Name: design and synthesis of a reconfigurable dna accordion rack
Uploaded: 2018-08-15T15:00:00
Description: Watch this Scientific Journal Video about Design and Synthesis of a Reconfigurable DNA Accordion Rack at JoVE.com

这项研究由科学和信息和通信技术部 (MSIT) (2015K1A4A3047345) 资助的韩国国家研究基金会 (NRF) 在全球研究发展中心的项目中得到部分支持, Nano·通过由科学和信息和通信技术部 (MSIT) 资助的韩国国家研究基金会 (NRF) 提供的材料技术发展方案 (2012M3A7A9671610)。首尔国立大学工程研究所为这项工作提供了研究设施。作者感谢泰青年尹 (生物科学, 首尔国立大学) 关于荧光光谱的烦恼分析。

1. 设计6由6个 DNA 手风琴架与 caDNAno14
<ol><li>下载并安装 caDNAno 2.0 软件14设计一个 DNA 手风琴架 (caDNAno 2.5 也可在 https://github.com/cadnano/cadnano2.5)。打开 caDNAno14并单击正方形工具以添加一个正方形格子的新零件。</li>
	<li>将手风琴架的每束光束编号, 并在 caDNAno14的左格子面板上绘制 (图 2)。</li>
	...

<ol>
	<li>Andersen, E. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-assembly+of+a+nanoscale+DNA+box+with+a+controllable+lid.">Self-assembly of a nanoscale DNA box with a controllable lid.</a> Nature. 459 (7243), 73-76 (2009).</li><li>Cha, T. -. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+principles+of+DNA+enzyme+based+walkers:+Translocation+kinetics+and+photo-regulation.">Design principles of DNA enzyme based walkers: Translocation kinetics and photo-regulation.</a> Journal of the American Chemical Society. 137 (29), 9429-9437 (2015).</li><li>Gerling, T., Wagenbauer, K. F., Neuner, A. M., Dietz, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+DNA+devices+and+assemblies+formed+by+shape-complementary,+non-base+pairing+3D+components.">Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components.</a> Science. 347 (6229), 1446-1452 (2015).</li><li>Pinheiro, A. V., Han, D., Shih, W. M., Yan, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Challenges+and+opportunities+for+structural+DNA+nanotechnology.">Challenges and opportunities for structural DNA nanotechnology.</a> Nature nanotechnology. 6 (12), 763-772 (2011).</li><li>Li, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exploring+the+speed+limit+of+toehold+exchange+with+a+cartwheeling+DNA+acrobat.">Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat.</a> Nature Nanotechnology. 1, (2018).</li><li>Krishnan, Y., Simmel, F. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nucleic+acid+based+molecular+devices.">Nucleic acid based molecular devices.</a> Angewandte Chemie International Edition. 50 (14), 3124-3156 (2011).</li><li>Liu, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+DNA+tweezer-actuated+enzyme+nanoreactor.">A DNA tweezer-actuated enzyme nanoreactor.</a> Nature communications. 4, 2127 (2013).</li><li>Douglas, S. M., Bachelet, I., Church, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+logic-gated+nanorobot+for+targeted+transport+of+molecular+payloads.">A logic-gated nanorobot for targeted transport of molecular payloads.</a> Science. 335 (6070), 831-834 (2012).</li><li>Kuzyk, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reconfigurable+3D+plasmonic+metamolecules.">Reconfigurable 3D plasmonic metamolecules.</a> Nature Materials. 13 (9), 862-866 (2014).</li><li>Zhou, C., Duan, X., Liu, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+plasmonic+nanorod+that+walks+on+DNA+origami.">A plasmonic nanorod that walks on DNA origami.</a> Nature communications. 6, 8102 (2015).</li><li>Choi, Y., Choi, H., Lee, A. C., Lee, H., Kwon, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Reconfigurable+DNA+Accordion+Rack.">A Reconfigurable DNA Accordion Rack.</a> Angewandte Chemie International Edition. 57 (11), 2811-2815 (2018).</li><li>Chen, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Understanding+the+Mechanical+Properties+of+DNA+Origami+Tiles+and+Controlling+the+Kinetics+of+their+Folding+and+Unfolding+Reconfiguration.">Understanding the Mechanical Properties of DNA Origami Tiles and Controlling the Kinetics of their Folding and Unfolding Reconfiguration.</a> Journal of the American Chemical Society. 136 (19), 6995-7005 (2014).</li><li>Han, D., Pal, S., Liu, Y., Yan, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+and+cutting+DNA+into+reconfigurable+topological+nanostructures.">Folding and cutting DNA into reconfigurable topological nanostructures.</a> Nature Nanotechnology. 5 (10), 712-717 (2010).</li><li>Douglas, S. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+prototyping+of+3D+DNA-origami+shapes+with+caDNAno.">Rapid prototyping of 3D DNA-origami shapes with caDNAno.</a> Nucleic Acids Research. 37 (15), 5001-5006 (2009).</li><li>Castro, C. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+primer+to+scaffolded+DNA+origami.">A primer to scaffolded DNA origami.</a> Nature methods. 8 (3), 221-229 (2011).</li><li>Ouldridge, T. E., Louis, A. A., Doye, J. P. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+Nanotweezers+Studied+with+a+Coarse-Grained+Model+of+DNA.">DNA Nanotweezers Studied with a Coarse-Grained Model of DNA.</a> Physical Review Letters. 104 (17), 178101 (2010).</li><li>Snodin, B. E. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+Simulation+of+the+Self-Assembly+of+a+Small+DNA+Origami.">Direct Simulation of the Self-Assembly of a Small DNA Origami.</a> ACS Nano. 10 (2), 1724-1737 (2016).</li><li>Amir, Y., Abu-Horowitz, A., Bachelet, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+and+Characterization+of+a+Bio-responsive+Robot+from+DNA+Origami.">Folding and Characterization of a Bio-responsive Robot from DNA Origami.</a> Journal of Visualized Experiments. (106), e51272 (2015).</li><li>Stahl, E., Martin, T. G., Praetorius, F., Dietz, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Facile+and+Scalable+Preparation+of+Pure+and+Dense+DNA+Origami+Solutions.">Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions.</a> Angewandte Chemie International Edition. 53 (47), 12735-12740 (2014).</li><li>Wei, B., Vhudzijena, M. K., Robaszewski, J., Yin, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-assembly+of+Complex+Two-dimensional+Shapes+from+Single-stranded+DNA+Tiles.">Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles.</a> Journal of Visualized Experiments. (99), e52486 (2015).</li><li>Clegg, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescence+resonance+energy+transfer+and+nucleic+acids.">Fluorescence resonance energy transfer and nucleic acids.</a> Methods in enzymology. 211, 353-388 (1992).</li><li>Kopperger, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+self-assembled+nanoscale+robotic+arm+controlled+by+electric+fields.">A self-assembled nanoscale robotic arm controlled by electric fields.</a> Science. 359 (6373), 296-301 (2018).</li><li>Lauback, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+magnetic+actuation+of+DNA+nanodevices+via+modular+integration+with+stiff+micro-levers.">Real-time magnetic actuation of DNA nanodevices via modular integration with stiff micro-levers.</a> Nature Communications. 9 (1), 1446 (2018).</li></ol>

