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DNA nanotechnology is a branch of nanotechnology which uses the unique molecular recognition properties of DNA and other nucleic acids to create designed, controllable structures out of DNA. This has possible applications in molecular self-assembly and in DNA computing. In this field, DNA is used as a structural material rather than as a carrier of genetic information, making it an example of bionanotechnology.

History

The M. C. Escher woodcut Depth (pictured) 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 concept of DNA nanotechnology was invented by Nadrian Seeman in early 1980's. A crystallographer, Seeman was frustrated with the haphazardness and guesswork involved with crystallizing centain molecules. In fall 1980, while at a campus pub, Seeman was inspired by the M. C. Escher woodcut Depth to realize that a three-dimensional DNA lattice could be used to orient target molecules, simplifying their crystallographic study. In 1991, Seeman's laboratory published the synthesis of a cube made of DNA, the first three-dimensional nanoscale object, for which he received the 1995 Feynman Prize in Nanotechnology, which was followed by a DNA truncated octahedron. However, it soon became clear that these objects were not rigid enough to form three-dimensional lattices.

Seeman developed the more rigid "DX" motif, and in collaboration with Erik Winfree, in 1998 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 Paul Rothemund in 2004, and for which they shared the 2006 Feynman Prize in Nanotechnology.

The field has continued to branch out. The first DNA nanomachine—a motif which changes its structure in response to an input—was demonstrated in 1999. Nanoarchitecture, first proposed by Seeman in 1987, was beginning to be demonstrated by 2006. Also in 2006, Rothemund first demonstrated the new DNA origami technique for easily and robustly creating folded DNA molecules of any shape. In 2009, Seeman published the synthesis of a three-dimensional lattice, nearly thirty years after he had set out to do so.^[1]

Fundamental concepts

DNA nanotechnology makes use of branched DNA structures to create DNA complexes with useful properties. DNA is normally a linear molecule, in that its axis is unbranched. However, DNA molecules containing junctions can also be made. For example, a four-arm junction can be made using four individual DNA strands which are complementary to each other in the correct pattern. Due to Watson-Crick base pairing, only portions of the strands which are complementary to each other will attach to each other to form duplex DNA. This four-arm junction is an immobile form of a Holliday junction.

Junctions can be used in more complex molecules. The most important of these is the "double-crossover" or DX motif. Here, two DNA duplexes lie next to each other, and share two junction points where strands cross from one duplex into the other. This molecule has the advantage that the junction points are now constrained to a single orientation as opposed to being flexible as in the four-arm junction. This makes the DX motif suitible as a structural building block for larger DNA complexes.^[2]

Structure of the 4-arm junction. Left: A schematic. Right: A more realistic model.[3] Each of the four separate DNA single strands are shown in different colors.

A double-crossover (DX) molecule. This molecule consists of five DNA single strands which form two double-helical domains, on the left and the right in this image. There are two crossover points where the strands cross from one domain into the other. Image from Mao, 2004. [1]

Design

A main goal of DNA nanotechnology is, given a target structure and/or functionality, to determine what sequences of DNA molecules will assemble into that structure. There are a number of different approaches which have been used to design DNA sequences that will form the desired structure.

Tile-based structures

Assembly of a DX array. Each bar represents a double-helical domain of DNA, with the shapes representing complimentary sticky ends. The DX molecule at top will combine into the two-dimensional DNA array shown at bottom. This is an example of the tile-based strategy for designing DNA nanostructures. Image from Mao, 2004. [2]

The earliest method for creating DNA nanostructures was to construct them out of smaller discrete units. This method has the advantage of being able to conceptually separate the stronger interactions which form each tile from the assembly of the larger complete structure. It is often used to make periodic lattices, but can also be used to implement algorithmic self-assembly, making them one platform for DNA computing.

