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出门在外也不愁From Wikipedia, the free encyclopedia
DNA nanotechnology involves the creation of artificial,
nanostructures out of , such as this
tetrahedron. Each edge of the tetrahedron is a 20
DNA , and each vertex is a three-arm junction. The 4 DNA strands that form the 4 tetrahedral faces are color-coded.
DNA nanotechnology is the design and manufacture of artificial
structures for technological uses. In this field, nucleic acids are used as non-biological engineering materials for
rather than as the carriers of genetic information in . Researchers in the field have created static structures such as two- and three-dimensional , nanotubes, , and arbitrary shapes, as well as functional devices such as
and . The field is beginning to be used as a tool to solve
problems in
and , including applications in
for protein structure determination. Potential applications in
are also being investigated.
The conceptual foundation for DNA nanotechnology was first laid out by
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
rules, which cause only portions of strands with
to bind together to form strong, rigid
structures. This allows for the
that will selectively assemble to form complex target structures with precisely controlled
features. A number of assembly methods are used to make these structures, including tile-based structures that assemble from smaller structures, folding structures using the
method, and dynamically reconfigurable structures using strand displacement techniques. While the field's name specifically references , 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.
These four strands associate into a DNA four-arm junction because this structure maximizes the number of correct , with
matched to
matched to . See
for a more realistic model of the four-arm junction showing its .
This double-crossover (DX)
consists of five
single strands that form two
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.
is often defined as the study of materials and devices with features on a scale below 100 . DNA nanotechnology, specifically, is an example of
, in which molecular components spontaneously organize in the particular form of these structures is induced by the physical and chemical properties of the components selected by the designers. 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
rules which are well understood, and form the specific nanoscale structure of the . These qualities make the assembly of nucleic acid structures easy to control through . This property is absent in other materials used in nanotechnology, including , for which
is very difficult, and , which lack the capability for specific assembly on their own.
of a nucleic acid molecule consists of a sequence of
distinguished by which
they contain. In DNA, the four bases present are
(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 , meaning that they form matching sequences of base pairs, with A only binding to T, and C only to G. Because the formation of correctly matched base pairs is , 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. While
is the dominant material used, structures incorporating other nucleic acids such as
(PNA) have also been constructed.
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,
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.
The complexes constructed in structural DNA nanotechnology use topologically branched nucleic acid structures containing junctions. (In contrast, most biological DNA exists as an unbranched .) 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 , each arm in the artificial immobile four-arm junction has a different , 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) , which contains two parallel double helical domains with individual strands crossing between the domains at two crossover points. Each crossover point is itself topologically a four-arm junction, but is constrained to a single orientation, as opposed to the flexible single four-arm junction, providing a rigidity that makes the DX motif suitable as a structural building block for larger DNA complexes.
Dynamic DNA nanotechnology uses a mechanism called
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
of a double-stranded complex, and then displaces one of the strands bound in the original complex through a
process. The overall effect is that one of the strands in the complex is replaced with another one. In addition, reconfigurable structures and devices can be made using functional nucleic acids such as
and , which are capable of performing chemical reactions, and , which can bind to specific proteins or small molecules.
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
has a robust, defined three-dimensional geometry that makes it possible to predict and design the structures of more complicated nucleic acid complexes. Many such structures have been created, including two- and three-dimensional structures, and periodic, aperiodic, and discrete structures.
The assembly of a DX array. Left, schematic diagram. Each bar represents a double-helical domain of , with the shapes representing
. The DX complex at top will combine with other DX complexes into the two-dimensional array shown at bottom. Right, an
of the assembled array. The individual DX tiles are clearly visible within the assembled structure. The field is 150  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.
