Characterization of 3D DNA Assemblies Using Cryogenic Electron Microscopy

Abstract

DNA nanotechnology utilizes DNA double strands as building units for self-assembly of DNA nanostructures. The specific base-pairing interaction between DNA molecules is the basis of these assemblies. After decades of development, this technology has been able to construct complex and programmable structures. With the increase in delicate nature and complexity of the synthesized nanostructures, a characterization technology that can observe these structures in three dimensions has become necessary, and developing such a technology is considerably challenging. DNA assemblies have been studied using different characterization methods including atomic force microscopy (AFM), scanning electron microscopy(SEM), and transmission electron microscopy(TEM). However, the three-dimensional(3D) DNA assemblies always collapse locally due to the dehydration during the drying process. Cryogenic electron microscopy(cryo-EM) can overcome the challenge by maintaining three-dimensional morphologies of the cryogenic samples and reconstruct the 3D models from cryogenic samples accordingly by collecting thousands of two-dimensional(2D) projection images, which can restore their original morphologies in solution. Here, we have reviewed several typical cases of 3D DNA-assemblies and highlighted the applications of cryo-EM in characterization of these assemblies. By comparing with some other characterization methods, we have shown how cryo-EM promoted the development of structural characterization in the field of DNA nanotechnology.