Charles Fracchia

Origami basics

DNA origami uses a scaffold strand -often from a bacteriophage (e.g: M13)- as the backbone DNA to be folded. This is a single-stranded piece of DNA (ssDNA) that is then guided into a precise 3D structure by complementary short strands called staples. These staples hybridise (Watson-Crick base pairing: A to T and C to G) to multiple specific regions of the scaffold The CADnano software is used to create these structures. The latest versions make use of the 3D modeling software Maya to give a 3D preview of the origami structure.

More links

Wikipedia article on DNA origami

Lego-style assembly of nanoBlocks


In order to achieve lego-style assembly of origami structures, an attachment strategy needs to be worked out. Intuitively, one would assume that increased number of linkers between two bricks results in increased rigidity. Unfortunately this has not been decisively shown in what is a relatively recent field and thus represents the goal for this class. The longer term goal is to create bricks that can self assemble into a large (1 µm3), user-defined structures.

General Design

Biological research is a slower-paced endeavor that often fails ungracefully and makes debugging impossible. It is therefore essential to think ahead a build structures that will easily be assessed through the available imaging technologies (TEM, AFM). To this end, I chose to build a rectangle with a 1:2 Width:Length ratio. Because DNA origami uses M13 virus DNA, there is a maximum length of DNA that can be used. This length varies with different mutants of the virus. A common sequence that is used in DNA origami is M13mp18 (7249 bp) because of its commercial availability. Some other variants like M13 p8634 (8634 bp) have a significantly larger DNA backbone and thus enable larger structures. However, commercial availability was considered to be a great advantage and thus the structure was build to not exceed the 7249 bp that M13mp18 allows.


In order to meet the design constraints put on the system (scaffold length, Width:Length ratio) while maximizing the size of the individual bricks, I made an excel spreadsheet to calculate the average length of the helices in the rectangular structure.

General design principles

Design grid selection

Seam placement

Helix stacking

Staple placement

Basepairs per turn and twist correction