/00-001M-0000-0010-9363-9 }}</ref><!--
--><ref>DNA boxes: {{cite journal | vauthors = Ke Y, Sharma J, Liu M, Jahn K, Liu Y, Yan H | title = Scaffolded DNA origami of a DNA tetrahedron molecular container | journal = Nano Letters | volume = 9 | issue = 6 | pages = 2445–2447 | date = June 2009 | pmid = 19419184 | doi = 10.1021/nl901165f | bibcode = 2009NanoL...9.2445K }}</ref>

{{Anchor|Nanoarchitecture}}

===Templated assembly===
Nucleic acid structures can be made to incorporate molecules other than nucleic acids, sometimes called heteroelements, including proteins, metallic nanoparticles, [[quantum dot]]s, [[Amine|amines]],<ref>{{Cite journal |last1=Zaborova |first1=O. V. |last2=Voinova |first2=A. D. |last3=Shmykov |first3=B. D. |last4=Sergeyev |first4=V. G. |title=Solid Lipid Nanoparticles for the Nucleic Acid Encapsulation |url=https://link.springer.com/10.1134/S2079978021030055 |journal=Reviews and Advances in Chemistry |year=2021 |language=en |volume=11 |issue=3–4 |pages=178–188 |doi=10.1134/S2079978021030055 |s2cid=246946068 |issn=2634-8276}}</ref> and [[fullerene]]s.  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.<ref name="ShihYanChallenges" /><!--
--><ref name="ChemicalReview">Overview: {{cite journal | vauthors = Endo M, Sugiyama H | title = Chemical approaches to DNA nanotechnology | journal = ChemBioChem | volume = 10 | issue = 15 | pages = 2420–2443 | date = October 2009 | pmid = 19714700 | doi = 10.1002/cbic.200900286 | s2cid = 205554125 }}</ref>
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 nanoparticle]]s on a DX-based array,<!--
--><ref>Nanoarchitecture: {{cite journal | vauthors = Zheng J, Constantinou PE, Micheel C, Alivisatos AP, Kiehl RA, Seeman NC | title = Two-dimensional nanoparticle arrays show the organizational power of robust DNA motifs | journal = Nano Letters | volume = 6 | issue = 7 | pages = 1502–1504 | date = July 2006 | pmid = 16834438 | pmc = 3465979 | doi = 10.1021/nl060994c | bibcode = 2006NanoL...6.1502Z }}</ref>
and to arrange [[streptavidin]] protein molecules into specific patterns on a DX array.<!--
--><ref>Nanoarchitecture: {{cite journal | vauthors = Park SH, Pistol C, Ahn SJ, Reif JH, Lebeck AR, Dwyer C, LaBean TH | title = Finite-size, fully addressable DNA tile lattices formed by hierarchical assembly procedures | journal = Angewandte Chemie | volume = 45 | issue = 5 | pages = 735–739 | date = January 2006 | pmid = 16374784 | doi = 10.1002/ange.200690141 | bibcode = 2006AngCh.118.6759P | doi-access = free }}</ref>
A non-covalent hosting scheme using [[Peter Dervan|Dervan]] polyamides on a DX array was used to arrange streptavidin proteins in a specific pattern on a DX array.<!--
--><ref>Nanoarchitecture: {{cite journal | vauthors = Cohen JD, Sadowski JP, Dervan PB | title = Addressing single molecules on DNA nanostructures | journal = Angewandte Chemie | volume = 46 | issue = 42 | pages = 7956–7959 | date = 22 October 2007 | pmid = 17763481 | doi = 10.1002/anie.200702767 | url = https://authors.library.caltech.edu/66743/ }}</ref> Carbon nanotubes have been hosted on DNA arrays in a pattern allowing the assembly to act as a [[Molecular scale electronics|molecular electronic]] device, a [[carbon nanotube field-effect transistor]].<!--
--><ref>Nanoarchitecture: {{cite journal | vauthors = Maune HT, Han SP, Barish RD, Bockrath M, Goddard WA, Rothemund PW, Winfree E | title = Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates | journal = Nature Nanotechnology | volume = 5 | issue = 1 | pages = 61–66 | date = January 2010 | pmid = 19898497 | doi = 10.1038/nnano.2009.311 | bibcode = 2010NatNa...5...61M | url = https://resolver.caltech.edu/CaltechAUTHORS:20100305-145736806 }}</ref>  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,<ref>Nanoarchitecture: {{cite journal | vauthors = Liu J, Geng Y, Pound E, Gyawali S, Ashton JR, Hickey J, Woolley AT, Harb JN | display-authors = 6 | title = Metallization of branched DNA origami for nanoelectronic circuit fabrication | journal = ACS Nano | volume = 5 | issue = 3 | pages = 2240–2247 | date = March 2011 | pmid = 21323323 | doi = 10.1021/nn1035075 }}</ref> and schemes for using nucleic acid nanostructures as [[lithography]] masks, transferring their pattern into a solid surface.<ref>Nanoarchitecture: {{cite journal | vauthors = Deng Z, Mao C | title = Molecular lithography with DNA nanostructures | journal = Angewandte Chemie | volume = 43 | issue = 31 | pages = 4068–4070 | date = August 2004 | pmid = 15300697 | doi = 10.1002/anie.200460257 }}</ref>

==Dynamic DNA nanotechnology==
[[File:Strand displacement.svg|thumb|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.<ref name="ShihYanChallenges" /><ref name="nanomachines" />

