Assembly of a DNA Origami Chinese Knot by Only 15% of the Staple Strands

• Published in: Chembiochem : a European journal of chemical biology Vol. 21; no. 15; pp. 2132 - 2136
• Main Authors: He, Kai, Li, Zhe, Liu, Longfei, Zheng, Mengxi, Mao, Chengde
• Format: Journal Article
• Language: English
• Published: Germany Wiley Subscription Services, Inc 03.08.2020
• Subjects: Assembly; Atomic force microscopy; Deoxyribonucleic acid; DNA; DNA polymerase; DNA structure; DNA-directed DNA polymerase; Folding; Nanostructure; Prototyping; Scaffolds; Strands; Topology
• ISSN: 1439-4227; 1439-7633
• DOI: 10.1002/cbic.202000106

As a giant leap in DNA self‐assembly, DNA origami has exhibited an unprecedented ability to construct nanostructures with arbitrary shapes and sizes. In typical DNA origami, hundreds of short DNA staple strands fold a long, single‐stranded (ss) DNA scaffold cooperatively into designed nanostructures. However, large numbers of DNA strands are expensive and would hinder applications such as pharmaceutical investigations because of the complicated components. Therefore, one challenge is how to reduce the number of staple strands needed to construct DNA origami. For a DNA origami structure, the scale‐free folding pattern of the scaffold strand is determined by staple strands at the branching vertexes. Simple duplex regions help to define the size‐related features of the origami geometry. In this study, we hypothesized that a scaffold strand can be correctly folded into a designed topology by using only staple strands involved in branching vertexes. After assembly, any remaining, flexible, single‐stranded regions of the scaffold could be converted into rigid duplexes by DNA polymerase to achieve the designed geometric structures. To demonstrate the concept, we used only 18 staple strands (covering 15 % of the scaffold strand) to assemble a porous DNA nanostructure, which was visualized by atomic force microscopy (AFM). This study helps understanding of the role of cooperativity in origami folding, and provides a cost‐effective approach for small‐scale prototyping DNA origami. A DNA nanostructure with large pores was prepared by a cost‐effective fold‐and‐fill (F&F) strategy. A small number of chemically synthesized DNA strands defined the routing path of a long scaffold DNA strand, then the majority of the supporting strands were enzymatically synthesized in situ to define the final geometry.