Materials and Methods
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.
Read more about this topic: DNA Nanotechnology
Famous quotes containing the words materials and/or methods:
“Herein is the explanation of the analogies, which exist in all the arts. They are the re-appearance of one mind, working in many materials to many temporary ends. Raphael paints wisdom, Handel sings it, Phidias carves it, Shakspeare writes it, Wren builds it, Columbus sails it, Luther preaches it, Washington arms it, Watt mechanizes it. Painting was called “silent poetry,” and poetry “speaking painting.” The laws of each art are convertible into the laws of every other.”
—Ralph Waldo Emerson (1803–1882)
“A writer who writes, “I am alone” ... can be considered rather comical. It is comical for a man to recognize his solitude by addressing a reader and by using methods that prevent the individual from being alone. The word alone is just as general as the word bread. To pronounce it is to summon to oneself the presence of everything the word excludes.”
—Maurice Blanchot (b. 1907)