Citation:
[D-1]
Kuzuya, A. and M. Komiyama, DNA origami: fold, stick, and beyond. Nanoscale, 2010. 2(3): p.310- 22.
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Scaffold and Staple
caDNAno is an open-accessed software which simplify the process of designing three-dimension DNA origami. It is a convenient tool that we can draw the blueprint of DNA origami. After we determine a kind of scaffold, caDNAno can automatically generate each complementary staple to fit the design of structure, and then export the sequence result to a file.
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Scaffold
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The size of DNA origami structures depends on scaffold length. The most common scaffold used in DNA origami is a 7249bp M13mp18 genome which is a circular single-stranded DNA isolated from bacteriophage. However, due to the structure we designed, we chose a longer scaffold, p7560, isolated from M13mp18 derivative. Figure D2 shows the backbone and the shape of a monomer of NanoMuscle in caDNAno.
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Scaffold + Staple
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After we added staples on scaffold in caDNAno, many staple sequences were generated, and we were able to do primer synthesis according to these sequences. Figure D3 illustrates the total nanostructure composed of scaffold and staples in caDNAno. There are three basic components in NanoMuscle, which will be mentioned in Structure page.
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Figure D1. The basic structure of DNA origami：Staple strands + Scaffold. [D-1]
Figure D2. Scaffold design
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Figure D3. Scaffold + staple design. Red part is Ring; green part is Axle; blue part is Base.
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DNA origami is a nanoscale folding of DNA to create 2D or 3D structure. There are two key elements in this technique. One is a backbone DNA called “scaffold” and the other is a small section of DNA called “staple” which can stick on scaffold by Watson-Crick base pairing as Figure D1. As a result, researchers can design staples to bind specific complementary position on scaffold and fold a unique structure.
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