这项工作是由海军研究青年学者计划奖N000141110914，海军研究基金N000141010827局，美国国家科学基金会职业奖CCF1054898，美国国立卫生研究院主任的新的创新奖1DP2OD007292办公室和威斯研究所生物启发工程学院启动基金（以PY）出资清华 - 北京中心生命科学基金启动（到BW）。

1. DNA序列设计<ol><li>使用UNIQUIMER软件27通过指定双螺旋中，顶部和底部螺旋每个双螺旋长度的数目，并且交叉图案创建24H×28T帆布设计一个SST-有限结构。定义这些参数之后，整体架构（链组合物与互补的安排）被在节目中以图形方式示出。 </li><li>产生用于特定结构的链可满足互补安排和附加要求（如果有的话）的序列。通过最小化所述序列的对称性28（对于大多数的结构）设计DNA序列。 <ol><li>产生的核苷酸（A，C，G和T）随机一个接一个。 </li><li>比赛核苷酸互补的产生遵循碱基配对的规则:A至T，反之亦然; C至G和反之亦然。 </li><li>不要使用重复段超越八九个核苷酸。当这样的代表吃在设计过程中出现细分，变异最近生成的核苷酸，直到重复段的要求得到满足。 </li><li>不要使用连续四个A，C，G或T碱基。 </li><li>使用预先指定的核苷酸的单链连接点（例如T和G作为第二十一和第二十二个核苷酸，分别用于大多数股线），以避免周围的联动点滑动碱（ 例如，如果这两个第二十一和第二十二核苷酸是T，它是可能的第二十一核苷酸结合的核苷酸的第二十二核苷酸应该结合）。 </li></ol></li><li>手动修改DNA序列为链霉抗标签，矩形的转化成管，不同的矩形和在不同尺度管的形成，并防止因上的SST暴露域聚集。 <ol><li>更换暴露域分子帆布与聚-T TRA的边界上CTS。 </li><li>对于链霉抗标签，设计手柄段（额外段附加到该组件链可以结合到互补配对如抗手柄链），使得它们可以容纳一个抗手柄链3&#39;生物素修饰。 </li><li>对于一个长方形的转化成管，从该矩形除去顶部和底部的行和插入新行的自助服务具有特定的互补性在第二顶部行和第二上下行对应的瓦片。 </li><li>对于不同形状的暴露的单链结构域，替换为10-11个核苷酸长度的poly-T段，或由该互补的暴露域和终止与一个10-11个核苷酸长的poly-T段边缘保护盖。 </li></ol></li></ol> 2.准备分子画布<ol><li>得到溶解于不含RNA酶的水从oligonucleoti指定序列的DNA的成分丝德商以V底96孔板与寡核苷酸在10纳摩尔规模标准脱盐合成。离心96孔板与大约10秒，在600×g的DNA链。 <ol><li>吸管1μl的来自各362孔与用于24H×28T矩形（ 图3A），在100μM每链（制造商说明书）DNA链到2ml试管中。 138微升蒸馏水去离子水2 O添加到2 ml的试验管，使该线材的混合物以每链200nM的浓度的储液。 </li></ol></li><li>添加50μl的链混合物，10微升10X退火缓冲液A（50毫摩尔Tris，pH值7.9，10mM的EDTA，250mM的MgCl 2的），和40μl蒸馏水去离子水的2 O到0.2的200nM的原液的毫升PCR管。这使得在1X退火缓冲液A中的分子画布的100微升样品（5毫摩的Tris，pH值7.9，1mM EDTA中，25毫的MgCl 2）。 </li><li>退火SAMPLE对于17小时的热循环从90℃冷却到25℃。程序的热循环如下:从90℃斜坡下降至61℃，以每℃下5分钟的恒定速度;从60℃斜坡下降至25℃，以每℃下20分钟的恒定速度;孵育在4℃下直到样品可以取出的热循环仪的。 </li><li>制备天然2％琼脂糖凝胶。 <ol><li>测量2.4克琼脂糖放入600ml烧杯中。再加入120毫升0.5X TBE缓冲液（44.5毫Tris-硼酸，pH值8.3，1mM EDTA中）和30毫升去离子蒸馏水至烧杯中。 </li><li>微波3分钟（或40 - 60秒以上煮沸后）。补充蒸发通过加入30毫升的水，这有助于保持琼脂糖凝胶中的浓度在2％时失去水。 </li><li>摇动烧杯中的内容为在冷水浴1分钟。加入1毫升1.2M的MgCl 2的（做出的10mM MgCl 2的浓度在凝胶中）和预染色的凝胶机智H 6微升SYBR安全染料（1:20,000）。 </li><li>倒入凝胶溶液变成干凝胶盒，并插入一个1.5mm厚的12孔凝胶电泳梳。让解决方案巩固15 - 30分钟在一个平台上，甚至。 </li><li>倾凝胶电泳缓冲液（44.5毫Tris-硼酸，pH值8.3，1毫摩尔EDTA和10mM的MgCl 2）到凝胶盒。负载2 - 3微升1 kb的DNA梯进琼脂糖凝胶的孔中。