title: Computational and experimental characterization of RNA cubic nanoscaffolds.
abstract: 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.affiliation: Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA.
authors.forename: Kirill A
authors.initials: KA
authors.lastname: Afonin
authors.affiliation: Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
authors.forename: Wojciech
authors.initials: W
authors.lastname: Kasprzak
authors.affiliation: Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
authors.forename: Eckart
authors.initials: E
authors.lastname: Bindewald
authors.affiliation: Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA.
authors.forename: Praneet S
authors.initials: PS
authors.lastname: Puppala
authors.affiliation: Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA.
authors.forename: Alex R
authors.initials: AR
authors.lastname: Diehl
authors.affiliation: Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA.
authors.forename: Kenneth T
authors.initials: KT
authors.lastname: Hall
authors.affiliation: Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA.
authors.forename: Tae Jin
authors.initials: TJ
authors.lastname: Kim
authors.affiliation: Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Zimmermann
authors.affiliation: Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Jernigan
authors.affiliation: Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA. Electronic address: jaeger@chem.ucsb.edu.
authors.forename: Luc
authors.initials: L
authors.lastname: Jaeger
authors.affiliation: Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA. Electronic address: shapirbr@mail.nih.gov.
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Shapiro
mesh_terms: D016880:Anisotropy; D003198:Computer Simulation; D020285:Cryoelectron Microscopy; D008027:Light; D008956:Models, Chemical; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure; D012542:Scattering, Radiation
chemical_list: D012313:RNA
keywords: Anisotropic network model; Nanostructure design; Native PAGE; RNA architectonics; RNA nanostructure characterization; RNA nanostructure dynamics; RNA nanotechnology; TGGE