Folding structures

An alternative to the tile-based approach, two-dimensional DNA structures can be made from a single, long DNA strand of arbitrary sequence which is folded into the desired shape by using shorter, "staple" strands. This allows the creation of two-dimensional shapes at the nanoscale using DNA. Demonstrated designs have included the smiley face and a coarse map of North America. DNA origami was the cover story of Nature on March 15, 2006.^[4]

Kinetic assembly

Most design in DNA nanotechnology only focuses on designing sequences so that the target structure is a thermodynamic minimum, without regard to the assembly pathway. Recently, there has been interest in controlling the kinetics of DNA self-assembly, so that transient dynamics can also be programmed into the assembly. Such a method also has the advantage of proceeding isothermally and thus not requiring a thermal annealing step required by solely thermodynamic approaches.^[5]

Primary sequence design

After any of the above approaches are used to design the secondary structure of a target molecule, an actual sequence of nucleotides must be devised which will form into the desired structure. Nucleic acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation (see, for example, RNA structure). Nucleic acid design is central to the field of DNA nanotechnology.

Nucleic acid design has similar goals to protein design: in both, the sequence of monomers is designed to favor the desired folded or associated structure and to disfavor alternate structures. Nucleic acid design has the advantage of being a much computationally simpler problem, since the simplicity of Watson-Crick base pairing rules leads to simple heuristic methods which yield experimentally robust designs. However, nucleic acid structures are less versitile than proteins in their functionality.^[6]

Target structures

Many structures made from DNA have been synthesized and characterized.

Two-dimensional lattices

Left, a model of a DNA tile used to make a two-dimensional periodic lattice. Right, an atomic force migrograph of the assembled lattice. Image from Strong, 2004. [3]

DX, or Double Crossover, molecules can be equipped with sticky ends in order to combine them into a two-dimenstional periodic lattice. Each DX molecule has four termini, one at each end of the two double-helical domains, and these can be equipped with sticky ends that program them to combine into a specific pattern. More than one type of DX can be used which can be made to arrange in rows or any other tessellated pattern. They thus form extended flat sheets which are essentially two-dimensional crystals of DNA.^[7]

Two-dimensional arrays have been made out of other motifs as well, including the Holliday junction rhombus array as well as various DX-based arrays in the shapes of triangles and hexagons.^[8]

Discrete three-dimensional structures

A number of three-dimensional DNA molecules have been made which have the connectivity of a polyhedron such as an octahedron or cube. In other words, the DNA duplexes trace the edges of a polyhedron with a DNA junction at each vertex.

The earliest demonstrations of DNA polyhedra involved multiple ligations and solid-phase synthesis steps to create catenated polyhedra. More recent work has yielded polyhedra whose synthesis is much easier. These include a DNA truncated octahedron made from a long single strand designed to fold into the correct conformation, as well as a tetrahedron which can be produced from four DNA strands in a single step.^[9]

DNA structures with solid faces have also been constructed, using the DNA origami method. These can be programmed to open and release their cargo in response to a stimulus, making them potentially useful as programmable molecular cages.^[10]

DNA nanotubes

In addition to flat sheets, DX arrays have been made to form hollow tubes of 4-20 nm diameter. These DNA nanotubes are somewhat similar in size and shape to carbon nanotubes, but the carbon nanotubes are stronger and better conductors, whereas the DNA nanotubes are more easily modified and connected to other structures.^[11]

Extended three-dimensional lattices

Creating three-dimensional lattices out of DNA was the earliest goal of DNA nanotechnology, but proved to be one of the most difficult to realize. Success in constructing three-dimensional DNA lattices was finally reported in 2009 using a motif based on the concept of tensegrity, a balance between tension and compression forces.^[12]

Applications

DNA nanotechnology focuses on creating molecules with designed functionalities as well as structures. Many classes of functional systems have been demonstrated.

Nanoarchitecture

The idea of using DNA arrays to template the assembly of other functional molecules has been around for a while, but only recently has progress been made in reducing these kinds of schemes to practice. In 2006, researchers covalently attached gold nanoparticles to a DX-based tile and showed that self-assembly of the DNA structures also assembled the nanoparticles hosted on them. A non-covalent hosting scheme was shown in 2007, using Dervan polyamides on a DX array to arrange streptavidin proteins on specific kinds of tiles on the DNA array.^[13] Previously in 2006 LaBean demonstrated the letters "D" "N" and "A" created on a 4x4 DX array using streptavidin. ^[14]

DNA has also been used to assemble a single walled carbon nanotube Field-effect transistor.^[15]

Algorithmic self-assembly

The Sierpinski gasket.