===Nanomechanical devices===
{{Main|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.<ref name="DDNreview" /><ref name="nanomachines" />  The earliest such device made use of the transition between the [[B-DNA]] and [[Z-DNA]] forms to respond to a change in [[Buffer solution|buffer]] conditions by undergoing a twisting motion.<!--
--><ref>DNA machines: {{cite journal | vauthors = Mao C, Sun W, Shen Z, Seeman NC | title = A nanomechanical device based on the B-Z transition of DNA | journal = Nature | volume = 397 | issue = 6715 | pages = 144–146 | date = January 1999 | pmid = 9923675 | doi = 10.1038/16437 | s2cid = 4406177 | bibcode = 1999Natur.397..144M }}</ref>
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,<!--
--><ref>DNA machines: {{cite journal | vauthors = Yurke B, Turberfield AJ, Mills AP, Simmel FC, Neumann JL | title = A DNA-fuelled molecular machine made of DNA | journal = Nature | volume = 406 | issue = 6796 | pages = 605–608 | date = August 2000 | pmid = 10949296 | doi = 10.1038/35020524 | s2cid = 2064216 | bibcode = 2000Natur.406..605Y }}</ref> 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,<!--
--><ref>DNA machines: {{cite journal | vauthors = Yan H, Zhang X, Shen Z, Seeman NC | title = A robust DNA mechanical device controlled by hybridization topology | journal = Nature | volume = 415 | issue = 6867 | pages = 62–65 | date = January 2002 | pmid = 11780115 | doi = 10.1038/415062a | s2cid = 52801697 | bibcode = 2002Natur.415...62Y }}</ref> and a two-dimensional array that could dynamically expand and contract in response to control strands.<ref>DNA machines: {{cite journal | vauthors = Feng L, Park SH, Reif JH, Yan H | title = A two-state DNA lattice switched by DNA nanoactuator | journal = Angewandte Chemie | volume = 42 | issue = 36 | pages = 4342–4346 | date = September 2003 | pmid = 14502706 | doi = 10.1002/ange.200351818 | bibcode = 2003AngCh.115.4478F }}</ref>  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.<ref name="AndersenBox" /><ref>DNA machines: {{cite journal | vauthors = Goodman RP, Heilemann M, Doose S, Erben CM, Kapanidis AN, Turberfield AJ | title = Reconfigurable, braced, three-dimensional DNA nanostructures | journal = Nature Nanotechnology | volume = 3 | issue = 2 | pages = 93–96 | date = February 2008 | pmid = 18654468 | doi = 10.1038/nnano.2008.3 | bibcode = 2008NatNa...3...93G }}</ref><ref name="DouglasRobot">Applications: {{cite journal | vauthors = Douglas SM, Bachelet I, Church GM | title = A logic-gated nanorobot for targeted transport of molecular payloads | journal = Science | volume = 335 | issue = 6070 | pages = 831–834 | date = February 2012 | pmid = 22344439 | doi = 10.1126/science.1214081 | s2cid = 9866509 | bibcode = 2012Sci...335..831D }}</ref> 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.<ref>{{Cite journal |last1=Centola |first1=Mathias |last2=Poppleton |first2=Erik |last3=Ray |first3=Sujay |last4=Centola |first4=Martin |last5=Welty |first5=Robb |last6=Valero |first6=Julián |last7=Walter |first7=Nils G. |last8=Šulc |first8=Petr |last9=Famulok |first9=Michael |date=2023-10-19 |title=A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower |url=https://www.nature.com/articles/s41565-023-01516-x |journal=Nature Nanotechnology |language=en |pages=1–11 |doi=10.1038/s41565-023-01516-x |issn=1748-3395|doi-access=free |pmid=37857824 |pmc=10873200 }}</ref>

[[DNA walker]]s are a class of nucleic acid nanomachines that exhibit directional motion along a linear track. A large number of schemes have been demonstrated.<ref name="nanomachines" /> One strategy is to control the motion of the walker along the track using control strands that need to be manually added in sequence.<ref>DNA walkers: {{cite journal | vauthors = Shin JS, Pierce NA | title = A synthetic DNA walker for molecular transport | journal = Journal of the American Chemical Society | volume = 126 | issue = 35 | pages = 10834–10835 | date = September 2004 | pmid = 15339155 | doi = 10.1021/ja047543j | url = https://resolver.caltech.edu/CaltechAUTHORS:20170224-152823096 }}</ref><ref>DNA walkers: {{cite journal |doi=10.1021/nl049527q |title=A precisely controlled DNA biped walking device |date=July 2004 | vauthors = Sherman WB, Seeman NC |journal=Nano Letters |volume=4 |issue=7 |pages=1203–1207|bibcode= 2004NanoL...4.1203S}}</ref> It is also possible to control individual steps of a DNA walker by irradiation with light of different wavelengths.<ref>DNA walkers: {{cite journal | vauthors = Škugor M, Valero J, Murayama K, Centola M, Asanuma H, Famulok M | title = Orthogonally Photocontrolled Non-Autonomous DNA Walker | journal = Angewandte Chemie | volume = 58 | issue = 21 | pages = 6948–6951 | date = May 2019 | pmid = 30897257 | doi = 10.1002/anie.201901272 | s2cid = 85446523 }}</ref> Another approach is to make use of [[restriction enzyme]]s or [[deoxyribozyme]]s to cleave the strands and cause the walker to move forward, which has the advantage of running autonomously.<ref>DNA walkers: {{cite journal | vauthors = Tian Y, He Y, Chen Y, Yin P, Mao C | title = A DNAzyme that walks processively and autonomously along a one-dimensional track | journal = Angewandte Chemie | volume = 44 | issue = 28 | pages = 4355–4358 | date = July 2005 | pmid = 15945114 | doi = 10.1002/ange.200500703 | bibcode = 2005AngCh.117.4429T }}</ref><ref>DNA walkers: {{cite journal | vauthors = Bath J, Green SJ, Turberfield AJ | title = A free-running DNA motor powered by a nicking enzyme | journal = Angewandte Chemie | volume = 44 | issue = 28 | pages = 4358–4361 | date = July 2005 | pmid = 15959864 | doi = 10.1002/anie.200501262 }}</ref> A later system could walk upon a two-dimensional surface rather than a linear track, and demonstrated the ability to selectively pick up and move molecular cargo.<ref>Functional DNA walkers: {{cite journal | vauthors = Lund K, Manzo AJ, Dabby N, Michelotti N, Johnson-Buck A, Nangreave J, Taylor S, Pei R, Stojanovic MN, Walter NG, Winfree E, Yan H | display-authors = 6 | title = Molecular robots guided by prescriptive landscapes | journal = Nature | volume = 465 | issue = 7295 | pages = 206–210 | date = May 2010 | pmid = 20463735 | pmc = 2907518 | doi = 10.1038/nature09012 | bibcode = 2010Natur.465..206L }}</ref> In 2018, a [[Catenation|catenated]] DNA that uses rolling circle transcription by an attached [[T7 RNA polymerase]] was shown to walk along a DNA-path, guided by the generated RNA strand.<ref>Functional DNA walkers: {{cite journal | vauthors = Valero J, Pal N, Dhakal S, Walter NG, Famulok M | title = A bio-hybrid DNA rotor-stator nanoengine that moves along predefined tracks | journal = Nature Nanotechnology | volume = 13 | issue = 6 | pages = 496–503 | date = June 2018 | pmid = 29632399 | pmc = 5994166 | doi = 10.1038/s41565-018-0109-z | bibcode = 2018NatNa..13..496V }}</ref> Additionally, a linear walker has been demonstrated that performs [[Nucleic acid templated chemistry|DNA-templated synthesis]] as the walker advances along the track, allowing autonomous multistep chemical synthesis directed by the walker.<ref>Functional DNA walkers: {{cite journal | vauthors = He Y, Liu DR | title = Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker | journal = Nature Nanotechnology | volume = 5 | issue = 11 | pages = 778–782 | date = November 2010 | pmid = 20935654 | pmc = 2974042 | doi = 10.1038/nnano.2010.190 | bibcode = 2010NatNa...5..778H }}</ref> The synthetic DNA walkers' function is similar to that of the proteins dynein and kinesin.<ref>{{cite journal | vauthors = Pan J, Li F, Cha TG, Chen H, Choi JH | title = Recent progress on DNA based walkers | journal = Current Opinion in Biotechnology | volume = 34 | pages = 56–64 | date = August 2015 | pmid = 25498478 | doi = 10.1016/j.copbio.2014.11.017 }}</ref>

