Single Molecule Force Control Drives the Rapid Assembly of DNA Nanostructure

Abstract

DNA is an attractive material for building a nanostructure because of its programmability, stability and feasibility of mass production. The DNA origami technique has further advanced the DNA-based nanostructure by providing a platform to design and build versatile structures with site-specific modifications. Unlike protein and RNA whose folding landscapes are evolutionarily tailored, however, DNA nanostructures adopt their minimum energy conformations by navigating much more rugged and complex folding landscapes. Therefore, current thermal folding protocol is usually very time-consuming and the yield is not very high especially for complex 3d structures. Also, intermediate states and exact folding mechanism of DNA origami remains to be understood. Here, by using single molecule force instruments, we separated the binding of staple strands from folding process to avoid a multitude of kinetic traps in the rugged folding landscape and guide the rapid and efficient folding of DNA nanostructures. We stretched the scaffold DNA using 5 pN of tension and hybridized with its staple strands to create an intermediate state where the scaffold DNA is fully stretched and covered by staple strands. Following replacement process between redundant staple strands folds the DNA nanostructure within 5 minutes. Our study demonstrates that an active mechanical control of the folding landscape of biological polymer can promote both folding rate and yield. We anticipate that our ability to manipulate the folding pathway will lead to the better understanding and design of DNA origami technique.