Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures
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Bathe_Quantitative prediction.pdf
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Author(s)
Kilchherr, F.
Dietz, H.
Kim, Do-Nyun
Bathe, Mark
Date Issued
December 2011
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Citation
Kim, D.-N., F. Kilchherr, H. Dietz, and M. Bathe. “Quantitative Prediction of 3D Solution Shape and Flexibility of Nucleic Acid Nanostructures.” Nucleic Acids Research 40, no. 7 (April 1, 2012): 2862–2868.
Version
Author's final manuscript
Abstract
DNA nanotechnology enables the programmed synthesis of intricate nanometer-scale structures for diverse applications in materials and biological science. Precise control over the 3D solution shape and mechanical flexibility of target designs is important to achieve desired functionality. Because experimental validation of designed nanostructures is time-consuming and cost-intensive, predictive physical models of nanostructure shape and flexibility have the capacity to enhance dramatically the design process. Here, we significantly extend and experimentally validate a computational modeling framework for DNA origami previously presented as CanDo [Castro,C.E., Kilchherr,F., Kim,D.-N., Shiao,E.L., Wauer,T., Wortmann,P., Bathe,M., Dietz,H. (2011) A primer to scaffolded DNA origami. Nat. Meth., 8, 221–229.]. 3D solution shape and flexibility are predicted from basepair connectivity maps now accounting for nicks in the DNA double helix, entropic elasticity of single-stranded DNA, and distant crossovers required to model wireframe structures, in addition to previous modeling (Castro,C.E., et al.) that accounted only for the canonical twist, bend and stretch stiffness of double-helical DNA domains. Systematic experimental validation of nanostructure flexibility mediated by internal crossover density probed using a 32-helix DNA bundle demonstrates for the first time that our model not only predicts the 3D solution shape of complex DNA nanostructures but also their mechanical flexibility. Thus, our model represents an important advance in the quantitative understanding of DNA-based nanostructure shape and flexibility, and we anticipate that this model will increase significantly the number and variety of synthetic nanostructures designed using nucleic acids.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
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Creative Commons Attribution Non-Commercial License
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DOI of Published Version
https://doi.org/10.1093/nar/gkr1173
