Scaffold & Staples
Background
DNA origami, a technology to create 2D or 3D structure with DNA, is mainly composed of two elements: “scaffold” and “staples”. The former functions as the backbone of the whole DNA structure, while the latter are binding pairs which stick to the scaffold. Scaffold is usually extracted from the DNA of bacteria or bacteriophage, which means that the sequences of scaffold is fixed. By designing the staples, researchers can bind these two components together and get the desired 3D structures.
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We choose the open-source software, caDNAno, as our tool to design the structures. First, we draw the outline and select an appropriate scaffold as the backbone. Second, caDNAno can calculate the stabilities and generate the most suitable staples for the structure. Third, we modify the staples at linking cross-sections and add the ssDNA(single-strand DNA) at specific positions. Finally, we export the sequences and complete the design. (You can find our caDNAno file here and all design related file here.)
Scaffold
The length of the scaffold we choose will limit the size of the origami structure. We use p7560 derived from M13mp18 because the size of our base is approximately 7400 base pairs.
Scaffold of base
Scaffold of right lid
Scaffold of left lid
Staples
After the scaffold is determined, caDNAno can generate staples sequences automatically. What we need to do is to link adjacent bars on the “honeycomb” together. All the staples are 10-60 bases long, and thus, the base in our structure is made up of 1 p7560 scaffold and 255 different staples.
Scaffold&Staple of base
Scaffold&Staples of right lid
Scaffold&Staples of left lid