An example of an aperiodic two-dimensional lattice that assembles into a fractal pattern. Left, the
fractal. Right, DNA arrays that display a representation of the Sierpinski gasket on their surfaces
Small nucleic acid complexes can be equipped with
and combined into larger two-dimensional periodic lattices containing a specific
pattern of the individual molecular tiles. 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. Two-dimensional arrays have been made from other motifs as well, including the
lattice, and various DX-based arrays making use of a double-cohesion scheme. 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. The DX tiles can have their sticky end sequences chosen so that they act as , allowing them to perform computation. A DX array whose assembly encodes an
operation h this allows the DNA array to implement a
that generates a
known as the . The third image at right shows this type of array. Another system has the function of a binary , displaying a representation of increasing binary numbers as it grows. These results show that computation can be incorporated into the assembly of DNA arrays.
DX arrays have been made to form hollow nanotubes 4–20  in diameter, essentially two-dimensional lattices which curve back upon themselves. These DNA nanotubes are somewhat similar in size and shape to , 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. 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 .
The creation of three-dimensional lattices out 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 , a balance between tension and compression forces, was finally reported in 2009.
Researchers have synthesized a number of three-dimensional DNA complexes that each have the connectivity of a , such as a
or , meaning that the DNA duplexes trace the
of a polyhedron with a DNA junction at each vertex. The earliest demonstrations of DNA polyhedra were very work-intensive, requiring multiple
steps to create
polyhedra. 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, and a tetrahedron that can be produced from four DNA strands in a single step, pictured at the top of this article.
Nanostructures of arbitrary, non-regular shapes are usually made using the
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
is predetermined by the scaffold strand sequence, and not requiring high strand purity and accurate , as most other DNA nanotechnology methods do. DNA origami was first demonstrated for two-dimensional shapes, such as a
and a coarse map of the Western Hemisphere. Solid three-dimensional structures can be made by using parallel DNA helices arranged in a honeycomb pattern, 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 .
Nucleic acid structures can be made to incorporate molecules other than nucleic acids, sometimes called heteroelements, including proteins, metallic nanoparticles, , and . 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. Many of these schemes use a covalent attachment scheme, using oligonucleotides with
functional groups as a chemical handle to bind the heteroelements. This covalent binding scheme has been used to arrange
on a DX-based array, and to arrange
protein molecules into specific patterns on a DX array. A non-covalent hosting scheme using
polyamides on a DX array was used to arrange streptavidin proteins in a specific pattern on a DX array. Carbon nanotubes have been hosted on DNA arrays in a pattern allowing the assembly to act as a
device, a . 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, and schemes for using nucleic acid nanostructures as
masks, transferring their pattern into a solid surface.
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
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 .
Dynamic DNA nanotechnology focuses on creating 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.
Main article:
DNA complexes have been made that change their conformation upon some stimulus, making them one form of . 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. The earliest such device made use of the transition between the
forms to respond to a change in
conditions by undergoing a twisting motion. This reliance on buffer conditions, however, 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, a device that could switch from a paranemic-crossover (PX) conformation to a double-junction (JX2) conformation, undergoing rotational motion in the process, and a two-dimensional array that could dynamically expand and contract in response to control strands. 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.
are a class of nucleic acid nanomachines that exhibit directional motion along a linear track. A large number of schemes have been demonstrated. One strategy is to control the motion of the walker along the track using control strands that need to be manually added in sequence. Another approach is to make use of
to cleave the strands and cause the walker to move forward, which has the advantage of running autonomously. 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. Additionally, a linear walker has been demonstrated that performs
as the walker advances along the track, allowing autonomous multistep chemical synthesis directed by the walker.
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
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
gain from disassembly reactions. Strand displacement cascades allow for isothermal operation of the assembly or computational process, as opposed 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
functionality of the initiator species, where less than one equivalent of the initiator can cause the reaction to go to completion.
Strand displacement complexes can be used to make
capable of complex computation. Unlike traditional electronic computers, which use
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
such as AND, OR, and NOT gates. More recently, a four-bit circuit was demonstrated that can compute the
of the integers 0–15, using a system of gates containing 130 DNA strands.
Another use of strand displacement cascades is to make dynamically assembled structures. These use a
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 .
