Name: folding and characterization of a bio-responsive robot from dna origami
Uploaded: 2015-12-03T10:45:00.000+00:00
Duration: 7 min 59 s
Description: Watch this Scientific Journal Video about Folding and Characterization of a Bio-responsive Robot from DNA Origami at JoVE.com

作者要感谢S.道格拉斯极有价值的讨论和建议，以及巴切莱特实验室的所有成员有益的讨论和工作。这项工作是由生命科学学院和纳米技术及先进材料研究所在巴伊兰大学的资助。

1.准备的斯台普斯池混合<ol><li>如表 1中所列的96孔板顺序冻干的DNA纳米机器人订书钉（ 见材料），并归一至10纳摩尔。将DNA纳米机器人的设计和结构的详细描述，请参见本- Ishay 等人 14和Douglas 等人15）。 </li><li>重构各订书钉以及用DNA酶/无RNase超纯至100μM的浓度。主食归到10纳摩尔，重组与100微升超纯水。 </li><li>池一起20微升各订书钉的使用多通道移液器和无菌55毫升解决方案盆地。 注:由于纳米机器人形状是由254短 ​​链（包括核心，边缘，手柄和指南序列， 表1），每个U形钉池中的订书钉的浓度为394纳米。从订书钉池中取出钉，或添加一些不同的卷超微电极，可降低产率相当，或者以其他方式导致展开聚集体。 </li></ol> 2.制备制作反应液<ol><li>对于一个标准的反应混合物用40微升的M13mp18病毒基因组的环状单链DNA中，对应于4皮摩尔脚手架的DNA（100nM的原液， 见材料）。支架在制造混合物的最终浓度为20nM的，最终体积200微升。 <ol><li>调整根据具体需要脚手架DNA的量;然而，保持在反应混合物中的DNA支架的最终浓度在恒定的20纳米。 </li></ol></li><li>添加订书钉达到支架为1订书钉比率至10。对于20纳米支架DNA浓度，每254订书钉&#39;最终浓度是200nM的。对于200微升最终反应体积加上102微升斯台普斯游泳池混合物（第1.2节）的。 <ol><li>添加特定的门序列，分别为thË折叠反应混合物在这个时候。这些寡单独订购，并要求HPLC纯化。确保门寡核苷酸存在于1:10支架到门序列比， 即 200nM的每种寡核苷酸的20nM的脚手架浓度。对于200微升折叠反应体积，在100微米的股票浓度增加0.4微升每个四门寡。 </li></ol></li><li>添加10倍TAE储备缓冲到达1×TAE（40mM的Tris-醋酸，1mM EDTA）中的最终浓度。对于200微升折叠反应体积，加入20微升的10X TAE。 </li><li>添加1M的MgCl 2的，以10mM的终浓度。对于200微升折叠反应体积，加入2微升的1M 氯化镁 。 </li><li>添加36微升DNA酶/ RNA酶游离超纯水，使达到200微升的最终体积。 </li><li>涡和分装100微升样品到PCR小瓶。 注:请有关最大反应体积中使用热循环仪规范。减少体积，以满足这些限制将不降低获得的收益率。反应体积上述规定将危及收益率的最大值。 </li></ol>制作反应3.温度退火斜坡<ol><li>程序热循环仪如下: <ol><li>坡道85℃至60℃，在5分钟/℃的速率。 </li><li>斜坡60℃至4℃下以75分钟/℃的速率。 </li><li>保持在4℃下去。 </li></ol></li><li>经过加工已经结束商店样品在-20℃。 </li></ol> 4.去除多余史泰博<ol><li>加入100微升的折叠反应混合物与0.5 ml的离心过滤器100 kDa的的MWCO。保存纳米机器人预纯化供以后分析的10微升样品。 </li><li>离心机在9,600×g的10分钟。 </li><li>加入400微升的折叠缓冲液（1×TAE，10毫米氯化镁2）。 </li><li>重复步骤4.2和4.3的两倍多。 </li><li>离心5分钟，在9,600×g的。 </li><li>通过将过滤器倒置在一个干净的离心管中，自旋为1分钟，在9600×g下恢复该浓缩物。最终体积可以根据制造反应混合物的初始体积被放入过滤器的不同而不同。通常浓缩纳米机器人样品的25-60微升最终体积被获得。 </li><li>测量通过分光光度计在样品中的DNA的浓度在260纳米。计算摩尔浓度的纳米机器人的样品时，应采用5.3微克/皮摩尔分子量。 注:摩尔消光系数为双链DNA，50微克/ OD 260，足以满足大多数应用。 48微克/ OD 260考虑到聚胸腺嘧啶的ssDNA延伸在边缘处缝合钉。 </li></ol>折叠纳米机器人的5琼脂糖凝胶电泳分析<ol><li>补充了10mM的MgCl 2 0.5×TBE（45毫摩尔Tris-硼酸盐，1mM EDTA中），2％琼脂糖凝胶的制备</suB&gt;（改编自埃内斯托·卡斯特罗等 [21]。）: <ol><li>在118.75双蒸2 O.毫升准备0.5X TBE缓冲液稀释6.25毫升10倍TBE储备缓冲</li><li>溶解2.5克琼脂糖在125毫升的0.5×TBE缓冲液。 </li><li>沸腾在微波直到琼脂糖完全溶解。 </li><li>加入1.25毫升的1M的MgCl 2的 10mM的最终浓度。 </li><li>加7微升10毫克/毫升的溴化乙锭。 </li><li>等待解决方案，以偏凉和琼脂糖凝胶固化前，填补了凝胶托盘。立即安装所需的梳子。 </li><li>制备1升0.5×TBE缓冲液加入50毫升10×TBE储备缓冲和10ml的1M MgCl 2的940至双蒸2 O中的溶液</li><li>一旦凝胶是固体加载运行缓冲液的电泳设备，并把设备在冰浴中。 </li></ol></li><li>在纳米机器人预净化负载1微克总DNA（步骤3.2），和纯化后（步骤4.7），旁边一个支架DNA样品和1 kb的DNA标记，凝胶上。给出一个例子在图2中。样品的实际量取决于纯化后得到的浓度。每个样品装入在1装载缓冲液:6终体积比。 </li><li>设置电源到80伏，并运行凝胶3小时。运行在装满冰和水的浴中的凝胶。纳米机器人将展开，如果琼脂糖凝胶电泳过程中加热出现一抹黑。电泳过程中添加额外的冰块，以保持设备的加热。 </li><li> （ 图2）紫外线表视图凝胶。 </li></ol>纳米机器人6.用铀甲酸盐负染色<ol><li> 2％的铀甲酸盐原液制备（改编自卡斯特罗等23）: <ol><li>权衡的双氧铀酸盐粉末100毫克到15毫升管。 </li><li>煮沸DNA酶/ RNA酶的超纯水进行3分钟脱含氧化合物。 </li><li>添加5毫升脱氧热水（〜60℃）入15ml试管中含有双氧铀酸盐粉末（来自之前的步骤）。紧紧合上机盖，包装在铝箔和涡严格的10分钟（系管涡流）。溶液应出现浑浊带有黄色。 </li><li>通过0.2微米注射器滤波器过滤解决方案。解决方法应该很清楚。 </li><li>分装200微升的溶液倒入离心管中。 </li><li>离心机中以最大速度为5分钟在台式离心机以池的样品在管的底部。 </li></ol></li><li>样品电网和消极染色加载: <ol><li>除霜2％铀甲酸盐溶液（6.1节准备）200微升等分。加入10微升0.5M的NaOH溶液和涡旋严格3分钟。离心机中以最大速度用台式离心机5分钟。 </li><li>同时，辉光放电网格使用室内空气在0.2毫巴和25 mA的30秒。 </li><li>添加15微升为2nM纳米机器人样品的纯化后（secti上4.7）到电网的顶侧（用镊子保持），并让吸收1分钟。使用滤波器纸张放置在网格上的滤纸的顶部以排出多余的液体。请勿触摸网格表面。 </li><li>加入10微升2％的铀甲酸盐（从步骤6.2.1）的网格上的顶面（用钳子举行）。 </li><li>快速使用滤波器纸张放置在网格上的滤纸的顶部以排出多余的液体。请勿触摸网格表面。 </li><li>重复步骤6.2.4和6.2.5。 </li><li>加入10微升2％的铀甲酸盐（从步骤6.2.1）的网格上的顶面（用钳子举行）。让染色溶液吸收30秒。 </li><li>使用滤波器纸张放置在网格上的滤纸的顶部以排出多余的液体。请勿触摸网格表面。 </li><li>让格完全干燥至少30分钟，面朝上的滤纸，注射入的TEM之前。 </li></ol></li></ol>

