Structural Biochemistry/Structural DNA Nanotechnology

Overview
Structural DNA nanotechnology is concentrated on synthesizing and building sequences of nucleic acid complexes with nano particles and nano materials. Structural DNA nanotechnology aims to achieve complete control of DNA with respect to its structure in space and time. With the use of SDN, scientists can manipulate the structure of DNA into any shape. Nanotechnology and nano science are inherent subjects of the construction of DNA, because the structure and dimensions are measured on the nano scale.

Fundamental concepts


DNA nanotechnology creates complex structures out of nucleic acids by taking advantage of the specificity of base pairing in nucleic acid molecules. The structure of a nucleic acid molecule consists of a sequence of nucleotides, distinguished by which nucleobase they contain (A,C,T,G). Nucleic acids have the property that two molecules will bind to each other to form a double helix only if the two sequences are complementary, meaning that they form matching sequences of base pairs, with A's only binding to T's, and C's only to G's. Because the formation of correctly matched base pairs is energetically favorable, nucleic acid strands are expected in most cases to bind to each other in the conformation that maximizes the number of correctly paired bases. This property, that the sequence determines the pattern of binding and the overall structure, is used by the field of DNA nanotechnology in that sequences are artificially designed so that a desired structure is favored to form.

Most if not all DNA nano-structures utilize the DNA branched structure, the most basic of which looks like a 4-way intersection. This simple rigid branched structure is made with 4 separate complementary DNA structures. Though there are naturally occurring branched structures the Holiday junction being an example, the difference between those and the artificially made branches for nanotechnology is that the base sequence of each arm in the artificial structure is different, meaning that the junction point is fixed in a certain position, giving rigidity and stability to the structure.

Initial DNA Nanotechnology Process
Motif design and sequence design are the two major steps needed for the initial process of structural DNA nanotechnology. It is essential to generate new DNA motifs that can self assemble from existing strands of DNA. Motif design relies upon the "reciprocal exchange" between the connections of two DNA double helix strands into the formation of new DNA motifs. Coinciding with motif design, a sequence design is necessary in order to classify individual strands. The sequence design is highly important and vital to the self assembly of the previously designed motif.

Constructs and DNA Origami
With the use of motif design, sequence design and nano materials, DNA can be (and has been) formed into numerous different constructs. Scaffolding strands and helper strands are utilized in the folding and formation of DNA origami. Paul W.K. Rothemund demonstrated that with strand folding, he was able to create a smiley face of DNA. One of the important discoveries of these constructs and origami creations is the increase in surface area available to the DNA. This can be utilized in the embedding of nano mechanical devices, building three dimensional objects and even potential therapeutic delivery uses.

DNA-Based Nanomechanical Devices
In addition to triumphs in the development of the structure of DNA nanomaterials in space, efforts have been made with considerable success to develop the controlled changing of these structures in time. Such DNA based structures fall under the study of nanomechanical devices. Nanomechanical motion can achieved by the exploitation of DNA structural transitions such as B-Z transition and the controlled conversion of a PX structure to that of a JX2 structure. Motion can also be achieved using DNA sequence dependency. Virtually every DNA sequence dependent device exploits a technique involving as the addition of an 8-nt "toehold" to a controlling strand in the device to allow for a change of state. Initially, this toehold in the controlling strand is unpaired, but when a complete complement is added to the strand, the toehold and its complement bind together, effectively removing the remainder of the strand by means of branch migration. Examples of devices that utilize this technique are the construction of a pair of molecular tweezers developed by Bernard Yurke and his co-workers, and nanomechanical devices constructed to walk on DNA "sidewalks" in a controlled manner by means of both human intervention, and more recently, autonomous action.