What is DNA origami?

DNA origami refers to an assembly technique that folds single-stranded DNA template molecules into target structures. This is done by annealing templates with hundreds of short ‘staple’ DNA strands.

Origami is a Japanese art of paper folding. The goal is to fold a flat sheet of paper into a finished sculpture. No cut, glue, or markings of the paper sheet should be used. Origami practitioners use a small number of basic folds to combine them into a variety of ways.  

Similarly to paper origami DNA origami uses intrinsic basic rules for folding DNA nanostructures. As XiaoZhi Lim recently pointed out in the Journal Nature, the double helix is a flexible, configurable rod, two (2) nanometers wide, and having a twist that repeats every 3.4 to 3.6 nm. However, the underlying principle for making DNA nanostructures are based on a simple rule: base-pair complementarity.

Hydrogen bonds that pair the bases adenine and thymine, and cytosine and guanine allow complementary DNA strands to form into a double helix spontaneously. In general, the two DNA strands are fully complementary. However, if the two strands are only partially complementary, both strands can accept multiple DNA molecules. DNA can form a four armed intermediary structure during cell division known as a Holliday junction. Over the years scientists were able to produce branched DNA structures containing six strands, stick cubes, branched DNA crystals and DNA tubes. Many different types of shapes can now be synthesized and folded.

Figure 1: Solved structures for DNA origami molecules. Left, ‘monoclonal stoichiometric’ single stranded DNA oligonucleotides, and, to the right, a 3D-origami object.

https://www.ncbi.nlm.nih.gov/Structure/pdb/4B8D;  https://www.ncbi.nlm.nih.gov/Structure/pdb/2YMF


DNA origami has now emerged as a new way for the design and synthesis of defined two-and three dimensional (2D and 3D) DNA nanostructures. The self-assembly reactions of DNA molecules enable the size expansion of the nanostructures.

Structural DNA nanotechnology is a new technology developed during the past 30 years. The nature of DNA molecules allowing for self-assembly makes it possible to construct novel DNA-based materials. For this approach, self-assembly protocols are utilized allowing the synthesis and folding of branched DNA molecules, for example, into polyhedral structures. Also, branched DNA motifs can be designed for the production of 2D and 3D periodic lattices of DNA or DNA crystals. Furthermore, DNA has been already used for the production of nanomechanical devices in which molecules can walk along strands of DNA or change their shapes.

DNA origami is created via self-assembly. The combination of heat and chemical denaturation of double-stranded DNA scaffold strands in the presence of staple strands, followed by a sudden drop in temperature and stepwise dialysis to remove chemical denaturant favors self-assembly. For DNA origami production DNA complementary reactions are exploited for controlling DNA structures. 


What is needed for the folding of DNA origami?

•  Typically a DNA scaffold or template DNA is needed. This will need to be designed first.

•  Before design select the desired shape of the final nanostructure. Software tools can help with the design, the placing of needed crossover points and the design of the short DNA stables required for folding.  

•  Single-stranded DNA sequences can be synthesized of up to 200 bases or somewhat  longer. Often, for longer DNA scaffold viral DNA is used.

•  Strands are mixed in the correct ratios with an excess of staple DNA.

•  Heating and cooling sometimes in combination with dialysis forms the structures via self-assembly.

•  Analysis via gelelectrophoresis allows detection of well-formed DNA nanostructures. DNA nanostructures are observed as sharp bands that migrate differently than the starting material.

•  Further characterization can be done using electron microscopy or atomic  force microscopy.