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
problems in
and . The earliest such application envisaged for the field, and one still in development, is in , 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
rods to replace
using DNA origami is advantageous because, unlike liquid crystals, they are tolerant of the detergents needed to suspend
in solution.
have been used as nanoscale assembly lines to move nanoparticles and direct . Furthermore, DNA origami structures have aided in the biophysical studies of
function and .
DNA nanotechnology is moving towards 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 a molecular electronic elements such as , providing a method for nanometer-scale control of the placement and overall architecture of the device analogous to a molecular . DNA nanotechnology has been compared to the concept of
because of the coupling of computation to its material properties.
In a study conducted by a group of scientists from
(), researchers were able to construct a small multi-switchable 3D DNA Box Origami. The proposed nanoparticle was characterized by ,
and . 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.".
There are potential applications for DNA nanotechnology in nanomedicine, making use of its ability to perform computation in a
format to make "smart drugs" for . One such system being investigated uses a hollow DNA box containing proteins that induce , or cell death, that will only open when in proximity to a . There has additionally been interest in expressing these artificial structures in engineered living bacterial cells, most likely using the
RNA for the assembly, although it is unknown whether these complex structures are able to efficiently fold or assemble in the cell's . If successful, this could enable
of nucleic acid nanostructures. Scientists at
reported the self-assembly of four short strands of synthetic DNA into a cage which is capable of entering cells and surviving for at least 48 hours. The fluorescently labeled DNA
were found to remain intact in the laboratory cultured human
cells despite the attack by cellular
after two days. This experiment showed the potential of drug delivery inside the living cells using the DNA ‘cage’. A DNA
was used to deliver
(RNAi) in a mouse model, reported a team of researchers in . Delivery of the interfering RNA for treatment has showed some success using
or , but there are limitations 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 a single strand of RNA affixed to each of the six edges. The tetrahedron is further equipped with targeting protein, three
molecules, which lead the DNA nanoparticles to the abundant
found on some tumors. The result showed that the gene expression targeted by the RNAi, , 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.
DNA nanostructures must be
so that the individual nucleic acid strands will assemble into the desired structures. This process usually begins with the specification of a desired
or functionality. Then, the overall
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
design, which is the specification of the actual base sequences of each nucleic acid strand.
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. 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 . This was the dominant design strategy used from the mid-1990s until the mid-2000s, when the DNA origami methodology was developed.
Folding structures. An alternative to the tile-based approach, folding approaches make the nanostructure from a single long strand. This long strand 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 , which allows the creation of nanoscale two- and three-dimensional shapes (see
Dynamic assembly. This approach directly controls the
of DNA self-assembly, specifying all of the
steps in the
in addition to the final product. This is done using starting materials whic these then assemble into the final conformation in a
reaction, in a specific order (see
below). This approach has the advantage of proceeding , at a constant temperature. This is in contrast to the thermodynamic approaches, which require a thermal
step where a temperature change is required to trigger the assembly and favor proper formation of the desired structure.
Main article:
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 , 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
methods such as , or by using a full
thermodynamic model, which is more accurate but slower and more computationally intensive. Geometric models are used to examine
of the nanostructures and to ensure that the complexes are not overly .
Nucleic acid design has similar goals to . 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. However, nucleic acid structures are less versatile than proteins in their functionality because of proteins' increased ability to fold into complex structures, as well as the limited chemical diversity of the four
as compared to the twenty .
methods, such as this
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 .
The sequences of the DNA strands making up a target structure are designed computationally, using
software. The nucleic acids themselves are then synthesized using standard
methods, usually automated in an , and strands of custom sequences are commercially available. Strands can be purified by
if needed, and precise concentrations determined via any of several
methods using .
The fully formed target structures can be verified using
gel electrophoresis, which gives size and shape information for the nucleic acid complexes. An
can assess whether a structure incorporates all desired strands.
(FRET) are sometimes used to characterize the structure of the complexes.
