Commentary and Perspective (Invited)
Constructing virtual DNA-nanomachines
2024 Volume 21 Issue Supplemental2 Article ID: e212011
Details
2024 Volume 21 Issue Supplemental2 Article ID: e212011
During the co-held 21st IUPAB Congress and 62nd Annual Meeting of the Biophysical Society of Japan (BSJ) [1,2], several satellite events were held in close proximity to the main event. Among these was “Hands-On Training Program D: DNA Nanomachine Tutorial,” hosted at the Senriyama Campus of Kansai University in Osaka [2]. The central theme was the creation of mechanical nanomachines constructed from DNA. The program was organized by Professor Shin-ichiro Nomura from Tohoku University, with lectures delivered by Professor Masayuki Endo (Kansai University), Professor Akinori Kuzuya (Kansai University), Professor Yuki Suzuki (Mie University), and Professor Ibuki Kawamata (currently at Kyoto University). These experts in DNA origami and nanomachines provided an overview of the historical context of DNA nanotechnology and a comprehensive tutorial on creating these structures, including tools for DNA origami structure prediction, as explained by Professor Kawamata.
The first lecture, presented by Professors Endo and Kuzuya, focused on the historical context of DNA hybridization discovery [3]. They discussed the initial observations of DNA hybridization and the pioneering designs by Professor Nadrian Seeman [4–7]. The lecture covered the formation of migratory immobile junctions of DNA (Figure 1), highlighting how these associations differ from the canonical duplex typically found in double-stranded nucleic acids in cells [3]. These insights were crucial for understanding the principles behind the formation and design of DNA nanostructures. The state-of-the-art in DNA origami was then presented, introducing new mechanical DNA structures [8–12]. The collaborative research groups led by the aforementioned Japanese researchers are at the forefront of developing nanomachines, including rotational devices [9,12], key-and-lock assemblies [13], and 4D structures [9,14]. Detailed guidelines for sequence design and structure prediction were provided for each case.
Following the theoretical introduction, the program transitioned to properly hands-on activities. Professor Kawamata provided tools for designing and predicting the structures discussed. The first tool, caDNAno [15], supports the design of 2D-4D DNA nanostructures and sequences, adhering to DNA origami design guidelines. The tutorial offered a step-by-step guide to developing simple nanomachines, serving as an excellent introduction to nanomachine system planning.
As in the tutorial, to design such tools, a long DNA strand (up to approximately 7 kb) acts as the main scaffold, shaped into the desired form by minor staple strands [11,15]. These strands align and crosslink different regions to shape the DNA origami into the intended structure. A more detailed picture can be seen in Figure 2, extracted from a nanotube design present in caDNAno YouTube channel [16]. As the color in the image, the long DNA strand is visualized in light blue, being folded by minor staples here represented in red, green and dark purple. The colors are under user’s choice,
Visualizing these complex systems requires significant imagination and creativity. While caDNAno provides only a 2D representation, creating complex systems can be challenging. To aid in 3D visualization, Professor Kawamata introduced CanDo [17–19], a finite element modeling framework which also provides a refined 2D-3D visualization. Students presented their newly designed structures, and promising 2D designs were simulated in CanDo. Models such as a Smiley Face, Trapezoid, Star, or simple duplex DNA were used as guides, helping students understand the construction process step-by-step.
As a scientist in the field of DNA nanotechnology, acquiring such skills in a condensed, one-day program was highly valuable. Additionally, comprehensive support was provided for beginners. For future programs, the following suggestions are proposed:
(i) Extend the program duration to include more thematic seminars and in vitro experiments, tailored to the number of participants.
(ii) Introduce and test new technologies and concepts, even for in silico experiments, such as DNA hybridization concepts, classifications, methods, and design.
The strongest aspects of the program were the presentation session at the end and the active interaction between lecturers and participants. This allowed students to quickly apply the lecture content, present their ideas, and receive immediate feedback from the professors, which greatly enhanced the learning process.
An additional strong feature for this event was the laboratory tour at Intelligent Molecules Lab. [20], under Professor Kuzuya supervision, in Kansai University. It is great for students to have the opportunity of closely seeing each set-up necessary for DNA nanotechnology experiments, such as Electrophoresis devices, Thermocyclers, Optical Microscopes, Atomic Force Microscope and Fluorescence Microscopes. It provided good clarification on daily work in DNA origami research, which enriched the lectures and tutorials.
In summary, the program was expertly designed, effectively explaining, applying, and refining the principles of DNA nanomachine tool creation. Any further changes to the program structure are minor and optional, as the primary objectives were clearly achieved. The comprehensive knowledge of DNA nanomachines we learned here would be applied as well to our current research on DNA droplets [21], being an extremely joyful and meaningful experience on this attendance.
The authors thank to the organizers of Hands-On Program D, for the careful preparation of all lecture materials and the kindly reception of each student. We also extend our pleasure to Professor Kumiko Hayashi, from University of Tokyo, for the management of Hands-On programs as satellite events for the IUPAB-BSJ joint congress.