<ol>
	<li>Watson, J. D., Crick, F. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetical+implications+of+the+structure+of+deoxyribonucleic+acid.">Genetical implications of the structure of deoxyribonucleic acid.</a> Nature. 171, 964-967 (1953).</li><li>Kosuri, S., 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=Large-Scale+de+novo.+DNA+synthesis:+technologies+and+applications.">Large-Scale de novo. DNA synthesis: technologies and applications.</a> Nature Meth. 11 (5), 499-507 (2014).</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 Nanotech. 6 (12), 763-772 (2011).</li><li>Seeman, N. 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+junctions+and+lattices.">Nucleic acid junctions and lattices.</a> J Theor Biol. 99 (2), 237-247 (1982).</li><li>Chen, J. H., Seeman, N. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synthesis+from+DNA+of+a+molecule+with+the+connectivity+of+a+cube.">Synthesis from DNA of a molecule with the connectivity of a cube.</a> Nature. 350 (6319), 631-633 (1991).</li><li>Wei, B., Dai, M., 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=Complex+shapes+self-assembled+from+single-stranded+DNA+tiles.">Complex shapes self-assembled from single-stranded DNA tiles.</a> Nature. 485 (7400), 623-626 (2012).</li><li>He, Y., 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=Hierarchical+self-assembly+of+DNA+into+symmetric+supramolecular+polyhedra.">Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra.</a> Nature. 452 (7184), 198-201 (2008).</li><li>Yin, P., Hariadi, R. F., Sahu, S., Choi, H. M. T., Park, S. H., Labean, T. H., Reif, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Programming+DNA+tube+circumferences.">Programming DNA tube circumferences.</a> Science. 321 (5890), 824-826 (2008).</li><li>Rothemund, P. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+DNA+to+create+nanoscale+shapes+and+patterns.">Folding DNA to create nanoscale shapes and patterns.</a> Nature. 440 (7082), 297-302 (2006).</li><li>Dietz, H., Douglas, S. M., Shih, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+DNA+into+twisted+and+curved+nanoscale+shapes.">Folding DNA into twisted and curved nanoscale shapes.</a> Science. 325 (5941), 725-730 (2009).</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=Self-assembly+of+DNA+into+nanoscale+three-dimensional+shapes.">Self-assembly of DNA into nanoscale three-dimensional shapes.</a> Nature. 459 (7245), 414-418 (2009).</li><li>Zhang, F., Nangreave, J., 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=Structural+DNA+nanotechnology:+state+of+the+art+and+future+perspective.">Structural DNA nanotechnology: state of the art and future perspective.</a> J Am Chem Soc. 136 (32), 11198-11211 (2014).</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=Prototyping+of+3D+DNA-origami+shapes+with+caDNAno.">Prototyping of 3D DNA-origami shapes with caDNAno.</a> Nucleic Acids Res. 37 (15), 5001-5006 (2009).</li><li>Ben-Ishay, E., 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=Designing+a+bio-responsive+robot+from+DNA+origami.">Designing a bio-responsive robot from DNA origami.</a> J Vis Exp. (77), e50268 (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>Tan, W., Donovan, M. J., Jiang, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aptamers+from+cell-based+selection+for+bioanalytical+applications.">Aptamers from cell-based selection for bioanalytical applications.</a> Chem Rev. 113 (4), 2842-2862 (2013).</li><li>Xiang, D., 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=Nucleic+Acid+Aptamer-Guided+Cancer+Therapeutics+and+Diagnostics:+The+Next+Generation+of+Cancer+Medicine.">Nucleic Acid Aptamer-Guided Cancer Therapeutics and Diagnostics: The Next Generation of Cancer Medicine.</a> Theranostics. 5 (1), 23-42 (2015).</li><li>Zhang, D. Y., Seelig, G. <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+nanotechnology+using+strand-displacement+reactions.">Dynamic DNA nanotechnology using strand-displacement reactions.</a> Nat Chem. 3 (2), 103-113 (2011).</li><li>Tang, Z., Parekh, P., Turner, P., Moyer, R. W., Tan, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generating+aptamers+for+recognition+of+virus-infected+cells.">Generating aptamers for recognition of virus-infected cells.</a> Clin Chem. 55 (4), 813-822 (2009).</li><li>Sefah, K., Shangguan, D., Xiong, X., O'Donoghue, M. B., Tan, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+DNA+aptamers+using+Cell-SELEX.">Development of DNA aptamers using Cell-SELEX.</a> Nature Prot. 5 (6), 1169-1185 (2010).</li><li>McKeague, M., DeRosa, M. C. <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+Small+Molecule+Aptamer+Development.">Challenges and Opportunities for Small Molecule Aptamer Development.</a> J Nucleic Acids. 2012, (2012).</li><li>Amir, Y., 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=Universal+computing+by+DNA+origami+robots+in+a+living+animal.">Universal computing by DNA origami robots in a living animal.</a> Nature Nanotech. 9 (5), 353-357 (2014).</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 Meth. 8 (3), 221-229 (2011).</li><li>Sobczak, J. P., Martin, T. G., Gerling, T., 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=Rapid+folding+of+DNA+into+nanoscale+shapes+at+constant+temperature.">Rapid folding of DNA into nanoscale shapes at constant temperature.</a> Science. 338 (6113), 1458-1461 (2012).</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> Angew Chem Int Ed Engl. 53 (47), 12735-12740 (2014).</li><li>Lin, C., Perrault, S. D., Kwak, M., Graf, F., Shih, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Purification+of+DNA-origami+nanostructures+by+rate-zonal+centrifugation.">Purification of DNA-origami nanostructures by rate-zonal centrifugation.</a> Nucleic Acids Res. 41 (2), (2012).</li><li>Bai, X. C., Martin, T. G., Scheres, S. H., 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=Cryo-EM+structure+of+a+3D+DNA-origami+object.">Cryo-EM structure of a 3D DNA-origami object.</a> Proc Natl Acad Sci U S A. 109 (49), 20012-20017 (2012).</li></ol>