Nucleic acid structures can be directly imaged by , 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 nu
are often used in this case. Extended three-dimensional lattices are analyzed by .
The woodcut Depth (pictured) by
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.
The conceptual foundation for DNA nanotechnology was first laid out by
in the early 1980s. Seeman's original motivation was to create a three-dimensional DNA lattice for orienting other large molecules, which would simplify their
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
and an array of DNA six-arm junctions. A number of natural branched DNA structures were known at the time, including the DNA
and the mobile , 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.
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 . This was followed by a DNA . However, it soon became clear that these structures, polygonal shapes with flexible junctions as their , were not rigid enough to form extended three-dimensional lattices. Seeman developed the more rigid double-crossover (DX) , and in 1998, in collaboration with , published the creation of two-dimensional lattices of DX tiles. These tile-based structures had the advantage that they provided the capability to implement DNA computing, which was demonstrated by Winfree and
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 , meaning that their assembly was capable of performing computation. 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.
New capabilities continued to be discovered for designed DNA structures throughout the 2000s. The first —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
the following year. The next advance was to translate this into mechanical motion, and in 2004 and 2005, a number of DNA walker systems were demonstrated by the groups of Seeman, , , and . 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, was demonstrated in 2006 and 2007 by the groups of , , and .
In 2006, Rothemund first demonstrated the
technique for easily and robustly creating 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 's DNA octahedron, which consisted mostly of one very long strand. Rothemund's DNA origami contains a long strand whose folding is assisted by a number of short strands. This method allowed the creation of much larger structures than were previously possible, and which are less technically demanding to design and synthesize. DNA origami was the cover story of
on March 15, 2006. 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, while the labs of
and Yan demonstrated hollow three-dimensional structures made out of two-dimensional faces.
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
experiments that extended the capabilities 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
after one reviewer praised its originality while another criticized it for its lack of biological relevance. By the early 2010s, however, the field was considered to have increased its capabilities 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. 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.
DNA polyhedra: Goodman, Russel P.; Schaap, Iwan A. T.; Tardin, C. F.; Erben, Christof M.; Berry, Richard M.; Schmidt, C.F.; Turberfield, Andrew J. (9 December 2005). "Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication". Science 310 (5754): . :. :.  .
Overview: Mao, Chengde (December 2004). . PLoS Biology 2 (12): . :.  .  .
Overview: Seeman, Nadrian C. (June 2004). . Scientific American 290 (6): 64–75. :.  .
Background: Pelesko, John A. (2007). Self-assembly: the science of things that put themselves together. New York: Chapman & Hall/CRC. pp. 5, 7.  .
Overview: Seeman, Nadrian C. (2010). . Annual Review of Biochemistry 79: 65–87. :.  .  .
Background: Long, Eric C. (1996). "Fundamentals of nucleic acids". In Hecht, Sidney M. Bioorganic chemistry: nucleic acids. New York: Oxford University Press. pp. 4–10.  .
RNA nanotechnology: Chworos, A Severcan, I Koyfman, Alexey Y.; Weinkam, P Oroudjev, E Hansma, Helen G.; Jaeger, Luc (2004). "Building Programmable Jigsaw Puzzles with RNA". Science 306 (5704): . :. :.  .
RNA nanotechnology: Guo, Peixuan (2010). . Nature Nanotechnology 5 (12): 833–842. :. :.  .  .
Dynamic DNA nanotechnology: Zhang, D. Y.; Seelig, G. (February 2011). "Dynamic DNA nanotechnology using strand-displacement reactions". Nature Chemistry 3 (2): 103–113. :.  .
Structural DNA nanotechnology: Seeman, Nadrian C. (November 2007). . Molecular Biotechnology 37 (3): 246–257. :.  .  .
Dynamic DNA nanotechnology: Lu, Y.; Liu, J. (December 2006). "Functional DNA nanotechnology: Emerging applications of DNAzymes and aptamers". Current Opinion in Biotechnology 17 (6): 580–588. :.  .
