In March 2006, Dr. Paul Rothemund published an article in Nature that caught the attention of the NanoEngineer-1 development team. Called "Folding DNA to create nanoscale shapes and patterns", Dr. Rothemund describes the scaffolded DNA origami method, a process he invented for synthesizing arbitrary 2D structures composed of DNA. The technique involves mixing hundreds of short "staple strands" with a long "scaffold strand" which gets folded into the desired shape. Using this method, it is possible to create any shape up to 100 nanometers across with a minimum feature size of 6 nanometers. The process is quick and simple (structures are created in a single-pot reaction in about an hour), it results in high yeild (60-90%) and can create large numbers of structure in parallel (50 billion structures in a 50 microliter drop of DNA solution).

For these reasons and others, the NE1 development team agreed that DNA origami (DNAO) was an important milestone in the field of structural DNA nanotechnology. After discussing it, we made the decision to develop a new DNAO design module for NE1. When complete, NE1 will make origami design much easier and accelerate research by reducing the time needed to model and synthesize custom structures.

After learning about our plans to develop a DNAO module for NE1, Dr. Rothemund invited me and my daughter to visit the Winfree Lab at Caltech to learn about scaffolded DNA origami first hand. He wanted to share the experience of designing, fabricating and imaging our own design. We jumped at the opportunity and soon after we arrived on campus to begin working with Paul. My daughter and I kept a detailed journal of what we did and published it (with photos) on the NE1 wiki.