DNA nanotech

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DNA nanotechnology is a subfield of nanotechnology which seeks to use the unique molecular recognition properties of DNA and other nucleic acids to create novel, controllable structures out of DNA. The DNA is thus used as a structural material rather than as a carrier of genetic information, making it an example of bionanotechnology. This has possible applications in molecular self-assembly and in DNA computing.

Introduction: DNA crossover molecules

Structure of the 4-arm junction.
Left: A schematic. Right: A more realistic model.[1]
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 antiparallel 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. [2]

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 antiparallel 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]

Tile-based arrays

Assembly of a DX array. Each bar represents a double-helical domain of DNA, with the shapes representing comlimentary sticky ends. The DX molecule at top will combine into the two-dimensional DNA array shown at bottom. Image from Mao, 2004. [3]

DX arrays

DX, 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.[3]

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.[4]

Other tile arrays

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.[5] Another motif, the six-helix bundle, has the ability to form three-dimensional DNA arrays as well.[6]

DNA origami

Main article: DNA origami

As 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.[7]

DNA polyhedra

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 recently, there have been demonstrations of 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.[8]

DNA nanomechanical devices

Main article: DNA machine

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.[9]

Stem Loop Controllers

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. [10] [11]These logic gates have been used to create the computers MAYA I and MAYA II which can play tick-tac-toe to some extent.[12]

Applications

[edit] Algorithmic self-assembly

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]

See also: DNA computing

DNA nanotechnology has been applied to the related field of DNA computing. A DX array has been demonstrated whose assembly encodes an XOR operation, which 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.[13]

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 convalently 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.[14] Previously in 2006 LaBean demonstrated the letters “D” “N” and “A” created on a 4×4 DX array using streptavidin. [15]

DNA has also been used to assemble a single walled carbon nanotube Field-effect_transistor.[16]

See also

External links

References

Note: Click on the doi to access the text of the referenced article.
  1. ^ Created from PDB 1M6G
  2. ^ Overview:
  3. ^ DX arrays:
    • Winfree, Erik; Liu, Furong; Wenzler, Lisa A. & Seeman, Nadrian C. (6 August 1998). “Design and self-assembly of two-dimensional DNA crystals”. Nature 394: 529–544. doi:10.1038/28998. ISSN 0028-0836.
  4. ^ DNA nanotubes:
  5. ^ Other arrays:
    • Constantinou, Pamela E.; Wang, Tong; Kopatsch, Jens; Israel, Lisa B.; Zhang, Xiaoping; Ding, Baoquan; Sherman, William B.; Wang, Xing; Zheng, Jianping; Sha, Ruojie & Seeman, Nadrian C. (2006). “Double cohesion in structural DNA nanotechnology”. Organic and Biomolecular Chemistry 4: 3414–3419. doi:10.1039/b605212f.
  6. ^ 3D arrays:
    • Mathieu, Frederick; Liao, Shiping; Kopatsch, Jens; Wang, Tong; Mao, Chengde & Seeman, Nadrian C. (April 2005). “Six-Helix Bundles Designed from DNA”. Nano Letters 5 (4): 661–665. doi:10.1021/nl050084f. ISSN 1530-6984.
  7. ^ DNA origami:
  8. ^ 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: 618–621. doi:10.1038/nature02307. ISSN 0028-0836.
    • Goodman, R.P.; Schaap, I.A.T.; Tardin, C.F.; Erben, C.M.; Berry, R.M.; Schmidt, C.F.; Turberfield, A.J. (9 December 2005). “Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication”. Science 310 (5754): 1661–1665. doi:10.1126/science.1120367. ISSN 0036-8075.
  9. ^ DNA machines:
    • Yurke, Bernard; 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: 605–609. doi:10.1038/35020524. ISSN 0028-0836.
    • Mao, Chengde; Sun, Weiqiong; Shen, Zhiyong & Seeman, Nadrian C. (14 January 1999). “A DNA Nanomechanical Device Based on the B-Z Transition”. Nature 397: 144–146. doi:10.1038/16437. ISSN 0028-0836.
    • Yan, Hao; Zhang, Xiaoping; Shen, Zhiyong & Seeman, Nadrian C. (3 January 2002). “A robust DNA mechanical device controlled by hybridization topology”. Nature 415: 62–65. doi:10.1038/415062a. ISSN 0028-0836.
  10. ^ DNA Logic Gates
  11. ^ [1]
  12. ^ MAYA II
  13. ^ Algorithmic self-assembly:
  14. ^ 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. ISSN 0269-2139. Link
    • Zheng, Jiwen; Constantinou, Pamela E.; Micheel, Christine; Alivisatos, A. Paul; Kiehl, Richard A. & Seeman Nadrian C. (2006). “2D Nanoparticle Arrays Show the Organizational Power of Robust DNA Motifs”. Nano Letters 6: 1502–1504. doi:10.1021/nl060994c. ISSN 1530-6984.
  15. ^ Finite-Size, Fully Addressable DNA Tile Lattices Formed by Hierarchical Assembly Procedures“. Angewandte Chemie 118 (40): 749–753. October 2006. doi:10.1002/ange.200690141. ISSN 1521-3757. http://www3.interscience.wiley.com/journal/113390879/abstract.
  16. ^ DNA-Templated Carbon Nanotube Field-Effect Transistor“. Science 302 (6549): 1380–1382. November 2003. doi:10.1126/science.1091022. ISSN 1095-9203. http://www.sciencemag.org/cgi/content/abstract/sci;302/5649/1380.

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