Other arrays: Strong, Michael (March 2004). . PLoS Biology 2 (3): e73. :.  .  .
Yan, H.; Park, S. H.; Finkelstein, G.; Reif, J. H.; Labean, T. H. (26 September 2003). "DNA-templated self-assembly of protein arrays and highly conductive nanowires". Science 301 (5641): . :.  .
Algorithmic self-assembly: Rothemund, Paul W. K.; Papadakis, N Winfree, Erik (December 2004). . PLoS Biology 2 (12): . :.  .  .
DX arrays: Winfree, E Liu, F Wenzler, Lisa A.; Seeman, Nadrian C. (6 August 1998). "Design and self-assembly of two-dimensional DNA crystals". Nature 394 (6693): 529–544. :. :.  .
DX arrays: Liu, F Sha, R Seeman, Nadrian C. (10 February 1999). "Modifying the surface features of two-dimensional DNA crystals". Journal of the American Chemical Society 121 (5): 917–922. :.
Other arrays: Mao, C Sun, W Seeman, Nadrian C. (16 June 1999). "Designed two-dimensional DNA Holliday junction arrays visualized by atomic force microscopy". Journal of the American Chemical Society 121 (23): . :.
Other arrays: Constantinou, Pamela E.; Wang, T Kopatsch, J Israel, Lisa B.; Zhang, X Ding, B Sherman, William B.; Wang, X Zheng, J Sha, R Seeman, Nadrian C. (21 September 2006). . Organic and Biomolecular Chemistry 4 (18): . :.  .  .
Other arrays: Mathieu, F Liao, S Kopatsch, J Wang, T Mao, C Seeman, Nadrian C. (April 2005). . Nano Letters 5 (4): 661–665. :. :.  .  .
History: Seeman, Nadrian (9 June 2010). . Nano Letters 10 (6): . :. :.  .  .
Algorithmic self-assembly: Barish, Robert D.; Rothemund, Paul W. K.; Winfree, Erik (December 2005). "Two computational primitives for algorithmic self-assembly: copying and counting". Nano Letters 5 (12): . :. :.  .
Design: Feldkamp, U.; Niemeyer, C. M. (13 March 2006). "Rational design of DNA nanoarchitectures". Angewandte Chemie International Edition 45 (12): . :.  .
DNA nanotubes: Rothemund, Paul W. K.; Ekani-Nkodo, A Papadakis, N Kumar, A Fygenson, Deborah Kuchnir & Winfree, Erik (22 December 2004). "Design and Characterization of Programmable DNA Nanotubes".
126 (50): 1. :.  .
DNA nanotubes: Yin, P.; Hariadi, R. F.; Sahu, S.; Choi, H. M. T.; Park, S. H.; Labean, T. H.; Reif, J. H. (8 August 2008). "Programming DNA Tube Circumferences". Science 321 (5890): 824–826. :. :.  .
Three-dimensional arrays: Zheng, J Birktoft, Jens J.; Chen, Yi; Wang, T Sha, R Constantinou, Pamela E.; Ginell, Stephan L.; Mao, C Seeman, Nadrian C. (3 September 2009). . Nature 461 (7260): 74–77. :. :.  .  .
Overview: Pinheiro, A. V.; Han, D.; Shih, W. M.; Yan, H. (December 2011). . Nature Nanotechnology 6 (12): 763–772. :.  .  .
DNA polyhedra: Zhang, Y Seeman, Nadrian C. (1 March 1994). "Construction of a DNA-truncated octahedron". Journal of the American Chemical Society 116 (5): . :.
DNA polyhedra: Shih, William M.; Quispe, Joel D.; Joyce, Gerald F. (12 February 2004). "A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron". Nature 427 (6975): 618–621. :. :.  .
DNA origami: Rothemund, Paul W. K. (16 March 2006). "Folding DNA to create nanoscale shapes and patterns". Nature 440 (7082): 297–302. :. :.  .
