Designing a Bio-responsive Robot from DNA Origami

Summary

DNA origami is a powerful method for fabricating precise nanoscale objects by programming the self-assembly of DNA molecules. Here, we describe how DNA origami can be utilized to design a robotic robot capable of sensing biological cues and responding by shape shifting, subsequently relayed to a desired effect.

Abstract

Nucleic acids are astonishingly versatile. In addition to their natural role as storage medium for biological information¹, they can be utilized in parallel computing^2,3 , recognize and bind molecular or cellular targets^4,5 , catalyze chemical reactions^6,7 , and generate calculated responses in a biological system^8,9. Importantly, nucleic acids can be programmed to self-assemble into 2D and 3D structures^10-12, enabling the integration of all these remarkable features in a single robot linking the sensing of biological cues to a preset response in order to exert a desired effect.

Creating shapes from nucleic acids was first proposed by Seeman¹³, and several variations on this theme have since been realized using various techniques^11,12,14,15 . However, the most significant is perhaps the one proposed by Rothemund, termed scaffolded DNA origami¹⁶. In this technique, the folding of a long (>7,000 bases) single-stranded DNA 'scaffold' is directed to a desired shape by hundreds of short complementary strands termed 'staples'. Folding is carried out by temperature annealing ramp. This technique was successfully demonstrated in the creation of a diverse array of 2D shapes with remarkable precision and robustness. DNA origami was later extended to 3D as well^17,18 .

The current paper will focus on the caDNAno 2.0 software¹⁹ developed by Douglas and colleagues. caDNAno is a robust, user-friendly CAD tool enabling the design of 2D and 3D DNA origami shapes with versatile features. The design process relies on a systematic and accurate abstraction scheme for DNA structures, making it relatively straightforward and efficient.

In this paper we demonstrate the design of a DNA origami nanorobot that has been recently described²⁰. This robot is 'robotic' in the sense that it links sensing to actuation, in order to perform a task. We explain how various sensing schemes can be integrated into the structure, and how this can be relayed to a desired effect. Finally we use Cando²¹ to simulate the mechanical properties of the designed shape. The concept we discuss can be adapted to multiple tasks and settings.

Protocol

The robot we will design in this paper responds to a protein P by making a cargo C available to bind to receptors on the surface of a chosen target cell. The robot is shown in Figure 1. C may be a receptor-blocking drug; a growth factor etc., and a way to chemically link it to a DNA oligonucleotide must be available that does not destroy its function. The robot has two states. When inactive, DNA gates on the two external 'lips' are hybridized, making sure the robot remains closed such that any cargo loaded within it is securely sequestered. In the presence of protein P, the gates open by either one of severa....

Results

Figures 1-25 are screenshots of the caDNAno 2.0 interface showing the design process step-by-step. The cross-section of the shape was first outlined (Figure 3), followed by automatic addition of scaffold strand fragments and completion of the entire scaffold path (Figure 7). Staple strands are automatically added (Figure 12), broken according to user-defined parameters (Figure 14), and manually edited to adapt the staples to the de.......

Discussion

DNA origami enables us to fabricate accurately defined objects with arbitrary features at the nanoscale. An important next step would be the integration of function into these designs. While many applications and challenges could be addressed with this technology, there is a particular interest in fabricating therapeutic and scientific robots from DNA origami, as these represent a natural milieu of DNA. DNA already interfaces with molecular machinery in cells as a genetic information storage medium. Interestingly,.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Autodesk Maya 2012	Autodesk		A student/academic account needs to be created first (see platform-specific instructions in http://cadnano.org)
caDNAno 2.0 (software)	(Open source)		Software for the design of DNA origami structures http://cadnano.org
Cando (webpage)	(Open source)		Webpage running a simulator of DNA origami shapes http://cando-dna-origami.org