该协议介绍了从设计、仿真、合成和分析基本的 2D DNA 手风琴机架的整个过程。修改后的设计和仿真规则被描述, 因为设计规则不同于标准的 dna 折纸, 因为 dna 手风琴架有额外的核苷酸在分频器为灵活性14,15。由此, 我们期望该协议可以加速各种研究使用 DNA 手风琴架。此外, 所描述的协议也可以应用于其他研究使用 dna 纳米结构, 而不是标准的 dna 折纸。</...

基于 dna 纳米结构或 dna nanomachines 的机械系统,1,2,3,4,5是独一无二的, 因为它们在纳米的2D 和3D 中产生复杂的纳米尺度运动, 以ångström 决议, 根据各种生物分子刺激2,3,6。通过在这些结构上附加功能材料并控制它们的位置, 这些结构可应用于各个领域。例如, 为分子反应器7, 药物交付8和 nanoplasmonic 系统9,10提出了 DNA nanomachines。
以前, 我们介绍了可重构的 DNA 手风琴架, 它可以操纵2D 或3D 元素11 (图 1A) 的纳米尺度网络。与其他仅控制少数元素的 DNA nanomachines 不同, 该平台可以将周期性地排列2D 或3D 元素的过程集体地操作到不同的阶段。我们预计, 可编程的化学和生物反应网络或分子计算系统可以建立从我们的系统, 通过增加数量的可控元素。dna 手风琴架是一种结构, 其中多个 dna 束网络连接到由单链 dna 组成的关节 (图 1B)。由 dna 束产生的手风琴架由 dna 锁重新配置, 杂交在光束的粘性部分, 根据锁 (锁定状态) 的桥接部分的长度改变光束之间的夹角。此外, 通过通过基于立足点的绞线12、13分离 DNA 锁, 在自由状态形成后添加新锁, 可以证明多步重构。
在本协议中, 我们描述了可重构 DNA 手风琴架的整个设计和合成过程。该协议包括设计, 模拟, 湿实验室实验, 并分析了 6 6 网格的 DNA 手风琴架的合成和重新配置这些。该协议所涵盖的结构是前一项研究的基本模型,11是 65 nm, 大小为65纳米, 由14束组成。在设计和仿真方面, 手风琴架的结构设计不同于传统的 DNA 折纸14、15 (即紧密包装)。因此, 采用传统的方法对设计规则和分子模拟进行了改进。为了演示, 我们用 caDNAno14的改进方法和使用 oxDNA16、17和附加脚本的手风琴机架的仿真来展示设计技术。最后, 介绍了该方法的基本原理和对所配置的手风琴架结构分析的烦恼。