作者什么都没有透露。

我们介绍的加工，净化，和可视化的DNA纳米机器人的。继装置的六边形底盘的制造中，所述纳米机器人的功能进行编程时将简单介绍的特定货物和传感链到机器人容易地找到它们的指定的位置，由于氢键互补可用单链对接位点14 ，15,22。 描述的制造协议使用缓慢退火坡道，其通常使用在我们的实验室折叠广泛折纸形状。如果生产时间成为关键因素的其它协议，如由Sobc...

的用途核酸纳米技术是惊人。在Watson-Crick碱基配对的易处理性以及大规模合成的定制寡核苷酸2的易用性和相对低的成本已生成的应用3中的DNA纳米技术领域的爆炸和研究。结构DNA纳米，基于所述不动的塞曼结4,5-作为基本构建块利用的DNA，作为任意形状6-8的结构的自组装基本单位。 脚手架DNA折纸9技术的最新发展使得复杂的2D / 3D纳米结构10-12亚纳米级精度的建设，是建设新的功能对象日益增长的复杂性和惊人的多样性的有效途径。施工过程是基于一个长脚手架单链DNA，通常是从病毒染色体组衍生即，它可以通过几百短单链DNA寡核苷酸的杂交被折叠称为订书钉。通过这种技术获得的高结构分辨率是DNA双螺旋的自然尺寸的直接结果，而制造的再现性剪裁短单链订书钉序列以促进最大的氢键互补达到的结果。与使用慢温度退火的斜坡设计最低能量，热力学优选的纳米结构中达到高的产率和保真度。在计算机代码轻松实现连接处的设计规则允许的CAD工具，如caDNAno 13的发展，也极其简化设计包含数百个路口相连的大，结构复杂的任务。 先前我们描述的DNA纳米机器人的设计与caDNAno工具14,15的助剂。在这里，我们描述的制造和可视化，通过透射电子显微镜（TEM），所述纳米机器人，一个三维空心六角纳米器件，具有尺寸为35×35×50纳米的三件设计成经受到预定刺激和本具体货物中，响应一个主要的构象变化，例如蛋白质或核酸的寡核苷酸，隔离内部。虽然12装载站可在空心机箱内部，束缚货物的实际数量与不同尺寸的货物。货物分子范围从小型DNA分子的酶，抗体和5-10纳米金纳米颗粒。 Cargocan要么是均匀的或异质的，使得每个纳米机器人包含不同的分子的混合物。感测通过两个双螺旋锁定门设计实现成感测蛋白质，核酸或其它化学品，或者基于适体传感器16,17或DNA链置换18的技术。在适体选择的协议19-21最近的事态发展使纳米机器人的设计响应到分子和细胞类型的不断增加的范围。 早期的工作表明一个纳米机器人携带的特异性抗体，其在结合其抗原可以中继既抑制性或多产的信号，以特定的细胞类型的内部以混合细胞群15。这些纳米器件的一个令人兴奋的特性是他们与一个单一的群体推出不同的纳米机器人亚型的执行更为复杂的任务和逻辑控制能力。最近，我们证明了在执行作为正或负调节纳米机器人的特定亚型，控制含活性货物分子22的效应器群体。 这里介绍的协议描述门控与选择性结合的PDGF以促进纳米机器人15,22的开口适体传感器序列的纳米机器人的制造中，纯化和成像。中描述的制造过程类似于n个anorobot制造工艺最初由Douglas 等人 15的变化旨在减少整个过程持续时间所描绘的，同时增加了产率和纯化率。

<table><tbody><tr><td>DNase/RNase free distilled water</td><td>Gibco</td><td>10977</td><td></td></tr><tr><td>M13mp18 ssDNA scaffold</td><td>NEB</td><td>N4040S</td><td></td></tr><tr><td>10x TAE</td><td>Gibco</td><td>15558-042</td><td></td></tr><tr><td>1 M MgCl&lt;sub&gt;2&lt;/sub&gt;</td><td>Ambion</td><td>AM9530G</td><td></td></tr><tr><td>Amicon Ultra 0.5 ml centrifugal filter 100K MWCO</td><td>Amicon</td><td>UFC510024</td><td></td></tr><tr><td>Agarose</td><td>Promega</td><td>V3125</td><td></td></tr><tr><td>TBE buffer</td><td>Promega</td><td>V4251</td><td></td></tr><tr><td>Ethidium bromide 10&amp;nbsp;mg/ml solution</td><td>Sigma Aldrich</td><td>E1510</td><td></td></tr><tr><td>1 kb DNA marker</td><td>NEB</td><td>N3232S</td><td></td></tr><tr><td>Loading Dye</td><td>NEB</td><td>B7021S</td><td></td></tr><tr><td>uranyl formate</td><td>polysciences</td><td>24762</td><td></td></tr><tr><td>carbon-coated TEM grids&amp;nbsp;</td><td>Science services</td><td>EFCF400-Cu-50</td><td></td></tr><tr><td>Thermal Cycler c1000 Touch</td><td>Bio-Rad</td><td></td><td></td></tr><tr><td>Glow Discharge K100X</td><td>Emitech</td><td></td><td></td></tr><tr><td>UV table Gel Doc EZ Imager</td><td>Bio-Rad</td><td></td><td></td></tr><tr><td>NanoDrop 2000c</td><td>Thermo Scientific</td><td></td><td></td></tr><tr><td>TEM FEI-G12</td><td>Tecnai</td><td></td><td></td></tr></tbody></table>

