Two Dimensional Ordering of DNA Origami Using Stacking Bonds

The ability to create rationally designed DNA nanostructures has grown significantly since the method of DNA origami was introduced by Paul Rothemund in 2006. In an effort to scale up the physical size we have designed structures in order to study the directed stacking behavior exhibited by DNA structures. These structures were made using a 7000 base single stranded DNA as a “scaffold” that is held in place by numerous short single stranded DNA molecules using Watson-Crick base pairings. In designing these structures, we made use of the computer programs caDNAno, and CanDo to predict the thermal stability and structural integrity of the design. The symmetry in our design affords the ability to create long chains of stacked origami structures. The implications of this method have the potential to solve problems facing nanotechnological advancements such as the organization of nanoparticles on a substrate.