DNA origami

DNA origami is the nanoscale folding of

DNA origami was the cover story of Nature on March 16, 2006.^[3] 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.^[4]

Overview

The idea of using DNA as a construction material was first introduced in the early 1980s by

One of the advantages of using a DNA Origami nanostructure over an otherwise classified DNA nanostructure is the ease of defining finite structures [9]. 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 ^[9].

Applications for DNA Origami are primarily focused around the ability to exert fine control on systems, especially by constraining positions of molecules, typically by attachment to the DNA Origami nanostructures. Current applications are primarily focused around sensing and drug delivery, but many additional applications have been investigated.

To produce a desired shape, images are drawn with a

Bottom-up self-assembly methods are considered promising alternatives that offer cheap, parallel synthesis of nanostructures under relatively mild conditions.

Since the creation of this method, software was developed to assist the process using CAD software. This allows researchers to use a computer to determine the way to create the correct staples needed to form a certain shape. One such software called caDNAno is an open source software for creating such structures from DNA. The use of software has not only increased the ease of the process but has also drastically reduced the errors made by manual calculations.^[10][5]

Dynamic Structures and Modifications

As in the broader field of DNA nanotechnology, DNA Origami may be made dynamic in nature through the use of a variety of methods. The three primary methods of creating a dynamic DNA Origami machine are toehold mediated strand displacement, enzymatic reactions, and base stacking ^[11]. 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 ^[12] or leveraging less commonly used DNA self-assembly phenomena like G-quadruplexes or i-motifs which can be pH sensitive. ^[13].

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 ^[14][15][16]. Other, less common applications comes in sensing moving mechanisms in vivo such as the unwinding of helicase^[17].

Applications

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.^[8][18] The following paragraphs list some of the reported applications conducted in the laboratories with clinical potential.

Researchers at the Harvard University Wyss Institute reported the self-assembling and self-destructing drug delivery vessels using the DNA origami in the lab tests. The DNA nanorobot they created is an open DNA tube with a hinge on one side which can be clasped shut. The drug filled DNA tube is held shut by a DNA aptamer, configured to identify and seek certain diseased related protein. Once the origami nanobots get to the infected cells, the aptamers break apart and release the drug. The first disease model the researchers used was leukemia and lymphoma.^[19]

Researchers in the National Center for Nanoscience and Technology in Beijing and Arizona State University reported a DNA origami delivery vehicle for Doxorubicin, a well-known anti-cancer drug. The drug was non-covalently attached to DNA origami nanostructures through intercalation and a high drug load was achieved. The DNA-Doxorubicin complex was taken up by human breast adenocarcinoma cancer cells (MCF-7) via cellular internalization with much higher efficiency than doxorubicin in free form. The enhancement of cell killing activity was observed not only in regular MCF-7, more importantly, also in doxorubicin-resistant cells. The scientists theorized that the doxorubicin-loaded DNA origami inhibits lysosomal acidification, resulting in cellular redistribution of the drug to action sites, thus increasing the cytotoxicity against the tumor cells.^[20][21]

In a study conducted by a group of scientists from

DNA is folded into an octahedron and coated with a single bilayer of phospholipid, mimicking the envelope of a virus particle. The DNA nanoparticles, each at about the size of a virion, are able to remain in circulation for hours after injected into mice. It also elicits much lower immune response than the uncoated particles. It presents a potential use in drug delivery, reported by researchers in Wyss Institute at Harvard University.^[25][26]

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.^[27]

Similar approaches

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.^[28][29]

See also

• RNA origami
• DNA nanotechnology
• Molecular self-assembly
• Folding@home
• Origami

References