拌4微升6X溴酚蓝染料（0.25％溴酚蓝，5毫摩尔Tris，1mM EDTA中，10毫的MgCl 2和30％甘油）与20μl的分子画布的样品并加载溶液到的另一个井琼脂糖凝胶。 </li></ol></li><li>运行的本机2％琼脂糖在100 V在冰水浴2小时（溴酚蓝，以蓝色显示，运行速度比成分丝快，因此它可以作为一个指标，如果2小时运行时间为宜）。 </li><li>图像使用凝胶扫描仪的SYBR安全污点适当的滤波器（ 图2B中的凝胶</s仲&gt;）。 </li><li>在蓝色的光透射，用锋利的干净的刀片切下具有类似的流动性的主导频带的1500个碱基对的1 kb的DNA梯的频带。将所需的凝胶片在旋转柱（多个），然后粉碎凝胶成使用微管杵细碎片。离心机在438×g离心3分钟，在4℃。 </li><li>使用紫外线分光光度计在260nm处测量DNA的浓度。 <ol><li>使用2微升超纯DNA酶/ RNA酶的蒸馏水作为空白校准机器。 </li><li>使用收集的样本的等效体积从所述旋转柱以获得DNA浓度的估计。在260纳米的紫外吸收得到的测定浓度值（"是"=纳克/微升）将有助于确定为AFM和TEM成像稀释因子。 </li><li>从"a"（毫微克/微升）以"b"的（纳米）以下B = A×10 6 /（330转换所测量的浓度＃215;核苷酸的数量）。 注意:一个核苷酸的分子量为330克/摩尔。所计算的摩尔浓度值将确定的AFM和TEM成像稀释因子。作为一个24H×28T矩形的情况下，公共测量纯化的样品是约10 - 60纳克/微升。作为核苷酸为这样的结构的数目为14616道尔顿，摩尔浓度为约2 - 12纳米。最终浓度是由收集收率测定 - 从离心（〜20 50％）和凝胶条带的卷切出（的体积越大，越稀纯化的样品）。 </li></ol></li></ol> 3.原子力显微镜成像<ol><li>剥离云母附连到使用透明胶带来获得一个平坦的表面上，并放置在试样圆盘到成像级检体金属盘。 </li><li>加入40微升1×退火缓冲液A后跟5微升 - 24H的28T×的纯化样品（2 5纳米）矩形的新鲜剥离的云母表面。允许混合物沉降约2分钟。 </li><li>安装AFM氮化硅悬臂芯片到悬臂支架。使用C三角尖（谐振频率f 0 = 40 - 75千赫;弹簧常数，K = 0.24牛顿米-1）成像。 </li><li>图像中的流体轻敲模式的样品。使用下面的摄像参数进行扫描:扫描为2μm大小，1024行的分辨率，和0.5的扫描速度- 1赫兹（ 图2C）。 </li><li>如果必要的话，加10微升或多种的10mM的NiCl 2溶液以增加DNA云母结合29的强度。 </li></ol> 4.样品制备链霉亲和标签<ol><li>手动设计24H×28T矩形，使得手柄股线在特定位置被结合到互补反手柄链用生物素修饰，这反过来又能够结合到streptavid在具体。 <ol><li>通过在底部附连，它由（TT）作为间隔物的两核苷酸序列的14张牌的顶部行和14瓦3&#39;17个核苷酸的片段和一个15碱基手柄（GGAAGGGATGGAGGA）修改分子画布矩形（ 图3A）的行来标记边界。该序列是互补的3&#39;生物素修饰的抗手柄链（TCCTCCATCCCTTCC生物素）。 </li></ol></li><li>对于内部的标签，附上3&#39;核苷酸17段8个内部瓷砖和矩形（ 图4A）的6边界瓷砖。 <ol><li>混合28链带把手（边界标记）与24H×28T矩形（334股）的成分丝的其余部分，以使一个200nM的储备溶液。混合14链带把手（内部标签）与24H×28T矩形（348股线），以获得一个200nM的原液的成分丝的其余部分。 </li></ol></li><li>对于博undary标签，添加50微升的股线的200nM的储备溶液，6微升100μM的生物素修饰的抗手柄股，10微升10X退火缓冲液A和34微升的去离子蒸馏水至0.1 - 0.2毫升的PCR试管中。组件链的最终浓度为100nM至反手柄生物素修饰链的最终浓度为6000纳米。需要注意的是28分子的反处理生物素修饰的链结合至24H×28T矩形，以便防处理生物素修饰的链是超过100％，使结合有利。 </li><li>对于内部标签，添加50微升的股线的200nM的原液，3微升内部反处理生物素修饰的链中的100μM为10微升10X退火缓冲液A，37微升的去离子蒸馏水至0.1 - 0.2毫升的PCR试管中。组件链的最终浓度为100nM至抗生物素手柄modifi的最终浓度<html> ED链是3000纳米。需要注意的是14分子的抗手柄生物素修饰的链结合到一个24H×28T矩形，以便防处理生物素修饰的链是超过100％，使结合有利。 </li><li>退火在热循环仪两个样品用于使用在2.3中描述的步骤17小时。 </li><li>如步骤2.4中所述制备的本机2％琼脂糖凝胶。 </li><li>纯化两种样品如步骤2.5中所述。 </li><li>如步骤2.6中所述测量所需DNA结构的浓度。 </li></ol> 5.原子力显微镜链霉标签<ol><li>图像使用AFM如在步骤3（ 图3B和4B）描述的每个样品。 </li><li>在第一轮的成像后，加入40微升1×退火缓冲液A，继以1微升链霉亲和的10毫克/毫升到样品中。使混合物重新映像（ 图3C和图4C）之前沉降约2分钟。 </li></ol>_title"&gt; 6。转换一个矩形管<ol><li>为了设计基于所述矩形的管中，保留所有代替组分自助服务以外的顶部和底部行。引入一个新的行，其自助服务是通过将顶部和底部半砖其相应列的环化原始矩形成管的构象（ 图5A）而设计的。 </li><li>与24H的成分丝×28T矩形不包括顶部和底部的行（336股线），以获得一个200nM的储备溶液混合股线的新行（14根纤维）。 </li><li>按照凝胶纯化步骤2.2 - 2.7（ 图5B）。 </li></ol> 7.透射电子显微镜成像<ol><li>权衡0.06克铀酸盐的3ml蒸馏水，以制备2％水溶液铀酸盐染色液。过滤使用连接到注射器一个0.2微米的过滤器的2％水溶液铀酸盐染色液。 <ol><li>加入5微升为5N NaOH中1毫升过滤染色液。短暂涡旋振荡以20,000×克溶液和离心机。 </li></ol></li><li> 25毫安，45秒，0.1毫巴，和负高张力极性:辉光使用以下设置排出碳包被的网格（涂层面朝上）。 </li><li>使用自闭钳抓住从边缘的光晕放处理网格。 </li><li>吸取3.5微升样品到网格为4分钟。使用一片滤纸通过使滤纸与来自侧面网格接触芯吸离开样品。 </li><li>立即加入3.5微升染色溶液到网格1分钟。 </li><li>灯芯掉污渍在7.4按住滤纸对电网1 - 2分钟。 </li><li>转移使用JEOL JEM-1400，在80千伏放大率范围从10 K至80度（ 图5C）的网格的TEM样品支架和图象。 </li></ol> 8.构建任意形状使用MoleculAR帆布<ol><li>识别的形状，并选择对应于该分子画布上的形状的股线。对于一个三角形状，例如，选择206出362股的分子画布。 </li><li>替换暴露域（即，沿所述三角形的斜边）与聚-T段10 - 11个核苷酸长（设计1在图6A中），或者添加一个边缘保护互补的暴露的结构域和与终止10 - 11个核苷酸长的poly-T段（设计2 图6A），以防止聚集。 注意:只要退火对应于三角形的像素的海面温度（不使用保护链）会导致聚合和凝胶上没有明显的产物带的形成。使用边缘保护设计各种形状，因为它是更有效利用资源;它仅需要四个额外链（ 图6C）相比，另外14套在更换设计的集（FIGURË6B）。 </li><li>对于310像素的画布分子，其中包括核心集（362 SST帆布），组1 *（即绑定SST为域1边缘保护）结合域2，设置2 *（边缘保护创建链库一SST）中，设置绑定到SST域3 3 *（边缘保护），并设置4 *（即绑定到SST域4）边缘保护，以使总数1344边缘保护。 </li><li>离心96孔板为不同组的大约10秒。吸管从所述板，以使原液为一定形状的所需链。 <ol><li>对于边缘保护，吸管1微升206股的核心集，从0 1集*，0起订2 *，0距离组3 *和4组* 24股成2 ml离心三角形的形状管。加入20微升的去离子蒸馏水到管以使DNA链的400nM的储备溶液。 </li></ol></li><li>加入50微升的DNA斯特拉的400nM的原液的<html>的nds，10微升10X退火缓冲液B（50毫摩尔Tris，pH值7.9，10毫摩尔EDTA，125毫的MgCl 2）储备溶液和40μl蒸馏水去离子H 2 O转发到0.2毫升PCR管中。这使得在1X退火缓冲液B中的三角形的100微升样品（5毫摩的Tris，pH值7.9，1mM EDTA中，12.5毫的MgCl 2）与股线以每链约200nM的浓度。 </li><li>如在步骤2.3中描述的17小时热循环退火混合物。 </li><li>如在步骤2.4中所述制备的本机2％琼脂糖凝胶。 </li><li>如在步骤2.5中所述纯化的样品。 </li><li>测量DNA的浓度如在步骤2.6中描述。 </li><li>图像如在步骤3（ 图7C和7D）中描述的AFM下的样品。 </li><li>挑选和混合链使用同一链库不同的形状。退火的不同的解决方案，并结合不同形状的纯化样品以在原子力显微镜成像节省时间。 </li></ol>jove_title"&gt; 9可选:机器人自动化外形设计和液体混合<ol><li>使用自定义MATLAB程序来辅助的复杂形状的设计。 </li><li>使用该软件，以提供在一个移液序列与机器人液体处理程序的形式的指令。使用机器人的液体处理程序来选择和组合构成目标形状的链。 注:外形设计和钢绞线混合是自动化，减少人为误差，使施工少劳力密集。 </li></ol> 10.矩形和​​不同尺度管<ol><li>通过简单地改变的平行螺旋（H）和螺旋圈（T）的数目的数目构造不同尺寸的矩形（ 图10）。 </li><li>跟随步骤3为特定大小的矩形。 </li><li>遵循步骤6为特定尺寸的管子。 </li></ol>

