Triggered contraction of self-assembled micron-scale DNA nanotube rings [Research Data] (doi:10.11588/data/ADYUNN)

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Part 2: Study Description
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Part 4: Variable Description
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Triggered contraction of self-assembled micron-scale DNA nanotube rings [Research Data]

doi:10.11588/data/ADYUNN

heiDATA

2024-02-16

1

Illig, Maja; Jahnke, Kevin; Weise, Lukas P.; Scheffold, Marlene; Mersdorf, Ulrike; Drechsler, Hauke; Zhang, Yixin; Diez, Stefan; Kierfeld, Jan; Göpfrich, Kerstin, 2024, "Triggered contraction of self-assembled micron-scale DNA nanotube rings [Research Data]", https://doi.org/10.11588/data/ADYUNN, heiDATA, V1, UNF:6:AJdXI51lTUqvs4V/XCVPZQ== [fileUNF]

Triggered contraction of self-assembled micron-scale DNA nanotube rings [Research Data]

doi:10.11588/data/ADYUNN

Illig, Maja (Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 329, 69120 Heidelberg, Germany, Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120 Heidelberg, Germany)

Jahnke, Kevin (Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120 Heidelberg, Germany, Harvard University, School of Engineering and Applied Sciences (SEAS), Cambridge, MA, USA)

Weise, Lukas P. (TU Dortmund University, Department of Physics, Otto-Hahn-Str. 4, 44221 Dortmund, Germany)

Scheffold, Marlene (Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120 Heidelberg, Germany)

Mersdorf, Ulrike (Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120 Heidelberg, Germany)

Drechsler, Hauke (B CUBE - Center for Molecular Bioengineering and Cluster of Excellence Physics of Life, Technische Universität Dresden, Tatzberg 41, 01307 Dresden, Germany, Tübingen University, Center for Plant Molecular Biology (ZMBP), Auf der Morgenstelle 32, 72076 Tübingen, Germany)

Zhang, Yixin (B CUBE - Center for Molecular Bioengineering and Cluster of Excellence Physics of Life, Technische Universität Dresden, Tatzberg 41, 01307 Dresden, Germany)

Diez, Stefan (B CUBE - Center for Molecular Bioengineering and Cluster of Excellence Physics of Life, Technische Universität Dresden, Tatzberg 41, 01307 Dresden, Germany, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany)

Kierfeld, Jan (TU Dortmund University, Department of Physics, Otto-Hahn-Str. 4, 44221 Dortmund, Germany)

Göpfrich, Kerstin (Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 329, 69120 Heidelberg, Germany, Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120 Heidelberg, Germany)

EXC-2082/1 -- 390761711

EXC-2082/1 -- 390761711

EXC-2082/1 -- 390761711

EXC-2082/1 -- 390761711

EXC-2082/1 -- 390761711

EXC-2082/1 -- 390761711

heiDATA

Illig, Maja

https://doi.org/10.11588/data/ADYUNN

Chemistry, Medicine, Health and Life Sciences, Physics, Bottom-up synthetic biology, DNA nanotubes, Contractile rings, Coarse-grained MD simulations

Contractile rings formed from cytoskeletal filaments mediate the division of cells. Ring formation is induced by specific crosslinkers, while contraction is typically associated with motor protein activity. Here, we engineer DNA nanotubes as mimics of cytoskeletal filaments and a synthetic crosslinker based on a peptide-functionalized starPEG construct. The crosslinker induces bundling of ten to hundred individual DNA nanotubes. Importantly, the DNA nanotube bundles curve into closed micron-scale rings in a one-pot self-assembly process yielding several thousand rings per microliter. Coarse-grained molecular dynamics simulations reproduce detailed architectural properties of the DNA rings as observed by electron microscopy. Furthermore, theory and simulations predict DNA ring contraction – without motor proteins – upon increasing attraction or decreasing bending rigidity of the DNA nanotubes, yielding mechanistic insights into the parameter space relevant for efficient nanotube sliding. We experimentally realize a variation of these parameters by addition of molecular crowders or temperature increase, respectively. In agreement between simulation and experiment, we obtain ring contraction to less than half of the initial ring diameter. DNA-based contractile rings could be a future element of an artificial division machinery in synthetic cells or of contractile muscle-like materials.

