EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.
ジャーナル・号・ページ	Nat Commun, Vol. 11, Issue 1, Page 6229, Year 2020
掲載日	2020年12月4日
著者	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 要旨	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.
リンク	Nat Commun / PubMed:33277481 / PubMed Central
手法	EM (単粒子)
解像度	7.4 - 28.0 Å
構造データ	EMDB-10993: 42 Helix Bundle with aligned Staple Breaks after UV Illumination 手法: EM (単粒子) / 解像度: 20.0 Å EMDB-11159: Dumbbell_1 手法: EM (単粒子) / 解像度: 21.0 Å EMDB-11168: Dumbbell_2 手法: EM (単粒子) / 解像度: 17.0 Å 11170 7as5 EMDB-11170, PDB-7as5: 126 helix bundle DNA nanostructure 手法: EM (単粒子) / 解像度: 9.8 Å EMDB-11294: 42hb with aligned staple breaks 手法: EM (単粒子) / 解像度: 17.5 Å EMDB-11295: 42hb with aligned staple breaks and 1T at staple termini 手法: EM (単粒子) / 解像度: 19.0 Å EMDB-11296: 42hb with aligned staple breaks and 1T at staple termini after UV illumination 手法: EM (単粒子) / 解像度: 20.0 Å EMDB-11297: 42hb with reduced staple density 手法: EM (単粒子) / 解像度: 19.0 Å EMDB-11298: 42hb with reduced staple density after UV illumination 手法: EM (単粒子) / 解像度: 17.0 Å EMDB-11343: 48hb brick with 1T at staple crossovers 手法: EM (単粒子) / 解像度: 13.0 Å EMDB-11344: 48hb brick with 2T at staple crossovers 手法: EM (単粒子) / 解像度: 15.0 Å EMDB-11345: 48hb brick with 4T at staple crossovers 手法: EM (単粒子) / 解像度: 26.0 Å EMDB-11346: hinged beam object v1 手法: EM (単粒子) / 解像度: 26.0 Å EMDB-11348: hinged beam object v2 手法: EM (単粒子) / 解像度: 19.0 Å EMDB-11349: hinged beam like object v3 手法: EM (単粒子) / 解像度: 26.0 Å EMDB-11350: hinged beam like object v4 手法: EM (単粒子) / 解像度: 17.0 Å EMDB-11351: six helix tube v1 手法: EM (単粒子) / 解像度: 17.0 Å EMDB-11352: six helix tube v2 手法: EM (単粒子) / 解像度: 18.0 Å EMDB-11353: six helix tube v3 手法: EM (単粒子) / 解像度: 19.0 Å EMDB-11354: six helix tube v4 手法: EM (単粒子) / 解像度: 25.0 Å EMDB-11355: 10 helix bundle 手法: EM (単粒子) / 解像度: 28.0 Å 11367 7arq EMDB-11367: 16 helix bundle PDB-7arq: Cryo EM of 3D DNA origami 16 helix bundle 手法: EM (単粒子) / 解像度: 10.0 Å 11378 7ary EMDB-11378: Twist-Tower_twist-corrected PDB-7ary: Twist-Tower_twist-corrected-variant 手法: EM (単粒子) / 解像度: 8.5 Å 11379 7arv EMDB-11379, PDB-7arv: TwistTower_native-twist 手法: EM (単粒子) / 解像度: 7.4 Å 11387 7art EMDB-11387, PDB-7art: 48 helix bundle DNA origami brick 手法: EM (単粒子) / 解像度: 9.9 Å 11881 7are EMDB-11881, PDB-7are: DNA origami pointer object v2 手法: EM (単粒子) / 解像度: 7.4 Å
由来	synthetic construct (人工物) Escherichia virus M13 (ウイルス)
キーワード	DNA (デオキシリボ核酸) / DNA Origami (DNAオリガミ)