folding and characterization of a bio-responsive robot from dna origami

该DNA纳米机器人是一个中空的六角纳米器件，设计成响应于特定的刺激和本货物内部隔离开。既刺激和货物可以根据具体需要量身定做。在这里，我们描述了DNA纳米机器人制造协议，与使用DNA折纸技术。该步骤首先短单链DNA订书钉混合到原料混合物中，然后加入到长圆形，单链DNA的支架中的折叠缓冲液中的存在。一个标准的热循环仪被编程，以逐渐降低所述混合反应温度，方便钉到脚手架退火，这是纳米机器人的折叠背后的导向力。一旦60小时折叠反应完成后，过剩的钉被使用离心过滤器，接着经由可视琼脂糖凝胶电泳（AGE）丢弃。最后，将纳米机器人的制造成功是由透射电子显微镜检验（TEM）与使用双氧铀酸盐作为负染色。

代表性的结果示于图2A。所有泳道含有1微克总DNA，通过分光光度计（OD 260）来测定。与环状单链DNA的支架（泳道2）相比，纳米机器人是受阻在凝胶由于它们的较高分子量，的订书钉杂交至骨架的DNA的结果（泳道3.红色箭头）。在泳道3的低分子量带代表其中不结合该支架的DNA（绿色箭头）过量订书钉。通过离心过滤纯化后大部分过量的订书钉被除去（泳道4-6）和纳米机器人准?...

Watch this Scientific Journal Video about Folding and Characterization of a Bio-responsive Robot from DNA Origami at JoVE.com

DNA 折纸生物响应机器人的折叠和表征 |化学|视频

Folding and Characterization of a Bio-responsive Robot from DNA Origami

DNA origami is a powerful method for fabricating precise nanoscale objects by programming the self-assembly of DNA molecules. Here we describe a protocol for the folding of a bio-responsive robot from DNA origami, its purification and negative staining for transmission electron microscopic imaging (TEM).

折叠的DNA折纸一个生物反应机器人与表征

The DNA nanorobot is a hollow hexagonal nanometric device, designed to open in response to specific stimuli and present cargo sequestered inside. Both ...

folding-characterization-bio-responsive-robot-from-dna

Research

Education

JoVE Journal

JoVE Core

Biology

Chemistry

Genetics

DNA Structure and Function

SCIENTISTS IN ACTION

14.5K 次观看.  Bar-Ilan University. DNA origami is a powerful method for fabricating precise nanoscale objects by programming the self-assembly of DNA molecules. Here we describe a protocol for the folding of a bio-responsive robot from DNA origami, its purification and negative staining for transmission electron microscopic imaging (TEM). 

视频: Folding and Characterization of a Bio-responsive Robot from DNA Origami

Origami Inspired Self-assembly of Patterned and Reconfigurable Particles

There are numerous techniques such as photolithography, electron-beam lithography and soft-lithography that can be used to precisely pattern two dimensional (2D) structures. These technologies are mature, offer high precision and many of them can be implemented in a high-throughput manner. We leverage the advantages of planar lithography and combine them with self-folding methods1-20 wherein physical forces derived from surface tension or residual stress, are used to curve or fold planar structures into three dimensional (3D) structures. In doing so, we make it possible to mass produce precisely patterned static and reconfigurable particles that are challenging to synthesize.
In this paper, we detail visualized experimental protocols to create patterned particles, notably, (a) permanently bonded, hollow, polyhedra that self-assemble and self-seal due to the minimization of surface energy of liquefied hinges21-23 and (b) grippers that self-fold due to residual stress powered hinges24,25. The specific protocol described can be used to create particles with overall sizes ranging from the micrometer to the centimeter length scales. Further, arbitrary patterns can be defined on the surfaces of the particles of importance in colloidal science, electronics, optics and medicine. More generally, the concept of self-assembling mechanically rigid particles with self-sealing hinges is applicable, with some process modifications, to the creation of particles at even smaller, 100 nm length scales22, 26 and with a range of materials including metals21, semiconductors9 and polymers27. With respect to residual stress powered actuation of reconfigurable grasping devices, our specific protocol utilizes chromium hinges of relevance to devices with sizes ranging from 100 &mu;m to 2.5 mm. However, more generally, the concept of such tether-free residual stress powered actuation can be used with alternate high-stress materials such as heteroepitaxially deposited semiconductor films5,7 to possibly create even smaller nanoscale grasping devices.

We describe experimental details of the synthesis of patterned and reconfigurable particles from two dimensional (2D) precursors. This methodology can be used to create particles in a variety of shapes including polyhedra and grasping devices at length scales ranging from the micro to centimeter scale.

