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- W2004348765 abstract "The emerging field of RNA-based nanotechnology can benefit from the development of new computational methods capable of helping in the design and characterization of nano-scale particles, leading to the development of qualitatively new structures and novel therapeutics. We have approached the computer-aided design process by creating a pipeline of tools, starting with a database of n-way junctions and kissing-loops called RNAJunction. This database provides building blocks for our programs, such as NanoTiler and RNA2D3D, which use them to design 3D models of RNA nanostructures. First, the building blocks are treated as rigid objects. Then, just as the natural RNA is shaped (deformed) by the larger structural contexts, our programs allow for deformations to be applied in order to produce fully assembled models. To assess the realistic limits of these deformations, we consider flexibility data available as alternative structures in databases as well as results of Molecular Dynamics (MD) simulations at the atomic resolution level and coarse-grained computational methods. Here we present an example of the modeling process including RNA flexibility information for three nanocube model variants and a novel application of a coarse-grained Anisotropic Network Model (ANM) to the RNA nanostructure characterization. The predictions of different efficiency of assembly for three nanocube variants, based on the exploratory modeling, were confirmed in in vitro experiments. The ANM simulations showed that the dynamics of the full nanostructure has to be considered in order to explain the differences between the size of the initial static models and that of the experimentally measured nanoparticles, thus bringing the computational and the experimental results into agreement. The ANM simulations also offered an additional insight into the assembly yields and the difference in the melting temperatures of the cube variants. Funded in part by HHSN261200800001E" @default.
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- W2004348765 date "2013-01-01" @default.
- W2004348765 modified "2023-09-27" @default.
- W2004348765 title "Coarse-Grained Computational Characterization of RNA Nanocube Flexibility Correlates with Experiments" @default.
- W2004348765 doi "https://doi.org/10.1016/j.bpj.2012.11.119" @default.
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