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• A - A
• B - B
• C - C
• D - D
• E - E
• F - F
• G - G
• H - H
• I - I
• J - J
• K - K
• L - L
• M - M
• 2207228DNA14.5k01 - 2207228DNA14.5k01
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• Mean - Mean
• X - X
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• Perim. - Perim.
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• AR - AR
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Summary Statistics: Valid 0.0; Min. NaN; Mean NaN; StDev NaN; Max. NaN;

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Variable Format: character

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f20646 Location:

Summary Statistics: StDev NaN; Min. NaN; Valid 0.0; Max. NaN; Mean NaN;

Variable Format: numeric

Notes: UNF:6:f5yeMayCVsovJYWD3yYtvA==

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Variable Format: character

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Summary Statistics: Min. 1.13514174; Valid 5.0; Max. 49.3897912; Mean 34.542385988; StDev 20.28300832096849;

Variable Format: numeric

Notes: UNF:6:YK6pGxas2nyo+MD8IeG8XA==

f20646 Location:

Summary Statistics: StDev 22.026442411942835; Valid 5.0; Min. 1.20203837; Mean 34.655579433999996; Max. 53.7855228

Variable Format: numeric

Notes: UNF:6:DF7uQntgoi0gHHYLAfofDg==

f20646 Location:

Summary Statistics: Valid 5.0; Min. 1.19174671; Mean 37.513587042; StDev 21.69019840289551; Max. 54.3612245;

Variable Format: numeric

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Summary Statistics: Min. 1.15498589; Mean 38.345095778; Max. 63.3703704; Valid 5.0; StDev 23.87522113329868

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Summary Statistics: Min. 34.5349794; Max. 54.2670895; Valid 4.0; StDev 9.196070259596887; Mean 45.799101725;

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Summary Statistics: StDev 8.742735406227615; Valid 4.0; Max. 55.1842105; Min. 34.6629213; Mean 46.7600436

Variable Format: numeric

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Summary Statistics: Min. 32.5352941; Max. 57.6752412; Mean 49.635167125; StDev 11.565350353598355; Valid 4.0;

Variable Format: numeric

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Summary Statistics: Mean 49.165999625; Min. 36.9233871; Max. 57.2075758; Valid 4.0; StDev 8.63113813254374;

Variable Format: numeric

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Summary Statistics: Valid 3.0; Mean 44.0861477; Max. 53.8505604; Min. 30.7979351; StDev 11.92345409715574

Variable Format: numeric

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Variable Format: character

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Variable Format: character

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Summary Statistics: Min. 0.0; Max. 25.0; Mean 14.583333333333332; Valid 12.0; StDev 8.050503466281228;

Variable Format: numeric

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f19881 Location:

Summary Statistics: Mean 15.384615384615383; StDev 25.493588937673664; Valid 13.0; Min. 5.0; Max. 100.0;

Variable Format: numeric

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f19881 Location:

Summary Statistics: Mean NaN; Valid 0.0; Max. NaN; StDev NaN; Min. NaN;

Variable Format: numeric

Notes: UNF:6:K1NCHP3PnX8R35PvIK/SSw==

f19881 Location:

Summary Statistics: Min. 1.0; Max. 10.0; StDev 2.716503992154979; Valid 100.0; Mean 4.88;

Variable Format: numeric

Notes: UNF:6:jXVC0ZIYmmSh8vGeU7L5mQ==

f19881 Location:

Variable Format: character

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f19881 Location:

Variable Format: character

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f19881 Location:

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f19881 Location:

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Variable Format: character

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f19403 Location:

Summary Statistics: Min. 1.576; Mean 3.0411428571428574; Max. 4.839; StDev 1.2242940045282462; Valid 7.0;

Variable Format: numeric

Notes: UNF:6:C0v1BDXuO+6iNOdeAMuqLg==

f19403 Location:

Summary Statistics: Valid 7.0; Min. 4.599; Mean 6.259285714285714; Max. 7.988; StDev 1.253873693038991;

Variable Format: numeric

Notes: UNF:6:wKADQ/fUtZRHtUqX7otUiw==

f19403 Location:

Summary Statistics: Max. 2.727; Min. 1.594; Mean 2.212857142857143; Valid 7.0; StDev 0.4080393888549766

Variable Format: numeric

Notes: UNF:6:g0AWi2PUYCNmEYXsHI913g==

f19403 Location:

Summary Statistics: Min. 1.083; Valid 7.0; Mean 1.6914285714285713; Max. 2.259; StDev 0.41292810396922486;

