Document Detail


Computational and Experimental Characterization of RNA Cubic Nanoscaffolds.
MedLine Citation:
PMID:  24189588     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
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.
Authors:
Kirill A Afonin; Wojciech K Kasprzak; Eckart Bindewald; Praneet S Puppala; Alex R Diehl; Kenneth T Hall; Tae Jin Kim; Michael T Zimmermann; Robert L Jernigan; Luc Jaeger; Bruce A Shapiro
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2013-11-1
Journal Detail:
Title:  Methods (San Diego, Calif.)     Volume:  -     ISSN:  1095-9130     ISO Abbreviation:  Methods     Publication Date:  2013 Nov 
Date Detail:
Created Date:  2013-11-5     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9426302     Medline TA:  Methods     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2013. Published by Elsevier Inc.
Affiliation:
Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA.
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