===Strand displacement cascades===
Cascades of strand displacement reactions can be used for either computational or structural purposes.  An individual strand displacement reaction involves revealing a new sequence in response to the presence of some initiator strand.  Many such reactions can be linked into a [[Biochemical cascade|cascade]] where the newly revealed output sequence of one reaction can initiate another strand displacement reaction elsewhere.  This in turn allows for the construction of chemical reaction networks with many components, exhibiting complex computational and information processing abilities.  These cascades are made energetically favorable through the formation of new base pairs, and the [[entropy]] gain from disassembly reactions. Strand displacement cascades allow isothermal operation of the assembly or computational process, in contrast to traditional nucleic acid assembly's requirement for a thermal annealing step, where the temperature is raised and then slowly lowered to ensure proper formation of the desired structure. They can also support [[Catalysis|catalytic]] function of the initiator species, where less than one equivalent of the initiator can cause the reaction to go to completion.<ref name="DDNreview" /><ref name="YinDynamic" />

Strand displacement complexes can be used to make [[molecular logic gate]]s capable of complex computation.<ref>Fuzzy and Boolean logic gates based on DNA: {{cite journal | vauthors = Zadegan RM, Jepsen MD, Hildebrandt LL, Birkedal V, Kjems J | title = Construction of a fuzzy and Boolean logic gates based on DNA | journal = Small | volume = 11 | issue = 15 | pages = 1811–1817 | date = April 2015 | pmid = 25565140 | doi = 10.1002/smll.201402755 }}</ref>  Unlike traditional electronic computers, which use [[electric current]] as inputs and outputs, molecular computers use the concentrations of specific chemical species as signals.  In the case of nucleic acid strand displacement circuits, the signal is the presence of nucleic acid strands that are released or consumed by binding and unbinding events to other strands in displacement complexes.  This approach has been used to make [[logic gates]] such as AND, OR, and NOT gates.<ref>Strand displacement cascades: {{cite journal | vauthors = Seelig G, Soloveichik D, Zhang DY, Winfree E | title = Enzyme-free nucleic acid logic circuits | journal = Science | volume = 314 | issue = 5805 | pages = 1585–1588 | date = December 2006 | pmid = 17158324 | doi = 10.1126/science.1132493 | s2cid = 10966324 | bibcode = 2006Sci...314.1585S | url = https://resolver.caltech.edu/CaltechAUTHORS:20110309-104200565 }}</ref>  More recently, a four-bit circuit was demonstrated that can compute the [[square root]] of the integers 0–15, using a system of gates containing 130 DNA strands.<ref>Strand displacement cascades: {{cite journal | vauthors = Qian L, Winfree E | title = Scaling up digital circuit computation with DNA strand displacement cascades | journal = Science | volume = 332 | issue = 6034 | pages = 1196–1201 | date = June 2011 | pmid = 21636773 | doi = 10.1126/science.1200520 | s2cid = 10053541 | bibcode = 2011Sci...332.1196Q }}</ref>

Another use of strand displacement cascades is to make dynamically assembled structures.  These use a [[Stem-loop|hairpin]] structure for the reactants, so that when the input strand binds, the newly revealed sequence is on the same molecule rather than disassembling.  This allows new opened hairpins to be added to a growing complex.  This approach has been used to make simple structures such as three- and four-arm junctions and [[dendrimer]]s.<ref name="YinDynamic" />

==Applications==
DNA nanotechnology provides one of the few ways to form designed, complex structures with precise control over nanoscale features.  The field is beginning to see application to solve [[basic science]] problems in [[structural biology]] and [[biophysics]].  The earliest such application envisaged for the field, and one still in development, is in [[crystallography]], where molecules that are difficult to crystallize in isolation could be arranged within a three-dimensional nucleic acid lattice, allowing determination of their structure. Another application is the use of [[DNA origami]] rods to replace [[liquid crystals]] in [[residual dipolar coupling]] experiments in [[Nuclear magnetic resonance spectroscopy of proteins|protein NMR spectroscopy]]; using DNA origami is advantageous because, unlike liquid crystals, they are tolerant of the detergents needed to suspend [[membrane protein]]s in solution.  [[#Nanomechanical devices|DNA walkers]] have been used as nanoscale assembly lines to move nanoparticles and direct [[chemical synthesis]].  Further, DNA origami structures have aided in the biophysical studies of [[enzyme]] function and [[protein folding]].<ref name="SDNreview" /><ref name="growsup" />