DNA arrays that display a representation of the Sierpinski gasket on their surfaces. Click the image for further details. Image from Rothemund et al., 2004. [4]

DNA nanotechnology has been applied to the related field of DNA computing. The DX tiles can have their sticky end sequences chosen so that they act as Wang tiles, allowing them to perform computation. A DX array has been demonstrated whose assembly encodes an XOR operation; this allows the DNA array to implement a cellular automaton which generates a fractal called the Sierpinski gasket. This shows that computation can be incorporated into the assembly of DNA arrays, increasing its scope beyond simple periodic arrays.

Note that DNA computing overlaps with, but is distinct from, DNA nanotechnology. The latter uses the specificity of Watson-Crick basepairing to make novel structures out of DNA. These structures can be used for DNA computing, but they do not have to be. Additionally, DNA computing can be done without using the types of molecules made possible by DNA nanotechnology.^[16]

Logic circuits

A design called a stem loop, consisting of a single strand of DNA which has a loop at an end, are a dynamic structure that opens and closes when a piece of DNA bonds to the loop part. This effect has been exploited to create several logic gates. These logic gates have been used to create the computers MAYA I and MAYA II which can play tic-tac-toe to some extent.^[17]

DNA nanomechanical devices

DNA complexes have been made which change their conformation upon some stimulus. These are intended to have applications in nanorobotics. One of the first such devices, called "molecular tweezers," changes from an open to a closed state based upon the presence of control strands.

DNA machines have also been made which show a twisting motion. One of these makes use of the transition between the B-DNA and Z-DNA forms to respond to a change in buffer conditions. Another relies on the presence of control strands to switch from a paranemic-crossover (PX) conformation to a double-junction (JX2) conformation.^[18]

Materials and methods

DNA of custom sequence is readily availible through oligonucleotide synthesis. This process is usually automated by using a DNA synthesizing machine, and custom DNA is commerically available from many vendors.

The sequences of the individual DNA strands which make up the target structure are designed computationally. Molecular modelling and thermodynamic modelling are sometimes used to optimize the DNA sequences.

The DNA molecules created by DNA nanotechnology are usually characterized by gel electrophoresis, which provides information about the size and shape of DNA molecules, indicating whether they have formed properly. Fluorescent labelling and Fluorescence resonance energy transfer are also used to characterize the structure of the molecules.

DNA structures can be directly imaged by atomic force microscopy, which images structures deposited on a flat surface. This method is well-suited to extended two-dimensional structures, but is less useful for discrete three-dimensional structures. For these latter structures cryo-electron microscopy is gaining popularity as an important method. Extended three-dimensional lattices are analyzed by X-ray crystallography.

See also

• DNA structure
• Molecular models of DNA

References

Note: Click on the doi to access the text of the referenced article.

External links

• Nanohedron.com images of DNA self assemblies

• Jørgen Kjems lab at Aarhus University [5]
• Thom LaBean lab at Duke University [6]
• Dan Luo lab at Cornell University [7]
• Chengde Mao page at Purdue University [8]
• John Reif lab at Duke University [9]
• Nadrian Seeman lab at NYU [10]
• William M. Shih lab at Harvard Medical School [11]
• Andrew Turberfield lab at Oxford University [12]
• Erik Winfree lab at Caltech [13]
• Hao Yan lab at Arizona State University [14]
• Peng Yin lab at Harvard Medical School [15]
• Bernard Yurke formerly at Bell Labs [16] now at Boise State University [17]

• Software for 3D DNA design, modeling and/or simulation:
  • Ascalaph Designer
  • caDNAno
  • GIDEON
  • NanoEngineer-1
• International Society for Nanoscale Science, Computation and Engineering [18]

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This page was last modified on 13 March 2010 at 01:53.

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