Группа авторов

DNA Origami


Скачать книгу

Smith, S.B., Cui, Y., and Bustamante, C. (1996). Overstretching B‐DNA: the elastic response of individual double‐stranded and single‐stranded DNA molecules. Science 271 (5250): 795–799.

      71 71 Suma, A., Poppleton, E., Matthies, M. et al. (2019). TacoxDNA: a user‐friendly web server for simulations of complex DNA structures, from single strands to origami. Journal of Computational Chemistry 40 (29): 2586–2595.

      72 72 Poppleton, E., Bohlin, J., Matthies, M. et al. (2020). Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation. Nucleic Acids Research.

       Yuki Suzuki

       Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan

      Atomic force microscopy (AFM) is a powerful tool for imaging individual bio‐macromolecules [1, 2]. In particular, its range of operation has been suitable for the morphological analysis of nucleic acid molecules ranging from a single DNA fragment (several tens of nanometers) to a large assembly of DNA nanostructures (several hundred nanometers to a few micrometers). Initial attempts to use the instrument for imaging DNA molecules date back to the early days of AFM. Throughout the late 1980s to the 1990s, it was notably applied to observe double‐stranded DNA [3–6], and new preparation methods for nucleic acid specimens amenable to AFM imaging were developed [7, 8]. These achievements greatly encouraged investigation of various DNA–protein assemblies [9, 10] and artificially designed DNA nanostructures [11]. In particular, in the field of structural nucleic acid nanotechnology, AFM has been routinely used to visualize various types of artificial DNA nanostructures, such as DNA tile motifs [11], DNA origamis [12], and DNA bricks [13], and it has become an almost indispensable tool.

      Although a variety of DNA‐based molecular machines had already been realized before the invention of the scaffolded DNA origami method [18–21], its excellent shape designability [12, 22, 23] brought remarkable progress in the development of DNA nanodevices and DNA nanorobots [24]. Representative examples include a nano‐sized box capable of being opened by reacting with a specific “key” DNA strand [25], pH‐ or photoresponsive nanocapsules [26, 27], and a capsule‐shaped nanorobot that recognizes specific proteins on the specific cell surface to expose its cargos [28]. In addition to these container‐like structures, researchers have attempted to imitate normal‐sized mechanical parts, such as bearings, sliders, and hinges with DNA origami [29–31]. Coordinated operations that combine multiple mechanical units have also been examined [30]. These mechanical motions are often regulated by strand displacement reactions [18], DNAzyme‐mediated cleavage [32], triplex formations [27], and quadruplex formations such as a guanine quadruplex (G‐quadruplex) and i‐Motifs [29, 33]. It is noteworthy that all of these can, in principle, be realized with natural nucleobases, exhibiting the great advantages of DNA as a material that not only enables the design of arbitrarily shaped nanostructures but also allows us to design responses to stimuli such as ions, pH changes, or small molecules, using only four fundamental nucleotides.

Schematic illustration of DNA origami nanoscissors exhibiting open/closed switching in response to Mg2+ concentration.

      Source: Willner et al. [34]/with permission from John Wiley & Sons, Inc.