DNA nanotechnology is moving toward potential real-world applications. The ability of nucleic acid arrays to arrange other molecules indicates its potential applications in molecular scale electronics.  The assembly of a nucleic acid structure could be used to template the assembly of molecular electronic elements such as [[molecular wire]]s, providing a method for nanometer-scale control of the placement and overall architecture of the device analogous to a molecular [[breadboard]].<ref name="SDNreview" /><ref name="ShihYanChallenges" />  DNA nanotechnology has been compared to the concept of [[programmable matter]] because of the coupling of computation to its material properties.<ref>Applications: {{cite book| vauthors = Rietman EA |title=Molecular engineering of nanosystems|year=2001|publisher=Springer|isbn=978-0-387-98988-4|pages=209–212|url=https://books.google.com/books?id=ga2DKYCm7xMC&pg=PA209|access-date=17 April 2011}}</ref>

In a study conducted by a group of scientists from [[Interdisciplinary Nanoscience Center|iNANO]] and [[Aarhus University#Research centres|CDNA centers]] in [[Aarhus University]], researchers were able to construct a small multi-switchable 3D DNA Box Origami. The proposed nanoparticle was characterized by [[atomic force microscopy]] (AFM), [[transmission electron microscopy]] (TEM) and [[Förster resonance energy transfer]] (FRET). The constructed box was shown to have a unique reclosing mechanism, which enabled it to repeatedly open and close in response to a unique set of DNA or RNA keys. The authors proposed that this "DNA device can potentially be used for a broad range of applications such as controlling the function of single molecules, controlled drug delivery, and molecular computing."<ref>{{cite journal | vauthors = Zadegan RM, Jepsen MD, Thomsen KE, Okholm AH, Schaffert DH, Andersen ES, Birkedal V, Kjems J | display-authors = 6 | title = Construction of a 4 zeptoliters switchable 3D DNA box origami | journal = ACS Nano | volume = 6 | issue = 11 | pages = 10050–10053 | date = November 2012 | pmid = 23030709 | doi = 10.1021/nn303767b }}</ref>

There are potential applications for DNA nanotechnology in nanomedicine, making use of its ability to perform computation in a [[Biocompatibility|biocompatible]] format to make "smart drugs" for [[targeted drug delivery]], as well as for [[diagnostic]] applications.  One such system being investigated uses a hollow DNA box containing proteins that induce [[apoptosis]], or cell death, that will only open when in proximity to a [[cancer cell]].<ref name="growsup" /><ref>Applications: {{cite journal | vauthors = Jungmann R, Renner S, Simmel FC | title = From DNA nanotechnology to synthetic biology | journal = HFSP Journal | volume = 2 | issue = 2 | pages = 99–109 | date = April 2008 | pmid = 19404476 | pmc = 2645571 | doi = 10.2976/1.2896331 }}</ref>  There has additionally been interest in expressing these artificial structures in engineered living bacterial cells, most likely using the [[Transcription (genetics)|transcribed]] RNA for the assembly, although it is unknown whether these complex structures are able to efficiently fold or assemble in the cell's [[cytoplasm]].  If successful, this could enable [[directed evolution]] of nucleic acid nanostructures.<ref name="ShihYanChallenges" />  
Scientists at [[Oxford University]] reported the self-assembly of four short strands of synthetic DNA into a cage which can enter cells and survive for at least 48 hours.  The fluorescently labeled DNA [[Tetrahedron|tetrahedra]] were found to remain intact in the laboratory cultured human [[kidney]] cells despite the attack by cellular [[enzymes]] after two days.  This experiment showed the potential of drug delivery inside the living cells using the DNA ‘cage’.<ref>{{cite web|url=http://www.fiercedrugdelivery.com/story/dna-cages-can-unleash-meds-inside-cells/2011-07-05|title=DNA cages can unleash meds inside cells|author=Lovy, Howard|publisher=fiercedrugdelivery.com|date=5 July 2011|access-date=22 September 2013}}{{Dead link|date=January 2024 |bot=InternetArchiveBot |fix-attempted=yes }}</ref><ref>{{cite journal | vauthors = Walsh AS, Yin H, Erben CM, Wood MJ, Turberfield AJ | title = DNA cage delivery to mammalian cells | journal = ACS Nano | volume = 5 | issue = 7 | pages = 5427–5432 | date = July 2011 | pmid = 21696187 | doi = 10.1021/nn2005574 }}</ref>  A DNA [[tetrahedron]] was used to deliver [[RNA Interference]] (RNAi) in a mouse model, reported a team of researchers in [[MIT]].  Delivery of the interfering RNA for treatment has showed some success using [[polymer]] or [[lipid]], but there are limits of safety and imprecise targeting, in addition to short shelf life in the blood stream.  The DNA nanostructure created by the team consists of six strands of DNA to form a tetrahedron, with one strand of RNA affixed to each of the six edges.  The tetrahedron is further equipped with targeting protein, three [[folate]] molecules, which lead the DNA nanoparticles to the abundant [[folate receptor]]s found on some tumors.  The result showed that the gene expression targeted by the RNAi, [[luciferase]], dropped by more than half.  This study shows promise in using DNA nanotechnology as an effective tool to deliver treatment using the emerging RNA Interference technology.<ref>{{cite web|url=http://web.mit.edu/newsoffice/2012/rna-interference-lightweight-nanoparticle-0604.html|title=Researchers achieve RNA interference, in a lighter package|author=Trafton, Anne|publisher=MIT News|date=4 June 2012|access-date=22 September 2013}}</ref><ref>{{cite journal | vauthors = Lee H, Lytton-Jean AK, Chen Y, Love KT, Park AI, Karagiannis ED, Sehgal A, Querbes W, Zurenko CS, Jayaraman M, Peng CG, Charisse K, Borodovsky A, Manoharan M, Donahoe JS, Truelove J, Nahrendorf M, Langer R, Anderson DG | display-authors = 6 | title = Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery | journal = Nature Nanotechnology | volume = 7 | issue = 6 | pages = 389–393 | date = June 2012 | pmid = 22659608 | pmc = 3898745 | doi = 10.1038/NNANO.2012.73 | bibcode = 2012NatNa...7..389L }}</ref> The DNA tetrahedron was also used in an effort to overcome the phenomena [[multidrug resistance]]. [[Doxorubicin]] (DOX) was conjugated with the tetrahedron and was loaded into MCF-7 breast cancer cells that contained the [[P-glycoprotein]] drug efflux pump. The results of the experiment showed the DOX was not being pumped out and apoptosis of the cancer cells was achieved. The tetrahedron without DOX was loaded into cells to test its biocompatibility, and the structure showed no cytotoxicity itself.<ref>{{cite journal | vauthors = Kim KR, Kim DR, Lee T, Yhee JY, Kim BS, Kwon IC, Ahn DR | title = Drug delivery by a self-assembled DNA tetrahedron for overcoming drug resistance in breast cancer cells | journal = Chemical Communications | volume = 49 | issue = 20 | pages = 2010–2012 | date = March 2013 | pmid = 23380739 | doi = 10.1039/c3cc38693g }}</ref> The DNA tetrahedron was also used as barcode for profiling the subcellular expression and distribution of proteins in cells for diagnostic purposes. The tetrahedral-nanostructured showed enhanced signal due to higher labeling efficiency and stability.<ref>{{cite journal | vauthors = Sundah NR, Ho NR, Lim GS, Natalia A, Ding X, Liu Y, Seet JE, Chan CW, Loh TP, Shao H | display-authors = 6 | title = Barcoded DNA nanostructures for the multiplexed profiling of subcellular protein distribution | journal = Nature Biomedical Engineering | volume = 3 | issue = 9 | pages = 684–694 | date = September 2019 | pmid = 31285580 | doi = 10.1038/s41551-019-0417-0 | s2cid = 195825879 }}</ref>