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The authors declare competing financial interests.

在结构形成步骤中，以保持镁阳离子的适当的浓度是很重要的（ 例如 ，15毫摩尔）的DNA链混合物自组装的DNA纳米结构。同样，在琼脂糖凝胶表征/纯化步骤，以保持适当的镁阳离子浓度是很重要的（ 例如 ，10毫摩尔）在凝胶和凝胶运行缓冲液电泳过程中保持该DNA的纳米结构。为24H×28T矩形结构，我们在不同的Mg ++的浓度下测试退火，发现通常形成在10的范围内的结构- 30mM的Mg ++的（具有最好形成收率约20毫Mg ++的）。 不像搭建折纸结构，SST结构具有一个模块化的架构。不同的形状可以从相同的画布通过选择SST瓦片的相应子集来设计。此外，SST结构组装来回米只有短的合成的DNA链的，不涉及所用的折纸方法长支架。因此，将SST结构的大小由可用支架的长度没有限制。然而，虽然DNA的折纸方法经常可以最优化，以产生折叠结构或展开单体，SST可能导致部分地形成的结构，因此，可能需要进行凝胶纯化以供后续使用。此外，由于缺乏一支架链的，在SST结构可以更"脆"，比它的DNA折纸对应。无论是SST方法和DNA折纸术的方法是快速变化的，并且建议用户选择最适合他或她的特殊功能需求的方法。 令人吃惊的是数百只由地方结合相互作用介导的小单体可自我组装成一个全球性规定的形状，就证明了SST方法。在SST方法笑所示的基本原则ULD推广到DNA链旁边材料，本文中所描述的基本方法，经过适当的修改，应使复杂的结构自组装来自不同材料的结构。

以前核酸自组装工作1-25已导致各种复杂的结构，包括DNA 2的成功构建- 5,8,10 - 13,17,23或RNA 7,22周期性3,4,7， 22和算法5二维晶格，彩带和10,12管4,12,13，3D晶体17，11多面体和有限，2D图形7,8。一种特别有效的方法是脚手架的DNA折纸，据此，单一支架链是由许多短的辅助订书钉链折叠以形成复杂形状9,14 - 16,18 - 21,25。 我们最近报道的方法构建与使用单链砖（SST）规定的2D形状离散纳米结构，并表现出与结构的复杂性堪比DNA折纸26。这article是我们以前的工作26的改编，并介绍安排单独寻址到自助服务有限精良2D形状与精确规定的尺寸（宽度和长度）和形态的详细方案。该SST方法的一个关键优势是其模块化。结构的每一个组成部分SST作为在装配模块化施工单位，而这些表层海水温度的不同子集产生不同的形状。因此，我们建立构造纳米结构与规定的尺寸和形状，从短，合成DNA链一个通用的平台。 自助服务包含四个畴，每次10或11个核苷酸长（ 图1A）。该表层海水温度结合使得它们平行螺旋通过创建交叉联系在一起的DNA点阵。各交叉是结构域2和3的磷酸盐在图中为清晰起见人工拉伸之间的磷酸盐。该交叉间隔两个螺旋形圈（21个碱基）分开（&lt;STRONG&gt;图1B）。该复合矩形在螺旋和螺旋的圈数提到了它们的尺寸。例如，一个矩形为六螺旋宽和八个螺旋变为长被引用作为6H×8T矩形。海表温度可以被排除在外，添加或以其他方式重新安排，以创建任意形状和大小（ 图1C）的结构。例如，矩形的设计可以卷成管具有所需长度和半径（ 图1D）。 可替代地，该矩形的SST晶格可以被看作是一个分子帆布组成的SST的像素，通过为7nm每3纳米。在这项研究中，我们使用的310全长内自助服务一个分子帆布，24全长自助服务构成的左和右边界，及28半身自助服务形成的顶部和底部的边界。画布具有由交叉链接24双螺旋和每个螺旋包含28个螺旋转角（294碱基），并因此被称为一24H×28T直角的画布。所述24H×28T帆布具有类似于从M13噬菌体脚手架创建的DNA折纸结构的分子量。