DNA origami: Douglas, Shawn M.; Dietz, H Liedl, T H?gberg, Bj? Graf, F Shih, William M. (21 May 2009). . Nature 459 (7245): 414–418. :. :.  .  .
DNA boxes: Andersen, Ebbe S.; Dong, M Nielsen, Morten M.; Jahn, K Subramani, R Mamdouh, W Golas, Monika M.; Sander, Bjoern et al. (7 May 2009). "Self-assembly of a nanoscale DNA box with a controllable lid". Nature 459 (7243): 73–76. :. :.  .
DNA boxes: Ke, Y Sharma, J Liu, M Jahn, K Liu, Y Yan, Hao (10 June 2009). "Scaffolded DNA origami of a DNA tetrahedron molecular container". Nano Letters 9 (6): . :. :.  .
Overview: Endo, M.; Sugiyama, H. (12 October 2009). "Chemical approaches to DNA nanotechnology". ChemBioChem 10 (15): . :.  .
Nanoarchitecture: Zheng, J Constantinou, Pamela E.; Micheel, C Alivisatos, A. P Kiehl, Richard A.; Seeman Nadrian C. (July 2006). . Nano Letters 6 (7): . :. :.  .  .
Nanoarchitecture: Park, Sung Ha; Pistol, C Ahn, Sang J Reif, John H.; Lebeck, Alvin R.; Dwyer, C LaBean, Thomas H. (October 2006). "Finite-size, fully addressable DNA tile lattices formed by hierarchical assembly procedures". Angewandte Chemie 118 (40): 749–753. :.
Nanoarchitecture: Cohen, Justin D.; Sadowski, John P.; Dervan, Peter B. (22 October 2007). "Addressing single molecules on DNA nanostructures". Angewandte Chemie International Edition 46 (42): . :.  .
Nanoarchitecture: Maune, Hareem T.; Han, Si-P Barish, Robert D.; Bockrath, M Goddard III, William A.; Rothemund, Paul W. K.; Winfree, Erik (January 2009). "Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates". Nature Nanotechnology 5 (1): 61–66. :. :.  .
Nanoarchitecture: Liu, J.; Geng, Y.; Pound, E.; Gyawali, S.; Ashton, J. R.; Hickey, J.; Woolley, A. T.; Harb, J. N. (22 March 2011). "Metallization of branched DNA origami for nanoelectronic circuit fabrication". ACS Nano 5 (3): . :.  .
Nanoarchitecture: Deng, Z.; Mao, C. (6 August 2004). "Molecular lithography with DNA nanostructures". Angewandte Chemie International Edition 43 (31): 4068. :.
DNA machines: Bath, J Turberfield, Andrew J. (May 2007). "DNA nanomachines". Nature Nanotechnology 2 (5): 275–284. :. :.  .
DNA machines: Mao, C Sun, W Shen, Z Seeman, Nadrian C. (14 January 1999). "A DNA nanomechanical device based on the B-Z transition". Nature 397 (6715): 144–146. :. :.  .
DNA machines: Yurke, B Turberfield, Andrew J.; Mills, Allen P., Jr; Simmel, Friedrich C.; Neumann, Jennifer L. (10 August 2000). "A DNA-fuelled molecular machine made of DNA". Nature 406 (6796): 605–609. :. :.  .
DNA machines: Yan, H Zhang, X Shen, Z Seeman, Nadrian C. (3 January 2002). "A robust DNA mechanical device controlled by hybridization topology". Nature 415 (6867): 62–65. :. :.  .
DNA machines: Feng, L.; Park, S. H.; Reif, J. H.; Yan, H. (22 September 2003). "A two-state DNA lattice switched by DNA nanoactuator". Angewandte Chemie 115 (36): 4478. :.
DNA machines: Goodman, R. P.; Heilemann, M.; Doose, S. R.; Erben, C. M.; Kapanidis, A. N.; Turberfield, A. J. (February 2008). "Reconfigurable, braced, three-dimensional DNA nanostructures". Nature Nanotechnology 3 (2): 93–96. :.  .
