multilayer DNA origami object consisting of 4 parts with crossections of 2x2, 4x4, 6x6, and 8x8 helices arranged on a square lattice. Native crossover spacing corresponding to 10.66bp/turn
ジャーナル: Nat Commun / 年: 2020 タイトル: Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution. 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 ...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 / 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.
ダウンロード / ファイル: emd_11379.map.gz / 形式: CCP4 / 大きさ: 381.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
multilayer DNA origami object consisting of 4 parts with crossections of 2x2, 4x4, 6x6, and 8x8 helices arranged on a square lattice. Native crossover spacing corresponding to 10.66bp/turn
ボクセルのサイズ
X=Y=Z: 1.39 Å
密度
表面レベル
登録者による: 0.051 / ムービー #1: 0.051
最小 - 最大
-0.2165063 - 0.40101093
平均 (標準偏差)
0.00082956726 (±0.017301481)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
0
0
0
サイズ
464
464
464
Spacing
464
464
464
セル
A=B=C: 644.96 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.39
1.39
1.39
M x/y/z
464
464
464
origin x/y/z
0.000
0.000
0.000
length x/y/z
644.960
644.960
644.960
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
464
464
464
D min/max/mean
-0.217
0.401
0.001
-
添付データ
-
追加マップ: Composite map from the four parts, obtained from...
名称: TwistTower_native-twist / タイプ: complex / ID: 1 / 親要素: 0 詳細: multilayer DNA origami object consisting of 4 parts with crossections of 2x2, 4x4, 6x6, and 8x8 helices arranged on a square lattice. Native crossover spacing corresponding to 10.66bp/turn