DNA Origami Design: A How-To Tutorial

Abstract

While the design and assembly of DNA origami are straightforward, its relative novelty as a nanofabrication technique means that the tools and methods for designing new structures have not been codified as well as they have for more mature technologies, such as integrated circuits. While design approaches cannot be truly formalized until design-property relationships are fully understood, this document attempts to provide a step-by-step guide to designing DNA origami nanostructures using the tools available at the current state of the art.

Generating DNA Origami Nanostructures through Shape Annealing

“…It would be interesting to apply more constraints, such as an outer mesh, for the coating application in order to automate the scaffold routing of DNA origami molds with tunable and uniform thickness. We will also explore other objective functions or constraints to address long standing challenges in the field of DNA origami design, such as limited knowledge in design-property relationships to decrease the design-iteration loop, increase design stability, and increase the yield in DNA origami nanostructures [16]. For example, Ke et al developed design rules empirically to increase the yield in multilayer DNA origami assemblies, which could be incorporated into our shape annealing platform in the future [42].…”

“…Currently, DNA origami design optimization is performed iteratively by human designers, where even veteran designers often get stuck in an infinite iterative design loop in search of the ideal design [16]. Here, we present a novel, formal approach for optimizing the design process for DNA origami through automation.…”

Translating DNA origami Nanotechnology to Middle School, High School, and Undergraduate Laboratories

“…The device is referred to as the "Horse," as in the original publication, inspired by the concept of the Trojan Horse. The basic DNA origami nanostructure design process 20 follows several common steps: 1) defining the geometry (i.e., cross-section in terms of dsDNA helices and the lengths of those helices); 2) scaffold routing; 3) staple routing; and 4) staple sequence determination. These steps are typically carried out using custom computer aided design (CAD) software.…”

“…However, current DNA origami methods are not suitable for translation to classrooms, even for well-equipped instructional laboratories. DNA origami development often require days, or up to several weeks of design and optimization [19][20][21] . Furthermore, fabrication typically takes many hours or days and is carried out on costly PCR thermocyclers 19,22 , while the analysis of structure folding and behavior can take several hours with the most common first step analysis carried out using laboratory gel electrophoresis equipment 19,23 .…”

Synthesizing the biochemical and semiconductor worlds: the future of nucleic acid nanotechnology

“…Origami is modular, simple to design, [29][30][31] does not require expensive oligomer purification, and has cooperative energetics leading to relatively high yields of correctly assembled structures. The same origami designs can be reused repeatedly for a wide variety of experiments.…”