<table><tbody><tr><td>DNA Strands&amp;nbsp;</td><td>Integrated DNA Technology</td><td></td><td>Section 3.1</td></tr><tr><td>SYBR Safe DNA gel stain</td><td>Invitrogen</td><td>S33102</td><td>Section 3.4.2</td></tr><tr><td>Freeze&#039;N Squeeze DNA Gel Extraction Spin Columns</td><td>BIO-RAD</td><td>731-6166</td><td>Section 3.6</td></tr><tr><td>Bruker&#039;s Sharp Nitride Lever Probes</td><td>Bruker AFM Probes</td><td>SNL10</td><td>Section 4.3</td></tr><tr><td>Safe Imager 2.0 Blue Light Transilluminator</td><td>Invitrogen</td><td>G6600</td><td>Section 3.6</td></tr><tr><td>Centrifuge 5430R</td><td>Eppendorf</td><td>5428 000.414</td><td>Section 3.6</td></tr><tr><td>Transmission Electron Microscope&amp;nbsp;</td><td>Jeol</td><td>Jem 1400</td><td>Section 7.4</td></tr><tr><td>Multimode 8</td><td>Veeco</td><td></td><td>Section 4</td></tr><tr><td>Typhoon FLA 9000 Laser Scanner</td><td>GE Heathcare Life Sciences</td><td>28-9558-08</td><td>Section 3.5</td></tr><tr><td>Ultrapure Distilled water</td><td>Invitrogen</td><td>10977-023</td><td>Section 3.7.1</td></tr><tr><td>Mica disk</td><td>SPI Supplies</td><td>12001-26-2</td><td>Section 4.1</td></tr><tr><td>Steel mounting disk</td><td>Ted Pella, Inc.</td><td>16218</td><td>Section 4.1</td></tr><tr><td>carbon coated copper grid for TEM</td><td>Electron Microscopy Sciences</td><td>FCF400-Cu</td><td>Section 7.2</td></tr><tr><td>tweezers</td><td>Dumont</td><td>0203-N5AC-PO</td><td>Section 7.31</td></tr><tr><td>glow discharge system</td><td>Quorum Technologies</td><td>K100X</td><td>Section 7.2</td></tr><tr><td>DNA Engine Tetrad 2 Peltier Thermal Cycler</td><td>BIO-RAD</td><td>PTC&amp;ndash;0240G</td><td>Section 3.3</td></tr><tr><td>Owl Easycast B2 Mini Gel Electrophoresis Systems</td><td>ThermoScientific</td><td>B2</td><td>Section 3.4.3</td></tr><tr><td>Seekam LE Agarose 500G</td><td>Lonza</td><td>50004</td><td>Section 3.4.1</td></tr><tr><td>GeneRuler 1kb Plus DNA Ladder, Ready-To-Use 75-20000bp</td><td>ThermoScientific</td><td>SM1333</td><td>Section 3.4.4</td></tr><tr><td>Nanodrop 2000c UV-vis Spectrophotometer</td><td>ThermoScientific</td><td></td><td>Section 3.7</td></tr><tr><td>0.2 um filter</td><td>Corning Inc.</td><td>431219</td><td>Section 7.1.2</td></tr></tbody></table>

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.

