Journal: Nanoscale / Year: 2020 Title: Truncated tetrahedral RNA nanostructures exhibit enhanced features for delivery of RNAi substrates. Authors: Paul Zakrevsky / Wojciech K Kasprzak / William F Heinz / Weimin Wu / Htet Khant / Eckart Bindewald / Nomongo Dorjsuren / Eric A Fields / Natalia de Val / Luc Jaeger / Bruce A Shapiro / Abstract: Using RNA as a material for nanoparticle construction provides control over particle size and shape at the nano-scale. RNA nano-architectures have shown promise as delivery vehicles for RNA ...Using RNA as a material for nanoparticle construction provides control over particle size and shape at the nano-scale. RNA nano-architectures have shown promise as delivery vehicles for RNA interference (RNAi) substrates, allowing multiple functional entities to be combined on a single particle in a programmable fashion. Rather than employing a completely bottom-up approach to scaffold design, here multiple copies of an existing synthetic supramolecular RNA nano-architecture serve as building blocks along with additional motifs for the design of a novel truncated tetrahedral RNA scaffold, demonstrating that rationally designed RNA assemblies can themselves serve as modular pieces in the construction of larger rationally designed structures. The resulting tetrahedral scaffold displays enhanced characteristics for RNAi-substrate delivery in comparison to similar RNA-based scaffolds, as evidenced by its increased functional capacity, increased cellular uptake and ultimately an increased RNAi efficacy of its adorned Dicer substrate siRNAs. The unique truncated tetrahedral shape of the nanoparticle core appears to contribute to this particle's enhanced function, indicating the physical characteristics of RNA scaffolds merit significant consideration when designing platforms for delivery of functional RNAs via RNA nanoparticles.
History
Deposition
Nov 22, 2019
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Header (metadata) release
Jan 29, 2020
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Map release
Feb 5, 2020
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Update
Feb 12, 2020
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Current status
Feb 12, 2020
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
#259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)
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Map
File
Download / File: emd_21026.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel size
X=Y=Z: 1.36 Å
Density
Contour Level
By AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum
-0.0018489175 - 0.021540685
Average (Standard dev.)
0.00016715552 (±0.0018350774)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
256
256
256
Spacing
256
256
256
Cell
A=B=C: 348.16 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.36
1.36
1.36
M x/y/z
256
256
256
origin x/y/z
0.000
0.000
0.000
length x/y/z
348.160
348.160
348.160
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-38
-19
-20
NX/NY/NZ
85
80
82
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
256
256
256
D min/max/mean
-0.002
0.022
0.000
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Supplemental data
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Sample components
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Entire : Tetrahedral RNA nanoparticle
Entire
Name: Tetrahedral RNA nanoparticle
Components
Complex: Tetrahedral RNA nanoparticle
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Supramolecule #1: Tetrahedral RNA nanoparticle
Supramolecule
Name: Tetrahedral RNA nanoparticle / type: complex / ID: 1 / Parent: 0 Details: Supra-molecular RNA structure assembled from rationally designed RNA strands produced by in vitro transcription of synthetic DNA templates
Source (natural)
Organism: unidentified, produced by invitro transcription of synthetic templates (unknown)
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Buffer
pH: 7.4
Grid
Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Particle selection
Number selected: 8862
CTF correction
Software - Name: CTFFIND
Final reconstruction
Applied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8862
Initial angle assignment
Type: RANDOM ASSIGNMENT
Final angle assignment
Type: RANDOM ASSIGNMENT
FSC plot (resolution estimation)
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Atomic model buiding 1
Refinement
Protocol: RIGID BODY FIT
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