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	Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.
Journal, issue, pages	Nat Commun, Vol. 11, Issue 1, Page 6229, Year 2020
Publish date	Dec 4, 2020
Authors	Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W Scheres / Hendrik Dietz /
PubMed Abstract	The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is ...The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions.
External links	Nat Commun / PubMed:33277481 / PubMed Central
Methods	EM (single particle)
Resolution	7.4 - 28.0 Å
Structure data	EMDB-10993: 42 Helix Bundle with aligned Staple Breaks after UV Illumination Method: EM (single particle) / Resolution: 20.0 Å EMDB-11159: Dumbbell_1 Method: EM (single particle) / Resolution: 21.0 Å EMDB-11168: Dumbbell_2 Method: EM (single particle) / Resolution: 17.0 Å 11170 7as5 EMDB-11170, PDB-7as5: 126 helix bundle DNA nanostructure Method: EM (single particle) / Resolution: 9.8 Å EMDB-11294: 42hb with aligned staple breaks Method: EM (single particle) / Resolution: 17.5 Å EMDB-11295: 42hb with aligned staple breaks and 1T at staple termini Method: EM (single particle) / Resolution: 19.0 Å EMDB-11296: 42hb with aligned staple breaks and 1T at staple termini after UV illumination Method: EM (single particle) / Resolution: 20.0 Å EMDB-11297: 42hb with reduced staple density Method: EM (single particle) / Resolution: 19.0 Å EMDB-11298: 42hb with reduced staple density after UV illumination Method: EM (single particle) / Resolution: 17.0 Å EMDB-11343: 48hb brick with 1T at staple crossovers Method: EM (single particle) / Resolution: 13.0 Å EMDB-11344: 48hb brick with 2T at staple crossovers Method: EM (single particle) / Resolution: 15.0 Å EMDB-11345: 48hb brick with 4T at staple crossovers Method: EM (single particle) / Resolution: 26.0 Å EMDB-11346: hinged beam object v1 Method: EM (single particle) / Resolution: 26.0 Å EMDB-11348: hinged beam object v2 Method: EM (single particle) / Resolution: 19.0 Å EMDB-11349: hinged beam like object v3 Method: EM (single particle) / Resolution: 26.0 Å EMDB-11350: hinged beam like object v4 Method: EM (single particle) / Resolution: 17.0 Å EMDB-11351: six helix tube v1 Method: EM (single particle) / Resolution: 17.0 Å EMDB-11352: six helix tube v2 Method: EM (single particle) / Resolution: 18.0 Å EMDB-11353: six helix tube v3 Method: EM (single particle) / Resolution: 19.0 Å EMDB-11354: six helix tube v4 Method: EM (single particle) / Resolution: 25.0 Å EMDB-11355: 10 helix bundle Method: EM (single particle) / Resolution: 28.0 Å 11367 7arq EMDB-11367: 16 helix bundle PDB-7arq: Cryo EM of 3D DNA origami 16 helix bundle Method: EM (single particle) / Resolution: 10.0 Å 11378 7ary EMDB-11378: Twist-Tower_twist-corrected PDB-7ary: Twist-Tower_twist-corrected-variant Method: EM (single particle) / Resolution: 8.5 Å 11379 7arv EMDB-11379, PDB-7arv: TwistTower_native-twist Method: EM (single particle) / Resolution: 7.4 Å 11387 7art EMDB-11387, PDB-7art: 48 helix bundle DNA origami brick Method: EM (single particle) / Resolution: 9.9 Å 11881 7are EMDB-11881, PDB-7are: DNA origami pointer object v2 Method: EM (single particle) / Resolution: 7.4 Å
Source	synthetic construct (others) Escherichia virus M13
Keywords	DNA / DNA Origami