Applications for DNA nanotechnology in nanomedicine also focus on mimicking the structure and function of naturally occurring [[membrane proteins]] with designed DNA nanostructures. In 2012, Langecker ''et al.''<ref name="LangeckerDNAchannel">DNA ion channels: {{cite journal | vauthors = Langecker M, Arnaut V, Martin TG, List J, Renner S, Mayer M, Dietz H, Simmel FC | display-authors = 6 | title = Synthetic lipid membrane channels formed by designed DNA nanostructures | journal = Science | volume = 338 | issue = 6109 | pages = 932–936 | date = November 2012 | pmid = 23161995 | pmc = 3716461 | doi = 10.1126/science.1225624 | bibcode = 2012Sci...338..932L }}</ref> introduced a pore-shaped DNA origami structure that can self-insert into [[Lipid bilayer|lipid membranes]] via hydrophobic [[cholesterol]] modifications and induce ionic currents across the membrane. This first demonstration of a synthetic DNA ion channel was followed by a variety of pore-inducing designs ranging from a single [[Nucleic acid double helix|DNA duplex]],<ref name="GoepfrichDuplex">DNA ion channels: {{cite journal | vauthors = Göpfrich K, Li CY, Mames I, Bhamidimarri SP, Ricci M, Yoo J, Mames A, Ohmann A, Winterhalter M, Stulz E, Aksimentiev A, Keyser UF | display-authors = 6 | title = Ion Channels Made from a Single Membrane-Spanning DNA Duplex | journal = Nano Letters | volume = 16 | issue = 7 | pages = 4665–4669 | date = July 2016 | pmid = 27324157 | pmc = 4948918 | doi = 10.1021/acs.nanolett.6b02039 | bibcode = 2016NanoL..16.4665G }}</ref> to small tile-based structures,<ref name="Burns2013_1">DNA ion channels: {{cite journal | vauthors = Burns JR, Stulz E, Howorka S | title = Self-assembled DNA nanopores that span lipid bilayers | journal = Nano Letters | volume = 13 | issue = 6 | pages = 2351–2356 | date = June 2013 | pmid = 23611515 | doi = 10.1021/nl304147f | citeseerx = 10.1.1.659.7660 | bibcode = 2013NanoL..13.2351B }}</ref><ref name="Burns2013_2">DNA ion channels: {{cite journal | vauthors = Burns JR, Göpfrich K, Wood JW, Thacker VV, Stulz E, Keyser UF, Howorka S | title = Lipid-bilayer-spanning DNA nanopores with a bifunctional porphyrin anchor | journal = Angewandte Chemie | volume = 52 | issue = 46 | pages = 12069–12072 | date = November 2013 | pmid = 24014236 | pmc = 4016739 | doi = 10.1002/anie.201305765 }}</ref><ref name="Seifert2015">DNA ion channels: {{cite journal | vauthors = Seifert A, Göpfrich K, Burns JR, Fertig N, Keyser UF, Howorka S | title = Bilayer-spanning DNA nanopores with voltage-switching between open and closed state | journal = ACS Nano | volume = 9 | issue = 2 | pages = 1117–1126 | date = February 2015 | pmid = 25338165 | pmc = 4508203 | doi = 10.1021/nn5039433 }}</ref><ref name="Goepfrich2015">DNA ion channels: {{cite journal | vauthors = Göpfrich K, Zettl T, Meijering AE, Hernández-Ainsa S, Kocabey S, Liedl T, Keyser UF | title = DNA-Tile Structures Induce Ionic Currents through Lipid Membranes | journal = Nano Letters | volume = 15 | issue = 5 | pages = 3134–3138 | date = May 2015 | pmid = 25816075 | doi = 10.1021/acs.nanolett.5b00189 | bibcode = 2015NanoL..15.3134G | url = https://www.repository.cam.ac.uk/handle/1810/259995 }}</ref><ref name="Burns2016">DNA ion channels: {{cite journal | vauthors = Burns JR, Seifert A, Fertig N, Howorka S | title = A biomimetic DNA-based channel for the ligand-controlled transport of charged molecular cargo across a biological membrane | journal = Nature Nanotechnology | volume = 11 | issue = 2 | pages = 152–156 | date = February 2016 | pmid = 26751170 | doi = 10.1038/nnano.2015.279 | bibcode = 2016NatNa..11..152B | url = https://discovery.ucl.ac.uk/id/eprint/1474103/ }}</ref> and large DNA origami transmembrane [[Porin (protein)|porins]].<ref name="GoepfrichPorin">DNA ion channels: {{cite journal | vauthors = Göpfrich K, Li CY, Ricci M, Bhamidimarri SP, Yoo J, Gyenes B, Ohmann A, Winterhalter M, Aksimentiev A, Keyser UF | display-authors = 6 | title = Large-Conductance Transmembrane Porin Made from DNA Origami | journal = ACS Nano | volume = 10 | issue = 9 | pages = 8207–8214 | date = September 2016 | pmid = 27504755 | pmc = 5043419 | doi = 10.1021/acsnano.6b03759 }}</ref> Similar to naturally occurring protein [[ion channels]], this ensemble of synthetic DNA-made counterparts thereby spans multiple orders of magnitude in conductance. The study of the membrane-inserting single [[Nucleic acid double helix|DNA duplex]] showed that current must also flow on the DNA-lipid interface as no central channel lumen is present in the design that lets ions pass across the [[lipid bilayer]]. This indicated that the DNA-induced lipid pore has a [[Torus|toroidal]] shape, rather than cylindrical, as [[Lipid|lipid headgroups]] reorient to face towards the membrane-inserted part of the DNA.<ref name="GoepfrichDuplex" /> Researchers from the [[University of Cambridge]] and the [[University of Illinois at Urbana-Champaign]] then demonstrated that such a DNA-induced toroidal pore can facilitate rapid [[Scramblase|lipid flip-flop]] between the lipid bilayer leaflets. Utilizing this effect, they designed a synthetic DNA-built [[enzyme]] that flips lipids in biological membranes orders of magnitudes faster than naturally occurring proteins called [[scramblases]].<ref name="OhmannDNAscramblase">DNA scramblase: {{cite journal | vauthors = Ohmann A, Li CY, Maffeo C, Al Nahas K, Baumann KN, Göpfrich K, Yoo J, Keyser UF, Aksimentiev A | display-authors = 6 | title = A synthetic enzyme built from DNA flips 10<sup>7</sup> lipids per second in biological membranes | journal = Nature Communications | volume = 9 | issue = 1 | pages = 2426 | date = June 2018 | pmid = 29930243 | pmc = 6013447 | doi = 10.1038/s41467-018-04821-5 | bibcode = 2018NatCo...9.2426O }}</ref> This development highlights the potential of synthetic DNA nanostructures for personalized drugs and therapeutics.

