ДНҚ оригами: Нанодәрежедегі ДНҚ құрылымдарын қалыптастыру

Folding of DNA to create two and three dimensional shapes at the nanoscale

DNA origami is the nanoscale folding of DNA to create arbitrary two and three dimensional shapes at the nanoscale. The specificity of the interactions between complementary base pairs make DNA a useful construction material, through design of its base sequences. DNA is a well understood material that is suitable for creating scaffolds that hold other molecules in place or to create structures all on its own. DNA origami was the cover story of Nature on March 16, 2006. Since then, DNA origami has progressed past an art form and has found a number of applications from drug delivery systems to uses as circuitry in plasmonic devices; however, most commercial applications remain in a concept or testing phase.

The idea of using DNA as a construction material was first introduced in the early 1980s by Nadrian Seeman. The method of DNA origami was developed by Paul Rothemund at the California Institute of Technology. In contrast to common top down fabrication methods such as 3D printing or lithography which involve depositing or removing material through a tool, DNA Nanotechnology, as well as DNA Origami as a subset, is a bottom up fabrication method. By rationally designing the constituent subunits of the DNA polymer, DNA can self assemble into a variety of shapes. The process of constructing DNA Origami involves the folding of a long single strand of viral DNA (typically the 7,249 bp genomic DNA of M13 bacteriophage) aided by multiple smaller "staple" strands. These shorter strands bind the longer in various places, resulting in the formation of a pre defined two or three dimensional shape. Examples include a smiley face and a coarse map of China and the Americas, along with many three dimensional structures such as cubes. There are several DNA properties that make the molecule an ideal building material for DNA origami. DNA strands have a natural tendency to bind to their complementary sequences through Watson–Crick base pairing. This allows staple strands to locate the position on the scaffold strand without any external manipulation, leading to self assembly of the desired structure. The specific sequence of bases in DNA gives the material an element of programmability by determining its binding behavior. Carefully designing the sequences of the staple strands enables scientists to precisely direct the scaffold strand’s folding into a predetermined shape with high precision. On a chemical level, the hydrogen bonds that exist between the complementary base pairs provide strength and stability to the folded DNA origami structures. Additionally, DNA is a relatively stable molecule, offering resilience in physiological conditions. In the design of some other DNA nanostructures, it can be impractical to design the extremely large number of individualized strands if the entire structure is composed of smaller strands. One method of bypassing the need for a huge number of different strands is to use repeating units, which comes with the disadvantage of a distribution of sizes and sometimes shapes. DNA Origami, however, forms discrete structures. While these methods are most commonly used, additional methods for creating dynamic DNA Origami machines exist, such as designing a directional component and using brownian motion to drive rotational movement of structures or leveraging less commonly used DNA self assembly phenomena like G quadruplexes or i motifs which can be pH sensitive. Modifications can be otherwise used to affect structural properties, to impart unique chemistry to the nanostructures, or to add stimuli responses to the nanostructures. Modifications to structures can be made through conjugation of molecules such as proteins, or through chemical modification of the DNA bases themselves. pH dependent responses, light dependent responses, and more have been shown through modified systems. One example application of creating dynamic structures is the ability to have a stimuli response resulting in drug release, which is presented by several groups. Other, less common applications comes in sensing moving mechanisms in vivo such as the unwinding of helicase.

Many potential applications have been suggested in literature, including enzyme immobilization, drug delivery systems, and nanotechnological self assembly of materials. Though DNA is not the natural choice for building active structures for nanorobotic applications, due to its lack of structural and catalytic versatility, several papers have examined the possibility of molecular walkers on origami and switches for algorithmic computing. The following paragraphs list some of the reported applications conducted in the laboratories with clinical potential. In a study conducted by a group of scientists from iNANO center and CDNA Center at Aarhus university, researchers were able to construct a small multi switchable 3D DNA Box Origami. The proposed nanoparticle was characterized by AFM, TEM and FRET. The constructed box was shown to have a unique reclosing mechanism, which enabled it to repeatedly open and close in response to a unique set of DNA or RNA keys. The authors proposed that this "DNA device can potentially be used for a broad range of applications such as controlling the function of single molecules, controlled drug delivery, and molecular computing." Nanorobots made of DNA origami demonstrated computing capacities and completed pre programmed task inside the living organism was reported by a team of bioengineers at Wyss Institute at Harvard University and Institute of Nanotechnology and Advanced Materials at Bar Ilan University. As a proof of concept, the team injected various kinds of nanobots (the curled DNA encasing molecules with fluorescent markers) into live cockroaches. By tracking the markers inside the cockroaches, the team found the accuracy of delivery of the molecules (released by the uncurled DNA) in target cells, the interactions among the nanobots and the control are equivalent to a computer system. The complexity of the logic operations, the decisions and actions, increases with the increased number of nanobots. The team estimated that the computing power in the cockroach can be scaled up to that of an 8 bit computer. A research group at the Indian Institute of Science used nanostructures to develop a platform to elucidate the coaxial stacking between DNA bases. This approach utilized DNA PAINT based super resolution microscopy for visualizing these DNA nanostructures and performed DNA binding kinetics analysis to elucidate the fundamental force of base stacking that helps stabilize the DNA double helical structure. They went on to assemble multimeric DNA origami nanostructures termed as a 'three point star' into a tetrahedral 3D origami structure. The assembly relied chiefly on base stacking interactions between each subunit. The group further showed that the knowledge of such interactions can be used to predict and thus tune the relative stabilities of these multimeric DNA nanostructures.

The idea of using protein design to accomplish the same goals as DNA origami has surfaced as well. Researchers at the National Institute of Chemistry in Slovenia are working on using rational design of protein folding to create structures much like those seen with DNA origami. The main focus of current research in protein folding design is in the drug delivery field, using antibodies attached to proteins as a way to create a targeted vehicle.