折纸灵感的图案和可重构颗粒自组装

There are numerous techniques such as photolithography, electron-beam lithography and soft-lithography that can be used to precisely pattern two ...

科研

化学

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Current methods in DNA nano-architecture have successfully engineered a variety of 2D and 3D structures using principles of self-assembly. In this article, we describe detailed protocols on how to fabricate sophisticated 2D shapes through the self-assembly of uniquely addressable single-stranded DNA tiles which act as molecular pixels on a molecular canvas. Each single-stranded tile (SST) is a 42-nucleotide DNA strand composed of four concatenated modular domains which bind to four neighbors during self-assembly. The molecular canvas is a rectangle structure self-assembled from SSTs. A prescribed complex 2D shape is formed by selecting the constituent molecular pixels (SSTs) from a 310-pixel molecular canvas and then subjecting the corresponding strands to one-pot annealing. Due to the modular nature of the SST approach we demonstrate the scalability, versatility and robustness of this method. Compared with alternative methods, the SST method enables a wider selection of information polymers and sequences through the use of de novo designed and synthesized short DNA strands.

DNA tiling is an effective approach to make programmable nanostructures. We describe the protocols to construct complex two-dimensional shapes by the self-assembly of single-stranded DNA tiles.

复杂的二维形状的从单链DNA的瓷砖自组装

Current methods in DNA nano-architecture have successfully engineered a variety of 2D and 3D structures using principles of self-assembly. In this ...

Preparation of Mica and Silicon Substrates for DNA Origami Analysis and Experimentation

The designed nature and controlled, one-pot synthesis of DNA origami provides exciting opportunities in many fields, particularly nanoelectronics. Many of these applications require interaction with and adhesion of DNA nanostructures to a substrate. Due to its atomically flat and easily cleaned nature, mica has been the substrate of choice for DNA origami experiments. However, the practical applications of mica are relatively limited compared to those of semiconductor substrates. For this reason, a straightforward, stable, and repeatable process for DNA origami adhesion on derivatized silicon oxide is presented here. To promote the adhesion of DNA nanostructures to silicon oxide surface, a self-assembled monolayer of 3-aminopropyltriethoxysilane (APTES) is deposited from an aqueous solution that is compatible with many photoresists. The substrate must be cleaned of all organic and metal contaminants using Radio Corporation of America (RCA) cleaning processes and the native oxide layer must be etched to ensure a flat, functionalizable surface. Cleanrooms are equipped with facilities for silicon cleaning, however many components of DNA origami buffers and solutions are often not allowed in them due to contamination concerns. This manuscript describes the set-up and protocol for in-lab, small-scale silicon cleaning for researchers who do not have access to a cleanroom or would like to incorporate processes that could cause contamination of a cleanroom CMOS clean bench. Additionally, variables for regulating coverage are discussed and how to recognize and avoid common sample preparation problems is described.

Reproducible cleaning processes for substrates used in DNA origami research are described, including bench-top RCA cleaning and derivatization of silicon oxide. Protocols for surface preparation, DNA origami deposition, drying parameters, and simple experimental set-ups are illustrated.

对于DNA折纸分析和实验准备云母和硅衬底

The designed nature and controlled, one-pot synthesis of DNA origami provides exciting opportunities in many fields, particularly nanoelectronics. Many of ...

Designing a Bio-responsive Robot from DNA Origami

Nucleic acids are astonishingly versatile. In addition to their natural role as storage medium for biological information1, they can be utilized in parallel computing2,3 , recognize and bind molecular or cellular targets4,5 , catalyze chemical reactions6,7 , and generate calculated responses in a biological system8,9. Importantly, nucleic acids can be programmed to self-assemble into 2D and 3D structures10-12, enabling the integration of all these remarkable features in a single robot linking the sensing of biological cues to a preset response in order to exert a desired effect.
Creating shapes from nucleic acids was first proposed by Seeman13, and several variations on this theme have since been realized using various techniques11,12,14,15 . However, the most significant is perhaps the one proposed by Rothemund, termed scaffolded DNA origami16. In this technique, the folding of a long (&gt;7,000 bases) single-stranded DNA 'scaffold' is directed to a desired shape by hundreds of short complementary strands termed 'staples'. Folding is carried out by temperature annealing ramp. This technique was successfully demonstrated in the creation of a diverse array of 2D shapes with remarkable precision and robustness. DNA origami was later extended to 3D as well17,18 .
 
The current paper will focus on the caDNAno 2.0 software19 developed by Douglas and colleagues. caDNAno is a robust, user-friendly CAD tool enabling the design of 2D and 3D DNA origami shapes with versatile features. The design process relies on a systematic and accurate abstraction scheme for DNA structures, making it relatively straightforward and efficient.
In this paper we demonstrate the design of a DNA origami nanorobot that has been recently described20. This robot is 'robotic' in the sense that it links sensing to actuation, in order to perform a task. We explain how various sensing schemes can be integrated into the structure, and how this can be relayed to a desired effect. Finally we use Cando21 to simulate the mechanical properties of the designed shape. The concept we discuss can be adapted to multiple tasks and settings.