<table>
	<tbody>
		<tr>
			<td>M13mp18 Single-stranded DNA</td>
			<td>NEB</td>
			<td>N4040s</td>
			<td></td>
		</tr>
		<tr>
			<td>1M MgCl2 Solution</td>
			<td>Biosesang</td>
			<td>M2001</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris-EDTA buffer</td>
			<td>Biosesang</td>
			<td>T2142</td>
			<td></td>
		</tr>
		<tr>
			<td>Nuclease-Free Water</td>
			<td>Qiagen</td>
			<td>129114</td>
			<td></td>
		</tr>
		<tr>
			<td>5M Sodium Chloride solution</td>
			<td>Biosesang</td>
			<td>s2007</td>
			<td></td>
		</tr>
		<tr>
			<td>PEG 8000</td>
			<td>Sigma Aldrich</td>
			<td>1546605</td>
			<td></td>
		</tr>
		<tr>
			<td>10N NaOH</td>
			<td>Biosesang</td>
			<td>S2038</td>
			<td></td>
		</tr>
		<tr>
			<td>Uranyl formate</td>
			<td>Thomas Science</td>
			<td>C993L42</td>
			<td></td>
		</tr>
		<tr>
			<td>Thermal cycler C1000</td>
			<td>Biorad</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Nanodropic 2000</td>
			<td>Thermo Fisher Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>TEM (LIBRA 120)&#160;&#160;</td>
			<td>Carl Zeiss</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorometer Enspire 2300</td>
			<td>Perkin-Elmer</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>Labogene</td>
			<td>LZ-1580</td>
			<td></td>
		</tr>
	</tbody>
</table>

design and synthesis of a reconfigurable dna accordion rack

基于 dna 纳米结构的机械系统或 dna nanomachines, 在纳米到ångström 分辨率的2D 和3D 中产生复杂的纳米尺度运动, 在纳米技术的各个领域, 如分子反应器、药物输送, 都显示出巨大的潜力,和 nanoplasmonic 系统。描述了可重构的 dna 手风琴机架, 它可以集体操纵2D 或3D 纳米元素网络, 在多个阶段响应 dna 输入。该平台有可能增加 DNA nanomachines 可以从几个元素控制到网络规模的元素数量, 并可重新配置多个阶段。
在本协议中, 我们描述了 6 6 网格可重构 DNA 手风琴架的整个实验过程。该协议包括结构的设计规则和仿真程序, 以及用于合成和重构的湿实验室实验。此外, 该协议还包括了透射电镜 (透射电子显微镜) 和焦虑 (荧光共振能量传递) 的结构分析。本协议所涵盖的新颖设计和仿真方法将帮助研究人员使用 DNA 手风琴机架进行进一步的应用。

设计的6由 6 DNA 手风琴机架模拟从 oxDNA16,17和结果显示在图 6。仿真结果表明, 该结构在不变形的情况下形成了拟合结构。
图 7中的 TEM 图像是配置结构的图像, 其锁定长度为2、8、13和 20 bp。在图像上, 当锁的长度变长时, 结构的角度 (<strong c...

Watch this Scientific Journal Video about Design and Synthesis of a Reconfigurable DNA Accordion Rack at JoVE.com

Design and Synthesis of a Reconfigurable DNA Accordion Rack

我们描述了设计, 模拟, 湿实验室实验的详细协议, 和分析的可重构的 DNA 手风琴架 6 6 网格。

可重构 DNA 手风琴架的设计与合成

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