Variable Format: numeric

Notes: UNF:6:8izKzKxQHPRJHSgx6k0Mzw==

f19403 Location:

Summary Statistics: Valid 7.0; Min. 0.181; Mean 111.75457142857142; StDev 70.84201382855879; Max. 174.668

Variable Format: numeric

Notes: UNF:6:0ceDcicMvvhd7ZGL6CEknA==

f19403 Location:

Summary Statistics: Valid 7.0; Mean 0.9367142857142857; Max. 0.966; Min. 0.856; StDev 0.036545470698452195

Variable Format: numeric

Notes: UNF:6:2U8C7PkDafXH6SorX5x8UQ==

f19403 Location:

Summary Statistics: Mean 1.334857142857143; Valid 7.0; Min. 1.133; StDev 0.18857485566871363; Max. 1.71;

Variable Format: numeric

Notes: UNF:6:KXGniULEflIegYtlgLKgng==

f19403 Location:

Summary Statistics: Max. 0.883; StDev 0.09581703795205092; Valid 7.0; Min. 0.585; Mean 0.7607142857142857;

Variable Format: numeric

Notes: UNF:6:wwCtl151xc8zyuX5fFuYRQ==

f19403 Location:

Summary Statistics: Max. 0.995; Mean 0.9887142857142857; Min. 0.981; StDev 0.004889249625940769; Valid 7.0;

Variable Format: numeric

Notes: UNF:6:mMdlrMUo8f6FlTLYi8B5aw==

f18560 Location:

Summary Statistics: StDev 3.358200693677312; Valid 29.0; Max. 18.541; Min. 3.057; Mean 6.672448275862069

Variable Format: numeric

Notes: UNF:6:W/jD5jcdhQjiJMIpYxEnIA==

f18560 Location:

Summary Statistics: Mean 9.518827586206896; Valid 29.0; StDev 2.2193466713840024; Max. 15.742; Min. 6.283

Variable Format: numeric

Notes: UNF:6:s03q12ZP67t4zjjujTzAJA==

f18560 Location:

Summary Statistics: Min. 0.601; Max. 0.973; Mean 0.8866896551724138; Valid 29.0; StDev 0.08403235067871856

Variable Format: numeric

Notes: UNF:6:wtDe7hRcdnfNoKnpps3HfQ==

f18560 Location:

Summary Statistics: Min. 1.086; StDev 0.5123355292982137; Max. 3.526; Valid 29.0; Mean 1.5648620689655173;

Variable Format: numeric

Notes: UNF:6:sMSJ0VCyWdKGYJahF/XCrQ==

f18560 Location:

Summary Statistics: StDev 0.15467422462565247; Min. 0.284; Mean 0.6844827586206896; Max. 0.921; Valid 29.0

Variable Format: numeric

Notes: UNF:6:OyWeUrQZKcZ3x9SEf62BUg==

f18560 Location:

Summary Statistics: Mean 0.988103448275862; Max. 0.996; Min. 0.967; Valid 29.0; StDev 0.007556193427467337;

Variable Format: numeric

Notes: UNF:6:svTgRwS/ZpwWuxxtBfgN8A==

f18528 Location:

Variable Format: character

Notes: UNF:6:3ND2YYr1AaDyhTmhoJ8pGQ==

f18528 Location:

Summary Statistics: Min. 3.467; Valid 32.0; Mean 8.215125; StDev 3.626004864060933; Max. 18.441

Variable Format: numeric

Notes: UNF:6:r+P2iSkAh8Pfd0QseaLgUA==

f18528 Location:

Summary Statistics: Min. 6.804; StDev 2.2703022444709866; Mean 10.32609375; Max. 15.654; Valid 32.0;

Variable Format: numeric

Notes: UNF:6:RlO8YUiiPDZV6cGG9pM5YQ==

f18528 Location:

Summary Statistics: Min. 0.759; Mean 0.9299375; Valid 32.0; Max. 0.975; StDev 0.0568790099614396

Variable Format: numeric

Notes: UNF:6:o1lgfGVR/aZu5gx9byo1+Q==

f18528 Location:

Summary Statistics: Min. 1.05; Mean 1.37128125; StDev 0.29778312463018475; Valid 32.0; Max. 2.258

Variable Format: numeric

Notes: UNF:6:D9gImkr7TBNBlqt3yQQ0Uw==

f18528 Location:

Summary Statistics: Min. 0.443; StDev 0.13140926205266432; Valid 32.0; Max. 0.952; Mean 0.75615625

