The Art of Designing DNA Nanostructures with CAD Software
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Peter Debye Institute for Soft Matter Physics, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany
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Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
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Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India
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Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
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Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
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Institute of Clinical Immunology, University of Leipzig Medical Faculty, 04103 Leipzig, Germany
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Authors to whom correspondence should be addressed.
Academic Editor: Ashok Kakkar
Molecules 2021, 26(8), 2287; https://doi.org/10.3390/molecules26082287
Received: 4 March 2021
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Revised: 9 April 2021
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Accepted: 12 April 2021
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Published: 15 April 2021
(This article belongs to the Special Issue Biomolecular Materials: Self-Assembly, Structure, and Application)
Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.
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Keywords:
DNA nanotechnology; CAD software; DNA origami; nanofabrication; DNA bricks; DNA tiles; self-assembly; simulation
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
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MDPI and ACS Style
Glaser, M.; Deb, S.; Seier, F.; Agrawal, A.; Liedl, T.; Douglas, S.; Gupta, M.K.; Smith, D.M. The Art of Designing DNA Nanostructures with CAD Software. Molecules 2021, 26, 2287. https://doi.org/10.3390/molecules26082287
AMA Style
Glaser M, Deb S, Seier F, Agrawal A, Liedl T, Douglas S, Gupta MK, Smith DM. The Art of Designing DNA Nanostructures with CAD Software. Molecules. 2021; 26(8):2287. https://doi.org/10.3390/molecules26082287
Chicago/Turabian StyleGlaser, Martin, Sourav Deb, Florian Seier, Amay Agrawal, Tim Liedl, Shawn Douglas, Manish K. Gupta, and David M. Smith. 2021. "The Art of Designing DNA Nanostructures with CAD Software" Molecules 26, no. 8: 2287. https://doi.org/10.3390/molecules26082287
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