Applications: Douglas, Shawn M.; Bachelet, I Church, George M. (17 February 2012). "A logic-gated nanorobot for targeted transport of molecular payloads". Science 335 (6070): 831–834. :.
DNA walkers: Shin, Jong-S Pierce, Niles A. (8 September 2004). "A synthetic DNA walker for molecular transport". Journal of the American Chemical Society 126 (35): 1. :.  .
DNA walkers: Sherman, William B.; Seeman, Nadrian C. (July 2004). "A precisely controlled DNA biped walking device". Nano Letters 4 (7): . :. :.
DNA walkers: Tian, Ye; He, Yu; Chen, Yi; Yin, P Mao, Chengde (11 July 2005). "A DNAzyme that walks processively and autonomously along a one-dimensional track". Angewandte Chemie 117 (28): . :.
DNA walkers: Bath, J Green, Simon J.; Turberfield, Andrew J. (11 July 2005). "A free-running DNA motor powered by a nicking enzyme". Angewandte Chemie International Edition 44 (28): . :.
Functional DNA walkers: Lund, K Manzo, Anthony J.; Dabby, N Michelotti, N Johnson-Buck, A Nangreave, J Taylor, S Pei, R Stojanovic, Milan N.; Walter, Nils G.; Winfree, E Yan, Hao (13 May 2010). . Nature 465 (7295): 206–210. :. :.  .  .
Functional DNA walkers: He, Yu; Liu, David R. (November 2010). . Nature Nanotechnology 5 (11): 778–782. :. :.  .  .
Kinetic assembly: Yin, P Choi, Harry M. T.; Calvert, Colby R.; Pierce, Niles A. (17 January 2008). "Programming biomolecular self-assembly pathways". Nature 451 (7176): 318–322. :. :.  .
Strand displacement cascades: Seelig, G.; Soloveichik, D.; Zhang, D. Y.; Winfree, E. (8 December 2006). "Enzyme-free nucleic acid logic circuits". Science 314 (5805): . :.  .
Strand displacement cascades: Qian, L Winfree, Erik (3 June 2011). "Scaling up digital circuit computation with DNA strand displacement cascades". Science 332 (6034): . :.  .
History/applications: Service, Robert F. (3 June 2011). "DNA nanotechnology grows up". Science 332 (6034): . :.
Applications: Rietman, Edward A. (2001). . Springer. pp. 209–212.   2011.
M. Zadegan, R et, al. (2012). .
6 (11): 1. :.
Applications: Jungmann, R Renner, S Simmel, Friedrich C. (March 2008). . HFSP journal 2 (2): 99–109. :.  .  .
Lovy, Howard (5 July 2011). .
Walsh, A Yin, H Erben, C Wood, M Turberfield, Andrew (2011). . ACS Nano (ACS Publications) 5 (7): . :.  .
Trafton, Anne (4 June 2012). . MIT News 2013.
Lee, H Lytton-Jean, A Chen, Yi; Love, K Park, A Karagiannis, E Sehgal, A Querbes, William et al. (2012).
(Nature) 7 (6): 389–393. :.
Design: Brenneman, A Condon, Anne (25 September 2002). "Strand design for biomolecular computation". Theoretical Computer Science 287: 39–58. :.
Overview: Lin, C Liu, Y Rinker, S Yan, Hao (11 August 2006). "DNA tile based self-assembly: building complex nanoarchitectures". ChemPhysChem 7 (8): . :.  .
Design: Dirks, Robert M.; Lin, M Winfree, E Pierce, Niles A. (15 February 2004). . Nucleic Acids Research 32 (4): . :.  .  .
Methods: Ellington, A.; Pollard, J. D. (1 May 2001). "Synthesis and purification of oligonucleotides". Current Protocols in Molecular Biology. :.  .
Methods: Ellington, A.; Pollard, J. D. (1 May 2001). "Purification of oligonucleotides using denaturing polyacrylamide gel electrophoresis". Current Protocols in Molecular Biology. :.  .