Variable Format: numeric

Notes: UNF:6:/VscKhrMa+ZkO6VNI8/w8g==

f18528 Location:

Summary Statistics: StDev 0.00701143938560868; Max. 0.998; Valid 32.0; Mean 0.98953125; Min. 0.958

Variable Format: numeric

Notes: UNF:6:VeJI3hv0n3cTxGi+DM3u0g==

f18319 Location:

Variable Format: character

Notes: UNF:6:3ND2YYr1AaDyhTmhoJ8pGQ==

f18319 Location:

Summary Statistics: Valid 32.0; Max. 18.441; Mean 8.215125; StDev 3.626004864060933; Min. 3.467

Variable Format: numeric

Notes: UNF:6:r+P2iSkAh8Pfd0QseaLgUA==

f18319 Location:

Summary Statistics: StDev 2.2703022444709866; Mean 10.32609375; Valid 32.0; Min. 6.804; Max. 15.654

Variable Format: numeric

Notes: UNF:6:RlO8YUiiPDZV6cGG9pM5YQ==

f18319 Location:

Summary Statistics: Valid 32.0; Max. 0.975; Min. 0.759; StDev 0.0568790099614396; Mean 0.9299375;

Variable Format: numeric

Notes: UNF:6:o1lgfGVR/aZu5gx9byo1+Q==

f18319 Location:

Summary Statistics: Valid 32.0; StDev 0.29778312463018475; Max. 2.258; Mean 1.37128125; Min. 1.05

Variable Format: numeric

Notes: UNF:6:D9gImkr7TBNBlqt3yQQ0Uw==

f18319 Location:

Summary Statistics: Valid 32.0; Mean 0.75615625; StDev 0.13140926205266432; Max. 0.952; Min. 0.443

Variable Format: numeric

Notes: UNF:6:/VscKhrMa+ZkO6VNI8/w8g==

f18319 Location:

Summary Statistics: Mean 0.98953125; Min. 0.958; Valid 32.0; StDev 0.00701143938560868; Max. 0.998;

Variable Format: numeric

Notes: UNF:6:VeJI3hv0n3cTxGi+DM3u0g==

f18960 Location:

Summary Statistics: Valid 30.0; StDev 2.945535615871554; Min. 2.33; Max. 12.925; Mean 7.208733333333333

Variable Format: numeric

Notes: UNF:6:opJmC4y8656131PQ9uAdiw==

f18960 Location:

Summary Statistics: Max. 121.846; StDev 23.259706367647798; Valid 30.0; Min. 33.537; Mean 74.40436666666666;

Variable Format: numeric

Notes: UNF:6:b1N+5xn3pq4VngK8jBHVOw==

f18960 Location:

Summary Statistics: StDev 0.6272390339791732; Max. 11.85; Mean 9.984233333333334; Min. 8.673; Valid 30.0;

Variable Format: numeric

Notes: UNF:6:hG7RLQHjC+D98mra9wUkRg==

f18960 Location:

Summary Statistics: Valid 30.0; Max. 11.881; StDev 0.7119427564809877; Min. 9.053; Mean 10.231166666666667

Variable Format: numeric

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f18960 Location:

Summary Statistics: Max. 15.482; Mean 9.884066666666667; StDev 2.1953121517629697; Min. 5.662; Valid 30.0

Variable Format: numeric

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f18960 Location:

Summary Statistics: Min. 2.076; Mean 3.536; Valid 30.0; Max. 4.944; StDev 0.7961060837298783;

Variable Format: numeric

Notes: UNF:6:3Yuh8b9m0Bt5uxCyPBU+cQ==

f18960 Location:

Summary Statistics: Valid 30.0; StDev 0.5928381580239208; Max. 3.639; Mean 2.5187666666666666; Min. 1.429

Variable Format: numeric

Notes: UNF:6:wV+gH7nChWbNf/Xq2URSDw==

f18960 Location:

Summary Statistics: Mean 92.21663333333333; StDev 52.881440453595125; Valid 30.0; Max. 179.013; Min. 13.118

Variable Format: numeric

Notes: UNF:6:V8VSFSt+c6V9wz1BkrAiTw==

f18960 Location:

Summary Statistics: StDev 0.07361109361671157; Max. 0.97; Min. 0.661; Mean 0.8984; Valid 30.0;

Variable Format: numeric

Notes: UNF:6:tdhSsa8goAIQrUb+orBpEA==

f18960 Location:

