DNA Origami as a Nanoscopic Ruler For Super-Resolution Microscopy

Abstract

The possibility of highly parallel formation of nanostructures using self-assembly of DNA molecules provides a powerful tool for bottom-up fabrication. The DNA origami technique, involves folding a long single-stranded DNA scaffold using short DNA staple strands that can only bind at particular points along this scaffold. With this technique large numbers of identical structures can be assembled simultaneously in a single experiment. One of the most attractive features of the origami technique is the precise addressability of the DNA structures formed. Each staple strand can serve as an attachment point for many different kinds of molecules or other objects. Due to their small size, DNA nanostructures are commonly imaged using atomic force microscopy or electron microscopy, but with recent advances in far-field fluorescence microscopy beyond the diffraction limit (super-resolution microscopy), structures in the sub-200 nm regime become amenable also to optical analysis. We here show that the distance between fluorescently labeled staple strands bound on specific positions of rectangular DNA origami structures can be accurately determined using a variety of super-resolution techniques such as single-molecule high-resolution imaging with photo-bleaching (SHRImP), direct stochastic optical reconstruction microscopy (dSTORM), and Blink-Microscopy.