自助服务（图1）的自组装将产生一个24H×28T矩形， 如图2所示。对于不同的自助服务的DNA序列可以被修改的/优化，以使链霉抗生物标记（图3和4）的一个，变换矩形成筒（ 图5），自助服务的可编程的自组装以形成管和不同大小的矩形（图10），并使用分子画布（图8）2D任意形状的结构。两种设计（域替代设计和边缘保护设计）进行测试作为解决方案，以沿任意的形状（图7）的暴露域汇聚。这两种设计具有相当凝胶产量和结构完整性，但边缘保护的设计更符合成本效益的，因为它需要较少的辅助物质（图6）。链采摘和混合可实现自动化， 如图9，以减少人为错误和节省时间。 <img alt="图1" src="/files/ftp_upload/52486/52486fig1.jpg" /> 分子形状图1.自组装使用单链砖。 （一）规范SST主题，改编自12（B）左，中:两个描写组装自助服务科技。内自助服务具有42个碱基的全长，并标记为"U"形，而边界自助服务有21个碱基，并标示为"L"​​。在左侧图中，颜色区分不同的域。在中间图中，颜色区分不同链。右:SST结构的砖墙视图的示意图。厚砖充满海表温度和薄砖是边界海面温度。圆边表示没有互补配对。由于在中间人物，颜色区分单个瓷砖。在所有的诊断公羊，每个瓦片具有独特的序列。（℃）预提适当选择构成该矩形设计在图B的结果在不同的所希望的形状的形成从将SST采集股如三角形（左）或矩形环（右）。（D）的具有预定宽度和长度的管的设计。（E）给定的预合成的SST序列（上），任意形状（底）的池可通过选择丝的一个子集来设计在链混合物（深蓝色像素）和消除其余的（淡蓝色像素）的使用。这个数字已被修改从先前公布的数字26。 <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/52486/52486fig1highres.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图2" src="/files/ftp_upload/52486/52486fig2.jpg" /> <s仲&gt;图2. 设计和24H×28T矩形的原子力显微镜图像。 （一）24H×28T矩形的示意图。一个放大的看法也显示了详细的局部结构。个人SST段安排为10新台币- 11 NT - 11 NT - 10 NT（ 如 A2.13-b2.13-A1.13 * -b1.12 *）或11 NT - 10 NT-10 NT - 11核苷酸（ 例如，a3.12-b3.12-A2.13 * -b2.12 *）。上矩形的左侧的三角形指示与10nt-11nt-11nt-10nt SST排列的行;其他内部表层海水温度有11 NT - 10 NT NT--10新台币11代替（NT是一个缩写核苷酸）。由于24H×28T SST矩形具有类似尺寸的DNA折纸结构，标准的DNA折纸作品推出，并考虑了SST矩形"良好的"，如果它在预期轮廓的直径大于15纳米的，没有缺陷采纳。此外，"良好的"矩形结构，哈哈S在其内部没有孔大于直径10纳米的是必要的。按照上述的标准中，得到55％（N = 163），一个"井地层"比率。红色星号（*）表示这里的矩形的左下角。（B）的 2％非变性琼脂糖凝胶电泳。 U，未纯化;磷，纯化（通过凝胶提取从泳道U）的（C）的原子力显微镜的晶格结构的图像。（扫描尺寸:2微米×2微米）。这个数字已被修改从先前公布的数字26。 <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/52486/52486fig2highres.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图3" src="/files/ftp_upload/52486/52486fig3.jpg" /> 24H×28T矩形图3.边界贴标。（A）特定的BI的示意图otin标记24H×28T矩形。在蓝色高亮显示的股线手柄股。在股以红色突出显示标有3&#39;生物素（黑点）的反手柄股。链霉描绘为橙色球（B）的 AFM图像中添加链霉（扫描尺寸:1微米×1微米）之前，加入链霉抗后（C）的 AFM图像。（扫描尺寸:1微米×1微米）。插图，一个放大视图显示成功的标签。