Summary Statistics: Max. 2.17; Valid 30.0; Mean 1.4368; StDev 0.31560848727716323; Min. 1.046;

Variable Format: numeric

Notes: UNF:6:fWgil95bYF1JVo2h1fsY8Q==

f18960 Location:

Summary Statistics: Max. 0.956; Mean 0.7260333333333333; Valid 30.0; Min. 0.461; StDev 0.1444097339668203

Variable Format: numeric

Notes: UNF:6:qOf596rsrHpL+06V5oFm7w==

f18960 Location:

Summary Statistics: Min. 0.843; StDev 0.025736172495393405; Max. 0.99; Valid 30.0; Mean 0.9758333333333333

Variable Format: numeric

Notes: UNF:6:F1CCZBTJSmEIYt1OyWY65w==

f18841 Location:

Variable Format: character

Notes: UNF:6:PDcOERlfEZ3wOf9OhkZSBA==

f18841 Location:

Variable Format: character

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f18841 Location:

Variable Format: character

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f18841 Location:

Variable Format: character

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f18841 Location:

Variable Format: character

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f18841 Location:

Variable Format: character

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f18841 Location:

Variable Format: character

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f18841 Location:

Summary Statistics: Max. NaN; Valid 0.0; Min. NaN; Mean NaN; StDev NaN

Variable Format: numeric

Notes: UNF:6:6kmqn29s8tU9RU5ii6WjOQ==

f18841 Location:

Variable Format: character

Notes: UNF:6:cvgoKysFaXPdv5xnpGXgCw==

f18841 Location:

Variable Format: character

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f18841 Location:

Variable Format: character

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Summary Statistics: StDev 2.2760243761698904; Mean 5.750733333333334; Max. 11.712; Min. 2.627; Valid 30.0;

Variable Format: numeric

Notes: UNF:6:29XBvZlXWJsxcrZmufwbHg==

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Summary Statistics: Mean 8.7034; Min. 5.99; Valid 30.0; Max. 12.456; StDev 1.6535708195213215;

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Summary Statistics: Max. 0.969; StDev 0.04791208423865479; Min. 0.762; Valid 30.0; Mean 0.9188666666666667

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Summary Statistics: StDev 0.26107224525287887; Max. 2.365; Valid 30.0; Min. 1.127; Mean 1.4408

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Summary Statistics: Valid 30.0; StDev 0.10726741746949402; Min. 0.423; Mean 0.7123333333333334; Max. 0.887

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Summary Statistics: Min. 0.976; Mean 0.9897; Max. 0.996; Valid 30.0; StDev 0.005408486307455265;

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Summary Statistics: Mean 0.894; StDev 0.062118351999810924; Max. 0.966; Valid 30.0; Min. 0.737;

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f18824 Location:

Summary Statistics: Min. 1.128; Mean 1.5449666666666666; Valid 30.0; StDev 0.34427159320085865; Max. 2.514;

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Summary Statistics: Valid 30.0; Mean 0.9833; Max. 0.998; StDev 0.008077853931455504; Min. 0.967

Variable Format: numeric

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Summary Statistics: StDev 2.6135739181830027; Min. 3.215; Valid 31.0; Max. 13.294; Mean 6.397677419354839;

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Summary Statistics: Max. 14.467; Min. 6.467; StDev 1.9754013186926025; Mean 9.413354838709678; Valid 31.0

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f18404 Location:

Summary Statistics: Max. 0.975; StDev 0.08843066660214048; Min. 0.661; Valid 31.0; Mean 0.8831290322580645

Variable Format: numeric

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f18404 Location:

Summary Statistics: Max. 2.724; Mean 1.583774193548387; Min. 1.047; StDev 0.4406048652838822; Valid 31.0;

Variable Format: numeric

Notes: UNF:6:5CzS5E41XR85Q/brvYfuhQ==

f18404 Location:

Summary Statistics: Mean 0.674483870967742; StDev 0.16495249234607762; Max. 0.955; Valid 31.0; Min. 0.367

Variable Format: numeric

Notes: UNF:6:law7kqYLwsbq6EnU1yTleQ==

f18404 Location:

Summary Statistics: Max. 1.001; Min. 0.965; StDev 0.00844361437157773; Mean 0.9851935483870967; Valid 31.0

Variable Format: numeric

Notes: UNF:6:d0OUNrPDHIfXR4yhaOL4sw==

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