Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structure, folding and flexibility of co-transcriptional RNA origami.
Journal, issue, pages	Nat Nanotechnol, Vol. 18, Issue 7, Page 808-817, Year 2023
Publish date	Feb 27, 2023
Authors	Ewan K S McRae / Helena Østergaard Rasmussen / Jianfang Liu / Andreas Bøggild / Michael T A Nguyen / Nestor Sampedro Vallina / Thomas Boesen / Jan Skov Pedersen / Gang Ren / Cody Geary / Ebbe Sloth Andersen /
PubMed Abstract	RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic biology. However, to advance the ...RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic biology. However, to advance the method further, an improved understanding of RNA structural properties and folding principles is required. Here we use cryogenic electron microscopy to study RNA origami sheets and bundles at sub-nanometre resolution revealing structural parameters of kissing-loop and crossover motifs, which are used to improve designs. In RNA bundle designs, we discover a kinetic folding trap that forms during folding and is only released after 10 h. Exploration of the conformational landscape of several RNA designs reveal the flexibility of helices and structural motifs. Finally, sheets and bundles are combined to construct a multidomain satellite shape, which is characterized by individual-particle cryo-electron tomography to reveal the domain flexibility. Together, the study provides a structural basis for future improvements to the design cycle of genetically encoded RNA nanodevices.
External links	Nat Nanotechnol / PubMed:36849548 / PubMed Central
Methods	EM (single particle) / EM (tomography)
Resolution	4.08 - 27.0 Å
Structure data	EMDB-13592: Cryo-EM SPA reconstruction of an extended RNA origami 5 helix tile (5HT-B-3X) Method: EM (single particle) / Resolution: 6.5 Å EMDB-13625: Mature conformer 2 of a 6-helix bundle of RNA with a clasp Method: EM (single particle) / Resolution: 7.43 Å EMDB-13626: Young conformer 2 of a 6-helix bundle of RNA with a clasp Method: EM (single particle) / Resolution: 7.04 Å EMDB-13627: 6-Helix bundle of RNA Method: EM (single particle) / Resolution: 6.61 Å 13628 7ptk EMDB-13628, PDB-7ptk: Young conformer of a 6-helix bundle of RNA with clasp Method: EM (single particle) / Resolution: 5.18 Å 13630 7ptl EMDB-13630, PDB-7ptl: Mature conformer of a 6-helix bundle of RNA with clasp Method: EM (single particle) / Resolution: 4.9 Å 13633 7ptq EMDB-13633, PDB-7ptq: RNA origami 5-helix tile Method: EM (single particle) / Resolution: 4.08 Å 13636 7pts EMDB-13636, PDB-7pts: RNA origami 5-helix tile Method: EM (single particle) / Resolution: 5.71 Å 13926 7qdu EMDB-13926, PDB-7qdu: Twist-corrected RNA origami 5-helix Tile A Method: EM (single particle) / Resolution: 5.14 Å EMDB-28669: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 01) Method: EM (tomography) / Resolution: 27.0 Å EMDB-28670: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 02) Method: EM (tomography) / Resolution: 25.0 Å EMDB-28671: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 03) Method: EM (tomography) / Resolution: 25.0 Å EMDB-28672: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 04) Method: EM (tomography) / Resolution: 24.0 Å EMDB-28673: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 05) Method: EM (tomography) / Resolution: 26.0 Å EMDB-28674: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 06) Method: EM (tomography) / Resolution: 27.0 Å EMDB-28675: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 07) Method: EM (tomography) / Resolution: 26.0 Å EMDB-28676: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 08) Method: EM (tomography) / Resolution: 25.0 Å EMDB-28677: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 09) Method: EM (tomography) / Resolution: 25.0 Å EMDB-28678: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 10) Method: EM (tomography) / Resolution: 26.0 Å EMDB-28679: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 11) Method: EM (tomography) / Resolution: 23.0 Å EMDB-28680: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 12) Method: EM (tomography) / Resolution: 23.0 Å EMDB-28681: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 13) Method: EM (tomography) / Resolution: 24.0 Å EMDB-28682: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 14) Method: EM (tomography) / Resolution: 27.0 Å EMDB-28683: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 15) Method: EM (tomography) / Resolution: 26.0 Å EMDB-28684: Single-Molecule 3D Image of 16 Helix RNA Origami Satellite by Individual Particle Electron Tomography (No. 16) Method: EM (tomography) / Resolution: 23.0 Å
Source	synthetic construct (others) unidentified (others)
Keywords	RNA / origami / nanostructure