Introducing DNA Origami

DNA is a molecule with many uses. All life on earth has used DNA for billions of years, encoding all form and function that exists, and has ever existed, in the chemical patterns of the four nucleotide bases.
DNA’s ubiquity means that a sequence from one organism can be put to use by another organism as if it were its own. Researchers in the field of synthetic biology use this property to confer new function to cells and organisms using chemically synthesised DNA that is equal in every way to natural DNA.
Synthetic DNA has been pivotal to molecular biology applications, including the development of model cells that provide a research platform to better understand disease, and the development of engineered microorganisms that act as microfactories, able to make useful chemicals from waste.
Recently, DNA’s use in research and industry has branched beyond biological systems. Microsoft, in collaboration with Twist Bioscience and the University of Washington, used the four nucleic acids that encode life to instead encode and store large volumes of computer data. Companies like SelectaDNA® are instead using the programmable and traceable nature of DNA sequences as a security tool. DNA of a specific sequence is stored in a spray that can be applied to objects or stored in anti-theft devices to deter and identify perpetrators in forensics.

The specific sequence of DNA makes the molecule traceable.
 
One of the most intriguing applications for DNA outside of biology is being upheld by a rapidly growing group of scientists in the emergent field of DNA origami. In this field, DNA is wholly abstracted from its biological role, where it is used solely as a building material.
Nadrain Seeman first proposed DNA as an ideal nano-scale building material in the Journal of Theoretical Biology in 1982, in which he imagined two and three-dimensional lattice structures that could possibly be built with DNA.
Contemporary DNA origami practices were introduced in the March 2006 edition of Nature. Paul Rothemund of the California Institute of Technology published a robust and repeatable DNA origami protocol and applied it to reliably construct multiple two dimensional shapes, including a smiley face, a square and a five-pointed star.
Today, DNA origami and its community are growing rapidly. Engineering practices underlie the field, which has a biohacker ethos. Researchers and tinkerers are designing and building nanoscale “things” with the vision of advancing the field or improving the world around us.
The principals behind DNA origami
First, let’s go through a few principal ideas required to understand how DNA origami works:
  • DNA comprises two strands of deoxyribonucleotides, which comprise four types of nucleotide base: A, T, C and G. Nucleotide bases pair with corresponding nucleotide bases always in the form A - T and C - G. Deoxyribose sugars form a double backbone housing the base pairs.
  • Any single strand of DNA can base pair with any other single strand of complementary sequence, forming a double helix with approximately 10.5 bases per complete helix twist.
  • With this base pairing property, cells occasionally produce different DNA structures with highly specialised functions. These are often branching structures formed from more than one double helix, examples being a Holliday junction and a replication fork.
  • Two independent, non-complementary single strands can be made rigid, and be connected to one another by another single strand that is complementary to both non-complementary strands. This principal is the cornerstone for all DNA origami.

DNA origami requires two ingredients: the scaffold and the staples. Staples are complementary to multiple parts of the scaffold, therefore can be designed to fold the scaffold into defined structures.

In current DNA Origami practices, there are two key ingredients required to turn DNA into a building material - scaffolds and staples. Scaffolds can be any long single stranded DNA with a known sequence. A well-studied strand that sees regular use in the field is the 7249-base genome of the M13 bacteriophage. Paul Rothemund first used this naturally occurring single stranded sequence in his seminal paper on DNA Origami. 
Staples on the other hand are small, single-stranded pieces of DNA. Typically, both halves of a staple are designed to base pair with different parts of the scaffold, forming double helices in these regions. When the staple forms base pairs across the scaffold, the scaffold bends and is held in place.
By adding multiple staples in solution with the scaffold, then heating the mixture and slowly cooling it, the scaffolds and staples form stable interactions across the entire scaffold length. As the mixture cools, a pre-defined shape made from many double helices begins to self-assemble.

Two-dimensional hollow triangle shapes formed by DNA origami, visualised by scanning probe microscopy. Each triangle is about 100 nm across. Source: wikicommons, Author: Mattias Fenner
 
As mentioned earlier, there are approximately 10.5 bases per complete 360° helix twist. Therefore, two- and three-dimensionality can be incorporated into the structures by altering the number of complementary bases between the staple and scaffold. For example, pairing every seven bases allows helices to be organised in a honeycomb lattice. Stacks of hexagons can then form three-dimensional structures.
Design of such structures is complex, requiring the careful planning of every staple position. It is standard practice for engineers to use computer-aided design to model and optimize their projects before they begin building. To make DNA origami simple and accessible, William Shih's laboratory in the Dana Faber Cancer Institute developed the open source 3D design tool caDNAno. Now in its second generation, caDNAno is being further developed by a collaboration between the Wyss institute and University of California, San Francisco. In this software suite it is possible to design staples and visualize nanostructures, making DNA origami open and accessible to wider communities of researchers.
Importantly any DNA sequence could be used as an origami scaffold in theory as the origami structure is driven by staple position and design. One of the first papers describing three dimensional DNA origami showed that, identical structures could be made with both the M13 genome and a plasmid encoding Green Fluorescent Protein. However, choosing a scaffold sequence requires consideration of the DNA synthesis properties. Repetitive sequences and sequences with an abundance of G’s and C’s are often impractical to synthesize with current technologies: always check with your provider first.  
What can be done with DNA origami?
 
For excellent DNA origami examples, check out BIOMOD. BIOMOD is an international competition between university students, where teams compete to produce innovative biomolecule-based constructions. DNA origami plays a big part in the competition, with many teams producing functional structures from DNA. For example, Team Tiny Trap from UNSW Australia, winners of the 2016 BIOMOD jamboree, created a 3D box with a spring-loaded hinge using DNA origami.
Researchers before Team Tiny Trap had shown that DNA origami boxes were possible. Other researchers had shown that DNA origami nanostructures could be designed to carry molecules of interest like the anti-cancer drug doxorubicin, and deliver this drug to cancer cells in a targeted fashion.
Team Tiny Trap aimed to build a DNA origami box that could snap closed on molecules of interest, safely carry the molecules inside to a target where the box opens to deliver a potent, directed molecule dose.
Their box was formed from layers of honeycomb lattices, with a depression in the center that would be able to be loaded with a molecule of interest.
A scanning electron micrograph of Team Tiny Trap’s Tiny box. These boxes can be seen to possess a dark region in the centre – the designed pit that will carry a payload. Source: BIOMOD. Author: Team Tiny Trap.
 
Not only was the team able to show that their design worked and nano-boxes could be made, they characterized how the trap worked in detail, as can be found on Team Tiny Trap’s website.
DNA origami is not just limited to boxes and 2D shapes. Other researchers have used DNA origami to design small bricks that snap together like legos to produce much larger structures, complex three-dimensional structures, including a rabbit, and increasingly complex DNA-based computers that are able to rapidly handle logic functions.
The field of DNA is only set to grow from here, powered by technologies like high throughput DNA synthesis, sophisticated CAD design tools and complementary efforts from open source collaboration like BIOMOD. Simply put, we are only scratching the surface of what is possible when treating DNA not as a biological material, but as a building material instead.