==Design==
DNA nanostructures must be [[Rational design|rationally designed]] so that individual nucleic acid strands will assemble into the desired structures. This process usually begins with specification of a desired [[Nucleic acid tertiary structure|target structure]] or function. Then, the overall [[Nucleic acid secondary structure|secondary structure]] of the target complex is determined, specifying the arrangement of nucleic acid strands within the structure, and which portions of those strands should be bound to each other. The last step is the [[Nucleic acid primary structure|primary structure]] design, which is the specification of the actual base sequences of each nucleic acid strand.<ref name="Feldkamp">Design: {{cite journal | vauthors = Feldkamp U, Niemeyer CM | title = Rational design of DNA nanoarchitectures | journal = Angewandte Chemie | volume = 45 | issue = 12 | pages = 1856–1876 | date = March 2006 | pmid = 16470892 | doi = 10.1002/anie.200502358 }}</ref><ref name="Brenneman02" />

===Structural design===
The first step in designing a nucleic acid nanostructure is to decide how a given structure should be represented by a specific arrangement of nucleic acid strands. This design step determines the secondary structure, or the positions of the base pairs that hold the individual strands together in the desired shape.<ref name="Feldkamp" />  Several approaches have been demonstrated:

*Tile-based structures. This approach breaks the target structure into smaller units with strong binding between the strands contained in each unit, and weaker interactions between the units. It is often used to make periodic lattices, but can also be used to implement algorithmic self-assembly, making them a platform for [[DNA computing]]. This was the dominant design strategy used from the mid-1990s until the mid-2000s, when the DNA origami methodology was developed.<ref name="Feldkamp" /><ref>Overview: {{cite journal | vauthors = Lin C, Liu Y, Rinker S, Yan H | title = DNA tile based self-assembly: building complex nanoarchitectures | journal = ChemPhysChem | volume = 7 | issue = 8 | pages = 1641–1647 | date = August 2006 | pmid = 16832805 | doi = 10.1002/cphc.200600260 }}</ref>
* Folding structures. An alternative to the tile-based approach, folding approaches make the nanostructure from one long strand, which can either have a designed sequence that folds due to its interactions with itself, or it can be folded into the desired shape by using shorter, "staple" strands. This latter method is called [[DNA origami]], which allows forming nanoscale two- and three-dimensional shapes (see [[#Discrete structures|Discrete structures]] above).<ref name="ShihYanChallenges" /><!--
--><ref name="rothemundorigami">DNA origami: {{cite journal | vauthors = Rothemund PW | title = Folding DNA to create nanoscale shapes and patterns | journal = Nature | volume = 440 | issue = 7082 | pages = 297–302 | date = March 2006 | pmid = 16541064 | doi = 10.1038/nature04586 | s2cid = 4316391 | bibcode = 2006Natur.440..297R | url = https://rothemundlab.caltech.edu/downloads/folding_dna.pdf }}</ref>
* Dynamic assembly. This approach directly controls the [[Chemical kinetics|kinetics]] of DNA self-assembly, specifying all of the [[Reaction intermediate|intermediate]] steps in the [[reaction mechanism]] in addition to the final product.  This is done using starting materials which adopt a [[Stem-loop|hairpin]] structure; these then assemble into the final conformation in a [[Biochemical cascade|cascade]] reaction, in a specific order (see [[#Strand displacement cascades|Strand displacement cascades]] below).  This approach has the advantage of proceeding [[Isothermal process|isothermally]], at a constant temperature.  This is in contrast to the thermodynamic approaches, which require a thermal [[Annealing (biology)|annealing]] step where a temperature change is required to trigger the assembly and favor proper formation of the desired structure.<!--
--><ref name="ShihYanChallenges" /><ref name="YinDynamic">Kinetic assembly: {{cite journal | vauthors = Yin P, Choi HM, Calvert CR, Pierce NA | title = Programming biomolecular self-assembly pathways | journal = Nature | volume = 451 | issue = 7176 | pages = 318–322 | date = January 2008 | pmid = 18202654 | doi = 10.1038/nature06451 | s2cid = 4354536 | bibcode = 2008Natur.451..318Y | url = https://resolver.caltech.edu/CaltechAUTHORS:20170224-143742507 }}</ref>