Methods: Gallagher, S. R.; Desjardins, P. (1 July 2011). "Quantitation of nucleic acids and proteins". Current Protocols Essential Laboratory Techniques. :.  .
Methods: Chory, J.; Pollard, J. D. (1 May 2001). "Separation of small DNA fragments by conventional gel electrophoresis". Current Protocols in Molecular Biology. :.  .
Methods: Walter, N. G. (1 February 2003). "Probing RNA structural dynamics and function by fluorescence resonance energy transfer (FRET)". Current Protocols in Nucleic Acid Chemistry. :.  .
Methods: Lin, C.; Ke, Y.; Chhabra, R.; Sharma, J.; Liu, Y.; Yan, H. (2011). "Synthesis and Characterization of Self-Assembled DNA Nanostructures". In Zuccheri, G. and Samorì, B. DNA Nanotechnology: Methods and Protocols. Methods in Molecular Biology 749. pp. 1–11. :.  .
Methods: Bloomfield, Victor A.; Crothers, Donald M.; Tinoco, Jr., Ignacio (2000). Nucleic acids: structures, properties, and functions. Sausalito, Calif: University Science Books. pp. 84–86, 396–407.  .
History: Pelesko, John A. (2007). Self-assembly: the science of things that put themselves together. New York: Chapman & Hall/CRC. pp. 201, 242, 259.  .
History: See . Nadrian Seeman Lab. for a statement of the problem, and . Nadrian Seeman Laboratory. for the proposed solution.
DNA origami: Rothemund, Paul W. K. (2006). "Scaffolded DNA origami: from generalized multicrossovers to polygonal networks". In Chen, J Jonoska, N Rozenberg, Grzegorz. Nanotechnology: science and computation. Natural Computing Series. New York: Springer. pp. 3–21. :.  .
Nanoarchitecture: Robinson, Bruche H.; Seeman, Nadrian C. (August 1987). "The design of a biochip: a self-assembling molecular-scale memory device". Protein Engineering 1 (4): 295–300. :.  .
History: Hopkin, Karen (August 2011). . The Scientist 2011.
Seeman, Nadrian C. (June 2004). . Scientific American 290 (6): 64–75. :.  .—An article written for laypeople by the founder of the field
Seeman, Nadrian C. (9 June 2010). . Nano Letters 10 (6): . :. :.  .  .—A review of results in the period
Seeman, Nadrian C. (2010). . Annual Review of Biochemistry 79: 65–87. :.  .  .—A more comprehensive review including both old and new results in the field
Service, Robert F. (3 June 2011). "DNA nanotechnology grows up". Science 332 (6034): . :. and :.—A news article focusing on the history of the field and development of new applications
Zadegan, Reza M.; Norton, Michael L. (June 2012). . Int. J. Mol. Sci. 13 (6): . :.  .  .—A very recent and comprehensive review in the field
Specific subfields:
Bath, J Turberfield, Andrew J. (5 May 2007). "DNA nanomachines". Nature Nanotechnology 2 (5): 275–284. :. :.  .—A review of nucleic acid nanomechanical devices
Feldkamp, U Niemeyer, Christof M. (13 March 2006). "Rational design of DNA nanoarchitectures". Angewandte Chemie International Edition 45 (12): 1856–76. :.  .—A review coming from the viewpoint of secondary structure design
Lin, C Liu, Y Rinker, S Yan, Hao (11 August 2006). "DNA tile based self-assembly: building complex nanoarchitectures". ChemPhysChem 7 (8): . :.  .—A minireview specifically focusing on tile-based assembly
Zhang, David Yu; Seelig, Georg (February 2011). "Dynamic DNA nanotechnology using strand-displacement reactions". Nature Chemistry 3 (2): 103–113. :. :.  .—A review of DNA systems making use of strand displacement mechanisms
—a video introduction to DNA nanotechnology
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