Jacob Magikes and Alex Liddle, researchers at the National Institute of Standards and Technology (NIST) who have studied DNA origami for many years, put together the first comprehensive guide to this technique. Their in-depth report provides a step-by-step guide to creating DNA origami nanostructures using state-of-the-art tools. They described their work in the Journal of Research.
In a new technique known as DNA origami, researchers fold long strands of DNA over and over to build many tiny three-dimensional structures, including miniature biosensors and drug delivery containers.
Pioneered at the California Institute of Technology in 2006, the DNA origami technique has attracted hundreds of new researchers over the past decade to create receivers and sensors that could detect and treat diseases in the human body, assess the impact of pollutants on the environment, and help many other biological applications.
Although DNA origami principles are simple, the tools and techniques of this technique for creating new structures are not always easy to understand and have not been well documented. Also, scientists new to this method did not have a single reference to find the most efficient way to build DNA structures and avoid the pitfalls that could have taken months or even years of research.
“We wanted to collect all the tools people developed in one place and explain things that cannot be said in a traditional magazine article. Review articles can tell you everything that everyone has done, but they won’t tell you how people did it.”
Jacob Magikes is a researcher at the National Institute of Standards and Technology (NIST).
DNA origami is based on complementary base pairs of DNA molecules to bind to each other. Among the four bases of DNA – adenine (A), cytosine (C), guanine (G), and thymine (T) – A binds to T and G to C. This means that a certain sequence of As, Ts, Cs, and Gs will find and will bind to its add-on.
Binding allows short strands of DNA to act like staples, holding portions of long strands folded or connecting individual strands. A typical origami design may require 250 staples. Thus, DNA can self-organize into various forms, forming a nanoscale framework. A set of nanoparticles can be attached, many of which are used for treatment, biological research, and environmental monitoring.
The use of DNA origami faces two challenges, according to Magix. First, the researchers create three-dimensional structures using base pairs A, G, T, and C. Also, they use these base-pair staples to twist and unwind the familiar double helix of DNA molecules so that they bend into specific shapes. It can be difficult to design and visualize. Majike and Liddle urge researchers to solidify their design intuition by creating 3D mock-ups, such as sculptures made with bar magnets, before they go into production. These models, which can show which aspects of the folding process are critical and less important, should then be flattened in 2D to be compatible with DNA origami CAD tools, which typically use 2D representations.
DNA folding can be done in several ways, some of which are less efficient than others, Magix notes. In fact, some strategies can be doomed to fail. Liddle and Magikes plan to complete their work with several additional manuscripts detailing how to create nanoscale devices with DNA successfully.