===Sequence design===
{{Main|Nucleic acid design}}
After any of the above approaches are used to design the secondary structure of a target complex, an actual sequence of nucleotides that will form into the desired structure must be devised. Nucleic acid design is the process of assigning a specific nucleic acid base sequence to each of a structure's constituent strands so that they will associate into a desired conformation. Most methods have the goal of designing sequences so that the target structure has the lowest [[Gibbs free energy|energy]], and is thus the most thermodynamically favorable, while incorrectly assembled structures have higher energies and are thus disfavored. This is done either through simple, faster [[heuristic]] methods such as [[sequence symmetry minimization]], or by using a full [[Nearest-neighbor thermodynamic parameters|nearest-neighbor]] thermodynamic model, which is more accurate but slower and more computationally intensive. Geometric models are used to examine [[Nucleic acid tertiary structure|tertiary structure]] of the nanostructures and to ensure that the complexes are not overly [[Strain (chemistry)|strained]].<!--
--><ref name="Brenneman02">Design: {{cite journal |doi=10.1016/S0304-3975(02)00135-4 |title=Strand design for biomolecular computation |date=25 September 2002 | vauthors = Brenneman A, Condon A |journal=Theoretical Computer Science |volume=287 |pages=39–58|doi-access=free }}</ref><ref name="paradigms" />

Nucleic acid design has similar goals to [[protein design]]. In both, the sequence of monomers is designed to favor the desired target structure and to disfavor other structures. Nucleic acid design has the advantage of being much computationally easier than protein design, because the simple base pairing rules are sufficient to predict a structure's energetic favorability, and detailed information about the overall three-dimensional folding of the structure is not required. This allows the use of simple heuristic methods that yield experimentally robust designs. Nucleic acid structures are less versatile than proteins in their function because of proteins' increased ability to fold into complex structures, and the limited chemical diversity of the four [[nucleotide]]s as compared to the twenty [[proteinogenic amino acid]]s.<ref name="paradigms">Design: {{cite journal | vauthors = Dirks RM, Lin M, Winfree E, Pierce NA | title = Paradigms for computational nucleic acid design | journal = Nucleic Acids Research | volume = 32 | issue = 4 | pages = 1392–1403 | date = 15 February 2004 | pmid = 14990744 | pmc = 390280 | doi = 10.1093/nar/gkh291 }}</ref>

==Materials and methods==
[[File:DX formation gel.png|thumb|[[Gel electrophoresis]] methods, such as this [[electrophoretic mobility shift assay|formation assay]] on a DX complex, are used to ascertain whether the desired structures are forming properly.  Each vertical lane contains a series of bands, where each band is characteristic of a particular [[reaction intermediate]].]]

The sequences of the DNA strands making up a target structure are designed computationally, using [[molecular modeling]] and [[Nucleic acid thermodynamics|thermodynamic modeling]] software.<ref name="Brenneman02" /><ref name="paradigms" /> The nucleic acids themselves are then synthesized using standard [[oligonucleotide synthesis]] methods, usually automated in an [[Oligonucleotide synthesis|oligonucleotide synthesizer]], and strands of custom sequences are commercially available.<ref>Methods: {{Cite journal| vauthors = Ellington A, Pollard JD |title= Synthesis and Purification of Oligonucleotides| doi= 10.1002/0471142727.mb0211s42|journal= Current Protocols in Molecular Biology|pages= 2.11.1–2.11.25|date= 1 May 2001 |volume= 42|isbn= 978-0471142720 |pmid=  18265179|s2cid= 205152989}}</ref>  Strands can be purified by [[Denaturation (biochemistry)|denaturing]] [[gel electrophoresis]] if needed,<ref>Methods: {{Cite journal| vauthors = Ellington A, Pollard JD |title= Purification of Oligonucleotides Using Denaturing Polyacrylamide Gel Electrophoresis|doi= 10.1002/0471142727.mb0212s42 |journal= Current Protocols in Molecular Biology|pages= Unit2.12| date= 1 May 2001 |volume= 42|isbn= 978-0471142720 |pmid= 18265180|s2cid= 27187583}}</ref> and precise concentrations determined via any of several [[nucleic acid quantitation]] methods using [[Ultraviolet–visible spectroscopy|ultraviolet absorbance spectroscopy]].<ref>Methods: {{Cite book| vauthors = Gallagher SR, Desjardins P |doi= 10.1002/9780470089941.et0202s5 |chapter= Quantitation of nucleic acids and proteins |title= Current Protocols Essential Laboratory Techniques |date= 1 July 2011 |volume= 5 |isbn= 978-0470089934 |s2cid= 94329398 }}</ref>

The fully formed target structures can be verified using [[Native state|native]] gel electrophoresis, which gives size and shape information for the nucleic acid complexes.  An [[electrophoretic mobility shift assay]] can assess whether a structure incorporates all desired strands.<ref>Methods: {{Cite journal| vauthors = Chory J, Pollard JD |title= Separation of Small DNA Fragments by Conventional Gel Electrophoresis|doi= 10.1002/0471142727.mb0207s47 |journal= Current Protocols in Molecular Biology|pages= Unit2.7|date= 1 May 2001 |volume= 47|isbn= 978-0471142720 |pmid=  18265187|s2cid= 43406338}}</ref>  [[Fluorescent labeling]] and [[Förster resonance energy transfer]] (FRET) are sometimes used to characterize the structure of the complexes.<ref>Methods: {{Cite journal| vauthors = Walter NG |title= Probing RNA Structural Dynamics and Function by Fluorescence Resonance Energy Transfer (FRET) |doi= 10.1002/0471142700.nc1110s11 |journal= Current Protocols in Nucleic Acid Chemistry |pages= 11.10.1–11.10.23 |date= 1 February 2003|volume= 11 | isbn= 978-0471142706 |pmid=  18428904|s2cid= 9978415 }}</ref>

