Paul Rothemund’s Scaffolded DNA Origami Method

DNA Origami

Scaffolded DNA Origami Paul Rothemund invented a technique called Scaffolded DNA Origami that allows a person to synthesize flat DNA structures from a computer design. Here are six structures that he designed and synthesized using his method. The colored row shows the computer rendering of each designed origami shape. The computer then creates a recipe on how to make the structure out of DNA. The set of images in the third row were taken with an Atomic Force Microscope after Rothemund made the six origami shapes. Each square image is 165 nm by 165 nm. Paul Rothemund “Folding DNA to create nanoscale shapes and patterns” Nature, 440:297-302 (2006).

DNA Origami Folding Process This picture shows the process for DNA origami. The red strand is the M13 viral genome DNA, which is a single strand of DNA that is 7,249 bases long. M13 Viral DNA is different from human DNA because there is only one strand instead of two strands that are combined in a double helix structure. The M13 Virus Strand is also a loop like a rubber band instead of a string with two ends. Over 216 blue strands in the picture represent the shorter staple strands that are each 20-30 bases long. These staple strands have to be custom made and ordered from a DNA synthesis house. The M13 strand and the staple strands create a double helix structure when mixed together, heated up, and then cooled down back to room temperature. All the staple strands wind up making a double helix along the entire length of the M13 viral strand. M13 viral genome DNA & Staple Stands Self-assembles into designed structure

Staple crossover Here, a staple strand combines with a scaffold strand in two specific places. Each staple strand has two sections that connect to different places on the M13 scaffold strand. Each section of the staple strand is unique and can only bond to a certain place on the scaffold strand. The staple strand pinches the scaffold strand, which is how the folding process takes place. The place on the staple strand that pinches the two different spots on the scaffold strand is called the staple crossover.

Surface patterns with hairpin loops Patterns can be created on the surface of DNA origami by replacing a staple strand with a version that contains a hairpin loop. The hairpin loop is shown on the right in yellow. Staple without hairpin loop Staple with hairpin loop

Hairpin becomes a “pixel” on origami surface Staple Hairpin (yellow) The hairpin loop sticks above the origami surface, becoming a pixel of a pattern. Staple (blue) Scaffold (red)