DNA origami is a powerful method for fabricating precise nanoscale objects by programming the self-assembly of DNA molecules. Here, we describe how DNA origami can be utilized to design a robotic robot capable of sensing biological cues and responding by shape shifting, subsequently relayed to a desired effect.

DNA折纸设计生物反应灵敏的机器人

Nucleic acids are astonishingly versatile. In addition to their natural role as storage medium for biological information1, they can be utilized in ...

生物工程

Production of Dynein and Kinesin Motor Ensembles on DNA Origami Nanostructures for Single Molecule Observation

Cytoskeletal motors are responsible for a wide variety of functions in eukaryotic cells, including mitosis, cargo transport, cellular motility, and others. Many of these functions require motors to operate in ensembles. Despite a wealth of knowledge about the mechanisms of individual cytoskeletal motors, comparatively less is known about the mechanisms and emergent behaviors of motor ensembles, examples of which include changes to ensemble processivity and velocity with changing motor number, location, and configuration. Structural DNA nanotechnology, and the specific technique of DNA origami, enables the molecular construction of well-defined architectures of motor ensembles. The shape of cargo structures as well as the type, number and placement of motors on the structure can all be controlled. Here, we provide detailed protocols for producing these ensembles and observing them using total internal reflection fluorescence microscopy. Although these techniques have been specifically applied for cytoskeletal motors, the methods are generalizable to other proteins that assemble in complexes to accomplish their tasks. Overall, the DNA origami method for creating well-defined ensembles of motor proteins provides a powerful tool for dissecting the mechanisms that lead to emergent motile behavior.

The goal of this protocol is to form ensembles of molecular motors on DNA origami nanostructures and observe the ensemble motility using total internal reflection fluorescence microscopy.

生产用于单分子观察的DNA折纸纳米结构的Dynein和Kinesin电机组合

Cytoskeletal motors are responsible for a wide variety of functions in eukaryotic cells, including mitosis, cargo transport, cellular motility, and ...

生物化学

Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures

DNA origami nanostructures hold an immense potential to be used for biological and medical applications. However, low-salt conditions and nucleases in physiological fluids induce denaturation and degradation of self-assembled DNA nanostructures. In non-viral gene delivery, enzymatic degradation of DNA is overcome by the encapsulation of the negatively charged DNA in a cationic shell. Herein, inspired by gene delivery advancements, a simple, one-step and robust methodology is presented for the stabilization of DNA origami nanostructures by coating them with chitosan and linear polyethyleneimine. The polycation coating efficiently protects DNA origami nanostructures in Mg-depleted and nuclease-rich media. This method also preserves the full addressability of enzyme- and aptamer-based functionalization of DNA nanostructures.

Here, a protocol for the protection of DNA origami nanostructures in Mg-depleted and nuclease-rich media using natural cationic polysaccharide chitosan and synthetic linear polyethyleneimine (LPEI) coatings is presented.

基因治疗诱导聚化涂层保护 dna 折纸纳米结构

DNA origami nanostructures hold an immense potential to be used for biological and medical applications. However, low-salt conditions and nucleases in ...

Assembly of Gold Nanorods into Chiral Plasmonic Metamolecules Using DNA Origami Templates

The inherent addressability of DNA origami structures makes them ideal templates for the arrangement of metal nanoparticles into complex plasmonic nanostructures. The high spatial precision of a DNA origami-templated assembly allows controlling the coupling between plasmonic resonances of individual particles and enables tailoring optical properties of the constructed nanostructures. Recently, chiral plasmonic systems attracted a lot of attention due to the strong correlation between the spatial configuration of plasmonic assemblies and their optical responses (e.g., circular dichroism [CD]). In this protocol, we describe the whole workflow for the generation of DNA origami-based chiral assemblies of gold nanorods (AuNRs). The protocol includes a detailed description of the design principles and experimental procedures for the fabrication of DNA origami templates, the synthesis of AuNRs, and the assembly of origami-AuNR structures. In addition, the characterization of structures using transmission electron microscopy (TEM) and CD spectroscopy is included. The described protocol is not limited to chiral configurations and can be adapted for the construction of various plasmonic architectures.

We describe the detailed protocol for the DNA origami-based assembly of gold nanorods into chiral plasmonic metamolecules with strong chiroptical responses. The protocol is not limited to chiral configurations and can be easily adapted for the fabrication of various plasmonic architectures.

利用 dna 折纸模板将金纳米产物组装成手性质浆细胞分裂体

The inherent addressability of DNA origami structures makes them ideal templates for the arrangement of metal nanoparticles into complex plasmonic ...

DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications

Structural DNA nanotechnology provides a viable route for building from the bottom-up using DNA as construction material. The most common DNA nanofabrication technique is called DNA origami, and it allows high-throughput synthesis of accurate and highly versatile structures with nanometer-level precision. Here, it is shown how the spatial information of DNA origami can be transferred to metallic nanostructures by combining the bottom-up DNA origami with the conventionally used top-down lithography approaches. This allows fabrication of billions of tiny nanostructures in one step onto selected substrates. The method is demonstrated using bowtie DNA origami to create metallic bowtie-shaped antenna structures on silicon nitride or sapphire substrates. The method relies on the selective growth of a silicon oxide layer on top of the origami deposition substrate, thus resulting in a patterning mask for following lithographic steps. These nanostructure-equipped surfaces can be further used as molecular sensors (e.g., surface-enhanced Raman spectroscopy (SERS)) and in various other optical applications at the visible wavelength range owing to the small feature sizes (sub-10 nm). The technique can be extended to other materials through methodological modifications; therefore, the resulting optically active surfaces may find use in development of metamaterials and metasurfaces.

Here, we describe a protocol to create discrete and accurate inorganic nanostructures on substrates using DNA origami shapes as guiding templates. The method is demonstrated by creating plasmonic gold bowtie-shaped antennas on a transparent substrate (sapphire).

脱氧核糖核酸介导基板无机结构纳米图案用于传感应用

Structural DNA nanotechnology provides a viable route for building from the bottom-up using DNA as construction material. The most common DNA ...

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Recent advances in modular DNA assembly techniques have enabled synthetic biologists to test significantly more of the available &#34;design space&#34; represented by &#34;devices&#34; created as combinations of individual genetic components. However, manual assembly of such large numbers of devices is time-intensive, error-prone, and costly. The increasing sophistication and scale of synthetic biology research necessitates an efficient, reproducible way to accommodate large-scale, complex, and high throughput device construction.
Here, a DNA assembly protocol using the Type-IIS restriction endonuclease based Modular Cloning (MoClo) technique is automated on two liquid-handling robotic platforms. Automated liquid-handling robots require careful, often times tedious optimization of pipetting parameters for liquids of different viscosities (e.g. enzymes, DNA, water, buffers), as well as explicit programming to ensure correct aspiration and dispensing of DNA parts and reagents. This makes manual script writing for complex assemblies just as problematic as manual DNA assembly, and necessitates a software tool that can automate script generation. To this end, we have developed a web-based software tool, http://mocloassembly.com, for generating combinatorial DNA device libraries from basic DNA parts uploaded as Genbank files. We provide access to the tool, and an export file from our liquid handler software which includes optimized liquid classes, labware parameters, and deck layout. All DNA parts used are available through Addgene, and their digital maps can be accessed via the Boston University BDC ICE Registry. Together, these elements provide a foundation for other organizations to automate modular cloning experiments and similar protocols.
The automated DNA assembly workflow presented here enables the repeatable, automated, high-throughput production of DNA devices, and reduces the risk of human error arising from repetitive manual pipetting. Sequencing data show the automated DNA assembly reactions generated from this workflow are ~95% correct and require as little as 4% as much hands-on time, compared to manual reaction preparation.

Here, an automated workflow to perform modular DNA &#34;device&#34; assembly using a modular cloning DNA assembly method on liquid-handling robots is presented. The protocol uses an intuitive software tool for generating liquid handler picklists for combinatorial DNA device library generation, which we demonstrate using two liquid handling platforms.

模块化 DNA 设备的自动机器人液体处理组件

Recent advances in modular DNA assembly techniques have enabled synthetic biologists to test significantly more of the available &#34;design space&#34; ...

Design and Synthesis of a Reconfigurable DNA Accordion Rack

DNA nanostructure-based mechanical systems or DNA nanomachines, which produce complex nanoscale motion in 2D and 3D in the nanometer to &#229;ngstr&#246;m resolution, show great potential in various fields of nanotechnology such as the molecular reactors, drug delivery, and nanoplasmonic systems. The reconfigurable DNA accordion rack, which can collectively manipulate a 2D or 3D nanoscale network of elements, in multiple stages in response to the DNA inputs, is described. The platform has potential to increase the number of elements that DNA nanomachines can control from a few elements to a network scale with multiple stages of reconfiguration.
In this protocol, we describe the entire experimental process of the reconfigurable DNA accordion rack of 6 by 6 meshes. The protocol includes a design rule and simulation procedure of the structures and a wet-lab experiment for synthesis and reconfiguration. In addition, analysis of the structure using TEM (transmission electron microscopy) and FRET (fluorescence resonance energy transfer) is included in the protocol. The novel design and simulation methods covered in this protocol will assist researchers to use the DNA accordion rack for further applications.

We describe the detailed protocol for design, simulation, wet-lab experiments, and analysis for a reconfigurable DNA accordion rack of 6 by 6 meshes.

可重构 DNA 手风琴架的设计与合成

DNA nanostructure-based mechanical systems or DNA nanomachines, which produce complex nanoscale motion in 2D and 3D in the nanometer to &#229;ngstr&#246;m ...