Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures
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 exp...
| Main Authors: | , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Oxford University Press
2014
|
| Online Access: | http://hdl.handle.net/1721.1/88694 https://orcid.org/0000-0002-6199-6855 |
| _version_ | 1826211349804351488 |
|---|---|
| author | Kilchherr, F. Dietz, H. Kim, Do-Nyun Bathe, Mark |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Kilchherr, F. Dietz, H. Kim, Do-Nyun Bathe, Mark |
| author_sort | Kilchherr, F. |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T15:04:31Z |
| format | Article |
| id | mit-1721.1/88694 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T15:04:31Z |
| publishDate | 2014 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/886942022-09-29T12:29:43Z Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures Kilchherr, F. Dietz, H. Kim, Do-Nyun Bathe, Mark Massachusetts Institute of Technology. Department of Biological Engineering Kim, Do-Nyun Bathe, Mark 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 Faculty Start-up Fund 2014-08-13T14:23:43Z 2014-08-13T14:23:43Z 2011-12 2011-11 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/88694 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. https://orcid.org/0000-0002-6199-6855 en_US http://dx.doi.org/10.1093/nar/gkr1173 Nucleic Acids Research Creative Commons Attribution Non-Commercial License http://creativecommons.org/licenses/by-nc/3.0 application/pdf Oxford University Press Nucleic Acids Research |
| spellingShingle | Kilchherr, F. Dietz, H. Kim, Do-Nyun Bathe, Mark Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures |
| title | Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures |
| title_full | Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures |
| title_fullStr | Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures |
| title_full_unstemmed | Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures |
| title_short | Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures |
| title_sort | quantitative prediction of 3d solution shape and flexibility of nucleic acid nanostructures |
| url | http://hdl.handle.net/1721.1/88694 https://orcid.org/0000-0002-6199-6855 |
| work_keys_str_mv | AT kilchherrf quantitativepredictionof3dsolutionshapeandflexibilityofnucleicacidnanostructures AT dietzh quantitativepredictionof3dsolutionshapeandflexibilityofnucleicacidnanostructures AT kimdonyun quantitativepredictionof3dsolutionshapeandflexibilityofnucleicacidnanostructures AT bathemark quantitativepredictionof3dsolutionshapeandflexibilityofnucleicacidnanostructures |