DNA nanotechnology

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 biological information, making it an example of bionanotechnology. This has possible applications in molecular self-assembly and in DNA computing.

## Contents

* 1 Introduction: DNA crossover molecules
* 2 Tile-based arrays
* 2.1 DX arrays
* 2.2 DNA nanotubes
* 2.3 Other tile arrays
* 3 DNA origami
* 4 DNA polyhedra
* 5 DNA nanomechanical devices
* 6 Applications
* 6.1 Algorithmic self-assembly
* 6.2 Nanoarchitecture
* 7 External links
* 8 References

## Introduction: DNA crossover molecules

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File:Holliday Junction.png |

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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.

File:Mao-DX-schematic.jpgA 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. Template:Doi-inline

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 immoble 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

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File:Mao-DXarray-schematic.gifAssembly 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. Template:Doi-inline

### DX arrays

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DX 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 essentiallt two-dimensional crystals of DNA.[3]

### DNA nanotubes

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In addition to flat sheets, DX arrays have been made to form hollow tubes of 4-20 nm diameter. These have been dubbed DNA nanotubes by analogy with the similarly-shaped carbon nanotubes.[4]

### Other tile arrays

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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

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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

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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

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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 "molecuar tweezers," changes form 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]

## Applications

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### Algorithmic self-assembly

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File:SierpinskiTriangle.svgThe Sierpinski gasket. File:Rothemund-DNA-SierpinskiGasket.jpgDNA arrays that display a representation of the Sierpinski gasket on their surfaces. Click the image for further details. Image from Rothemund et al., 2004. Template:Doi-inline

Template:Seealso

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.[10]

### Nanoarchitecture

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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. The first report of assembly with a non-covalent hosting scheme came in 2007, using Dervan polyamides on a DX array to arrange streptavidin proteins on the DNA array.[11]

## External links

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* Nadrian Seeman lab at NYU [1]
* Erik Winfree lab at Caltech [2]
* Andrew Turberfield lab at Oxford University [3]
* Bernard Yurke page at Bell Labs [4]
* Chengde Mao page at Purdue University [5]
* International Society for Nanoscale Science, Computation and Engineering [6]
* Reza Mohammadzadegan, Mohammad Hossein sheikhi DNA Nano-Gears' Molecular Simulation 33(13); 1071-1081.
* A brief page on DNA self-assembly DNA Self Assembly for Nanotechnology'

## References

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

1. ↑ Created from PDB 1M6G
2. ↑ Overview:
* Seeman, Nadrian C. (1999). "DNA Engineering and its Application to Nanotechnology". Trends in Biotechnology. 17 (11): 437–443. ISSN 0167-7799. Unknown parameter `|month=` ignored (help) doi:10.1016/S0167-7799(99)01360-8
* Seeman, Nadrian C. (2001). "DNA Nicks and Nodes and Nanotechnology". Nano Letters. 1 (1): 22–26. ISSN 1530-6984. Unknown parameter `|month=` ignored (help) doi:10.1021/nl000182v
* Mao, Chengde (2004). "The Emergence of Complexity: Lessons from DNA". PLoS Biology. 2 (12): 2036–2038. ISSN 1544-9173. Unknown parameter `|month=` ignored (help) doi:10.1371/journal.pbio.0020431
3. ↑ DX arrays:
* Winfree, Erik (1998). "Design and self-assembly of two-dimensional DNA crystals". Nature. 394: 529–544. ISSN 0028-0836. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) doi:10.1038/28998
* Liu, Furong (1999). "Modifying the Surface Features of Two-Dimensional DNA Crystals". Journal of the American Chemical Society. 121 (5): 917–922. ISSN 0002-7863. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) doi:10.1021/ja982824a
4. ↑ DNA nanotubes:
* Rothemund, Paul W. K. (2004). "Design and Characterization of Programmable DNA Nanotubes". Journal of the American Chemical Society. 126 (50): 16344–16352. ISSN 0002-7863. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) doi:10.1021/ja044319l
5. ↑ Other arrays:
* Mao, Chengde (1999). "Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy". Journal of the American Chemical Society. 121 (23): 5437–5443. ISSN 0002-7863. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) doi:10.1021/ja9900398
* Constantinou, Pamela E. (2006). "Double cohesion in structural DNA nanotechnology". Organic and Biomolecular Chemistry. 4: 3414–3419. Unknown parameter `|coauthors=` ignored (help) doi:10.1039/b605212f
6. ↑ 3D arrays:
* Mathieu, Frederick (2005). "Six-Helix Bundles Designed from DNA". Nano Letters. 5 (4): 661–665. ISSN 1530-6984. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) doi:10.1021/nl050084f
7. ↑ DNA origami:
* Rothemund, Paul W. K. (2006). "Folding DNA to create nanoscale shapes and patterns". Nature. 440: 297–302. ISSN 0028-0836. doi:10.1038/nature04586
8. ↑ DNA polyhedra:
* Zhang, Yuwen (1994). "Construction of a DNA-truncated octahedron". Journal of the American Chemical Society. 116 (5): 1661–1669. ISSN 0002-7863. Unknown parameter `|coauthors=` ignored (help) doi:10.1021/ja00084a006
* Shih, William M. (2004). "A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron". Nature. 427: 618–621. ISSN 0028-0836. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) doi:10.1038/nature02307
* Goodman, R.P. (2005). "Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication". Science. 310 (5754): 1661–1665. ISSN 0036-8075. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) doi:10.1126/science.1120367
9. ↑ DNA machines:
* Yurke, Bernard (2000). "A DNA-fuelled molecular machine made of DNA". Nature. 406: 605–609. ISSN 0028-0836. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) doi:10.1038/35020524
* Mao, Chengde (1999). "A DNA Nanomechanical Device Based on the B-Z Transition". Nature. 397: 144–146. ISSN 0028-0836. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) doi:10.1038/16437
* Yan, Hao (2002). "A robust DNA mechanical device controlled by hybridization topology". Nature. 415: 62–65. ISSN 0028-0836. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) doi:10.1038/415062a
10. ↑ Algorithmic self-assembly:
* Rothemund, Paul W. K. (2004). "Algorithmic Self-Assembly of DNA Sierpinski Triangles". PLoS Biology. 2 (12): 2041–2053. ISSN 1544-9173. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) doi:10.1371/journal.pbio.0020424
11. ↑ Nanoarchitecture:
* Robinson, Bruche H. (1987). "The Design of a Biochip: A Self-Assembling Molecular-Scale Memory Device". Protein Engineering. 1 (4): 295–300. ISSN 0269-2139. Unknown parameter `|coauthors=` ignored (help); Unknown parameter `|month=` ignored (help) Link
* Zheng, Jiwen (2006). "2D Nanoparticle Arrays Show the Organizational Power of Robust DNA Motifs". Nano Letters. 6: 1502–1504. ISSN 1530-6984. Unknown parameter `|coauthors=` ignored (help) doi:10.1021/nl060994c
* Cohen, Justin D. (2007). "Addressing Single Molecules on DNA Nanostructures". Angewandte Chemie. ISSN 0570-0833. Unknown parameter `|coauthors=` ignored (help) doi:10.1002/anie.200702767

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