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Atomic force microscopy analysis of orientation and bending of oligodeoxynucleotides in polypod-like structured DNA

Nano Research 2015年第12期8卷 3764-3771页

作者： Tomoki Shiomi Mengmeng Tan Natsuki Takahashi Masayuki Endo tomoko emura Kumi Hidaka Hiroshi Sugiyama Yuki Takahashi Yoshinobu Takakura Makiya Nishikawa Department of Biopharmaceutics and Drug Metabolism Graduate School of Pharmaceutical Sciences Kyoto University Sakyo-ku Kyoto 606-8501 Japan Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Sakyo-ku Kyoto 606-8501 Japan Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto 606-8502 Japan

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 bend- type 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.

关键词： DNA nanostructure atomic force microscopy self-asse nanotechology structure-activity relationship

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A Photoresponsive DNA Nanodevices with Reversible Rotary Perfor mances

A Photoresponsive DNA Nanodevices with Reversible Rotary Per...

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第十届全国化学生物学学术会议

作者： Yangyang Yang Ryo Tashiro Yuki Suzuki tomoko emura Kumi Hidaka Hiroshi Sugiya ma Masayuki Endo Shanghai Key Laboratory of Chemical Biology School of PharmacyEast China University of Science and Technology Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Faculty of Pharmaceutical Sciences Suzuka University of Medical Science

Various DNA-based nanomachines have been developed to perform tasks on the nanometer scale using light as regulation input. However, the programmed controllability is still a major challenge. Here, we constructed a rotary DNA nanostructure in which the rotations were controlled by light input. A bar-shaped DNA rotor, fabricated as a stiff double-crossover molecule supported by a rigid shaft, was placed on the top of a rectangular DNA tile. Photoresponsive oligonucleotides modified with azobenzene molecules were employed as switching motifs and anchors. Two types of photoresponsive DNA switched based on the same switching principal were combined to regulate the rotary motions. The supported nanorotor could be regulated to rotate and then be trapped at specific angular locations by switching photo-irradiations UV and visible light, resulting in the formation of two reconfigurable states. The angular changes in the nanorotors were characterized by atomic force microscopy（AFM） and fluorescence quenching assays. Furthermore, the reversible rotary movements during the photoirradiation were directly visualized using a second-scale scanning of the high-speed AFM.

关键词： DNA origami rotary nanodevices high-speed AFM photoresponsive

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