Nucleic acid structures can be directly imaged by [[atomic force microscopy]], which is well suited to extended two-dimensional structures, but less useful for discrete three-dimensional structures because of the microscope tip's interaction with the fragile nucleic acid structure; [[transmission electron microscopy]] and [[cryo-electron microscopy]] are often used in this case.  Extended three-dimensional lattices are analyzed by [[X-ray crystallography]].<ref>Methods: {{cite book | vauthors = Lin C, Ke Y, Chhabra R, Sharma J, Liu Y, Yan H | chapter = Synthesis and Characterization of Self-Assembled DNA Nanostructures | title = DNA Nanotechnology | volume = 749 | pages = 1–11 | year = 2011 | pmid = 21674361 | doi = 10.1007/978-1-61779-142-0_1 | isbn = 978-1-61779-141-3 | series = Methods in Molecular Biology | veditors = Zuccheri G, Samorì B }}</ref><ref>Methods: {{cite book| vauthors = Bloomfield VA, Crothers DM, Tinoco Jr I |title=Nucleic acids: structures, properties, and functions|year=2000|publisher=University Science Books|location=Sausalito, Calif|isbn=978-0-935702-49-1|pages=84–86, 396–407}}</ref>

== See also ==
{{Portal|Science|Technology}}
* [[International Society for Nanoscale Science, Computation, and Engineering]]
* [[Comparison of nucleic acid simulation software]]
* [[Molecular models of DNA]]
* [[Nanobiotechnology]]

== References ==
{{Reflist|30em}}

== Further reading ==
General:
{{refbegin|30em}}
* {{cite journal | vauthors = Seeman NC | title = Nanotechnology and the double helix | journal = Scientific American | volume = 290 | issue = 6 | pages = 64–75 | date = June 2004 | pmid = 15195395 | doi = 10.1038/scientificamerican0604-64 | bibcode = 2004SciAm.290f..64S }}—An article written for laypeople by the founder of the field
* {{cite journal | vauthors = Seeman NC | title = Structural DNA nanotechnology: growing along with Nano Letters | journal = Nano Letters | volume = 10 | issue = 6 | pages = 1971–1978 | date = June 2010 | pmid = 20486672 | pmc = 2901229 | doi = 10.1021/nl101262u | bibcode = 2010NanoL..10.1971S }}—A review of results in the period 2001–2010
* {{cite journal | vauthors = Seeman NC | title = Nanomaterials based on DNA | journal = Annual Review of Biochemistry | volume = 79 | pages = 65–87 | year = 2010 | pmid = 20222824 | pmc = 3454582 | doi = 10.1146/annurev-biochem-060308-102244 }}—A more comprehensive review including both old and new results in the field
* {{cite journal | vauthors = Service RF | title = DNA nanotechnology. DNA nanotechnology grows up | journal = Science | volume = 332 | issue = 6034 | pages = 1140–1, 1143 | date = June 2011 | pmid = 21636754 | doi = 10.1126/science.332.6034.1140 | bibcode = 2011Sci...332.1140S }} and {{cite journal | vauthors = Service RF | title = DNA nanotechnology. Next step: DNA robots? | journal = Science | volume = 332 | issue = 6034 | pages = 1142 | date = June 2011 | pmid = 21636755 | doi = 10.1126/science.332.6034.1142 }}.—A news article focusing on the history of the field and development of new applications
* {{cite journal | vauthors = Zadegan RM, Norton ML | title = Structural DNA nanotechnology: from design to applications | journal = International Journal of Molecular Sciences | volume = 13 | issue = 6 | pages = 7149–7162 | date = June 2012 | pmid = 22837684 | pmc = 3397516 | doi = 10.3390/ijms13067149 | doi-access = free }}—A very recent and comprehensive review in the field
{{refend}}
Specific subfields:

{{refbegin|30em}}
* {{cite journal | vauthors = Bath J, Turberfield AJ | title = DNA nanomachines | journal = Nature Nanotechnology | volume = 2 | issue = 5 | pages = 275–284 | date = May 2007 | pmid = 18654284 | doi = 10.1038/nnano.2007.104 | bibcode = 2007NatNa...2..275B }}—A review of nucleic acid nanomechanical devices
* {{cite journal | vauthors = Feldkamp U, Niemeyer CM | title = Rational design of DNA nanoarchitectures | journal = Angewandte Chemie | volume = 45 | issue = 12 | pages = 1856–1876 | date = March 2006 | pmid = 16470892 | doi = 10.1002/anie.200502358 }}—A review coming from the viewpoint of secondary structure design
* {{cite journal | vauthors = Lin C, Liu Y, Rinker S, Yan H | title = DNA tile based self-assembly: building complex nanoarchitectures | journal = ChemPhysChem | volume = 7 | issue = 8 | pages = 1641–1647 | date = August 2006 | pmid = 16832805 | doi = 10.1002/cphc.200600260 }}—A minireview specifically focusing on tile-based assembly
* {{cite journal | vauthors = Zhang DY, Seelig G | title = Dynamic DNA nanotechnology using strand-displacement reactions | journal = Nature Chemistry | volume = 3 | issue = 2 | pages = 103–113 | date = February 2011 | pmid = 21258382 | doi = 10.1038/nchem.957 | bibcode = 2011NatCh...3..103Z }}—A review of DNA systems making use of strand displacement mechanisms
{{refend}}

== External links ==
{{Commons category}}
* [https://www.youtube.com/watch?v=ITtGJUGXFKc What is Bionanotechnology?]—a video introduction to DNA nanotechnology

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[[Category:DNA nanotechnology| ]]