Computational and Experimental Characterization of RNA Cubic Nanoscaffolds

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2014-05-15
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Afonin, Kirill
Kasprzak, Wojciech
Bindewald, Eckart
Puppala, Praneet
Diehl, Alex
Hall, Kenneth
Kim, Tae Jin
Zimmermann, Michael
Jaeger, Luc
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Jernigan, Robert
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The fast-developing field of RNA nanotechnology requires the adoption and development of novel and faster computational approaches to modeling and characterization of RNA-based nano-objects. We report the first application of Elastic Network Modeling (ENM), a structure-based dynamics model, to RNA nanotechnology. With the use of an Anisotropic Network Model (ANM), a type of ENM, we characterize the dynamic behavior of non-compact, multi-stranded RNA-based nanocubes that can be used as nano-scale scaffolds carrying different functionalities. Modeling the nanocubes with our tool NanoTiler and exploring the dynamic characteristics of the models with ANM suggested relatively minor but important structural modifications that enhanced the assembly properties and thermodynamic stabilities. In silico and in vitro, we compared nanocubes having different numbers of base pairs per side, showing with both methods that the 10 bp-long helix design leads to more efficient assembly, as predicted computationally. We also explored the impact of different numbers of single-stranded nucleotide stretches at each of the cube corners and showed that cube flexibility simulations help explain the differences in the experimental assembly yields, as well as the measured nanomolecule sizes and melting temperatures. This original work paves the way for detailed computational analysis of the dynamic behavior of artificially designed multi-stranded RNA nanoparticles.

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This is a manuscript of an article published as Afonin, Kirill A., Wojciech Kasprzak, Eckart Bindewald, Praneet S. Puppala, Alex R. Diehl, Kenneth T. Hall, Tae Jin Kim et al. "Computational and experimental characterization of RNA cubic nanoscaffolds." Methods 67, no. 2 (2014): 256-265. 10.1016/j.ymeth.2013.10.013. Posted with permission.

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Tue Jan 01 00:00:00 UTC 2013
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