Atomic force microscopy analysis of orientation and bending of oligodeoxynucleotides in polypod-like structured DNA
DNA nanostructure, atomic force microscopy, self-assembly, nanotechnology, structure–activity relationship
We previously demonstrated that polypod-like structured DNA, or polypodna, constructed with three or more oligodeoxynucleotides (ODNs), is efficiently taken up by immune cells such as dendritic cells and macrophages, depending on its structural complexity. The ODNs comprising the polypodna should bend to form the polypod-like structure, and may do so by adopting either a bendtype conformation or a cross-type conformation. Here, we tried to elucidate the orientation and bending of ODNs in polypodnas using atomic force microscopy (AFM). We designed two types of pentapodnas (i.e., a polypodna with five pods) using 60- to 88-base ODNs, which were then immobilized on DNA origami frames. AFM imaging showed that the ODNs in the pentapodna adopted bend-type conformations. Tetrapodna and hexapodna also adopted bend-type conformations when they were immobilized on frames under unconstrained conditions. These findings provide useful information toward the coherent design of, and the structure–activity relationships for, a variety of DNA nanostructures.
Tsinghua University Press
Tomoki Shiomi,Mengmeng Tan,Natsuki Takahashi,Masayuki Endo,Tomoko Emura,Kumi Hidaka,Hiroshi Sugiyama,Yuki Takahashi,Yoshinobu Takakura,Makiya Nishikawa, Atomic force microscopy analysis of orientation and bending of oligodeoxynucleotides in polypod-like structured DNA. NanoRes.2015, 8(12): 3764–3771