page_title: DNA nanotechnology
section_title: Materials and methods
hierarchical_section_title: DNA nanotechnology / Materials and methods
caption_attribution_description: English: Formation gel of a DAO double-crossover (DX) DNA molecule used in DNA nanotechnology. This is a polyacrylamide gel run under native conditions. The molecule has four strands, here labeled 1 through 4, and each lane contains a different combination of the strands. The lanes, from left to right, are: 10 base pair ladder, 1+2+3+4 (full DX), empty, 1+2+3, 1+2+4, 1+3+4, 2+3+4, empty, 1+2, 1+3, 1+4, 3+4, 2+4, 2+3, empty, 1, 2, 3, 4.
context_page_description: 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 cells. Researchers in the field have created static structures such as two- and three-dimensional crystal lattices, nanotubes, polyhedra, and arbitrary shapes, and functional devices such as molecular machines and 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.
context_section_description: The sequences of the DNA strands making up a target structure are designed computationally, using molecular modeling and thermodynamic modeling software. The nucleic acids themselves are then synthesized using standard oligonucleotide synthesis methods, usually automated in an oligonucleotide synthesizer, and strands of custom sequences are commercially available.  Strands can be purified by denaturing gel electrophoresis if needed, and precise concentrations determined via any of several nucleic acid quantitation methods using ultraviolet absorbance spectroscopy.
  The fully formed target structures can be verified using 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.  Fluorescent labeling and Förster resonance energy transfer (FRET) are sometimes used to characterize the structure of the complexes.
  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.
caption: Gel electrophoresis methods, such as this 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.
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