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_11168.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Dumbbell shaped DNA nanostructure with reduced helical twist density (by design) but without crossovers along the handle of the dumbbell
ボクセルのサイズ
X=Y=Z: 3.71 Å
密度
表面レベル
登録者による: 0.22 / ムービー #1: 0.22
最小 - 最大
-0.10804583 - 0.6097828
平均 (標準偏差)
0.0040700883 (±0.035247467)
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
300
300
300
Spacing
300
300
300
セル
A=B=C: 1113.0 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
3.71
3.71
3.71
M x/y/z
300
300
300
origin x/y/z
0.000
0.000
0.000
length x/y/z
1113.000
1113.000
1113.000
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
300
300
300
D min/max/mean
-0.108
0.610
0.004
-
添付データ
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試料の構成要素
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全体 : dumbbell-shaped multilayer DNA nanostructure with reduced twist d...
全体
名称: dumbbell-shaped multilayer DNA nanostructure with reduced twist density (by design) and without crossovers at the "handle"
要素
複合体: dumbbell-shaped multilayer DNA nanostructure with reduced twist density (by design) and without crossovers at the "handle"
-
超分子 #1: dumbbell-shaped multilayer DNA nanostructure with reduced twist d...
超分子
名称: dumbbell-shaped multilayer DNA nanostructure with reduced twist density (by design) and without crossovers at the "handle" タイプ: complex / ID: 1 / 親要素: 0 / 詳細: DNA Origami