需要注意的是链霉亲和表现为两种白色点或条纹由于他们提出的高度。这个数字已被修改从先前公布的数字26。 <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/52486/52486fig3highres.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图4" src="/files/ftp_upload/52486/52486fig4.jpg" /> 图4.在24H×28T矩形的ternal标签。 （一）具体的生物素标记的24H×28T矩形的示意图。在蓝色高亮显示的股线手柄股。在股以红色突出显示标有3&#39;生物素（黑点）的反手柄股。链霉描绘为橙色球（B）的 AFM图像中添加链霉（扫描尺寸:1微米×1微米）之前，加入链霉抗后（C）的 AFM图像。（扫描尺寸:1微米×1微米）。插图，一个放大视图显示成功的标签。需要注意的是链霉出现无论是作为白点或条纹由于凸起的高度。这个数字已被修改从先前公布的数字26。 <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/52486/52486fig4highres.jpg" target="_blank">请点击此处查看该图的放大版本。</a> 内页="总是"&gt; <img alt="图5" src="/files/ftp_upload/52486/52486fig5.jpg" /> 图5.设计和24H×28T管TEM照片。 （一）24H×28T桶的示意图。在前两名放大的意见和底部显示详细段的身份。需要注意的是段a24.x *（ 例如，a24.13 *）和b24.x *（ 例如，b24.12 *）排在前列的互补段a24.x（ 例如，a24.13）和b24.x底部行的（ 例如，b24.12）;这种互补性预期导致在管状结构的形成。（B）的 2％非变性琼脂糖凝胶电泳。 U，未纯化;磷，净化（通过车道ü凝胶提取）（C）桶结构的TEM照片（比例尺:100纳米）。这个数字已被修改从先前公布的数字26。ighres.jpg"目标="_空白"&gt;点击此处查看该图的放大版本。 <img alt="图6" src="/files/ftp_upload/52486/52486fig6.jpg" /> 图6.两个设计，以防止聚集的暴露粘域造成的。 （A）并排侧示范两种方法来覆盖暴露域。未配对的粘性域（4）表示用红色，虚线框。设计1是域替代设计，其中未配对的域由一个聚-T域取代的（显示为红色，标有"T"）。设计图2是所述边缘保护件设计，这涉及覆盖有边缘保护链的不成对域（显示为红色，标有"T-4 *"）。边缘保护链是由聚-T部分和补充的暴露域。（B）中的不同的可能的边界与域取代（设计1）相关联的配置。有14个不同的方式的内部SST（以蓝色显示）可以留下暴露的域或域。适当的链取代示于红色的每个的情况。（C）中的边缘保护器设计（设计2）。一个内部SST（蓝色）只需要四个边缘保护股（红色），以支付采用这种设计暴露域。这个数字已被修改从先前公布的数字26。 <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/52486/52486fig6highres.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图7" src="/files/ftp_upload/52486/52486fig7.jpg" /> 图7.两种设计的SST三角。 （A）和（B）的描绘图8的基础上设计1（域替换）和设计2（边缘保护）的原理图，分别。使用聚-T的区域（T10或T11中所示）被描述为圆角的框图。插图显示用虚线框所表示的结构的放大图。比例尺为100nm。（C）和（D）是在原子力显微镜图像。这个数字已被修改从先前公布的数字26。 <img alt="图8" src="/files/ftp_upload/52486/52486fig8.jpg" /> 图8.图和AFM的100个不同形状的图像。结构设计都显示在顶部面板。淡蓝色的颜色表明冷落混合物的帆布股，而深蓝色着色表示股包括在内。为清楚起见，边缘保护股线被省略。每个结构的相应的AFM图像示出低于设计。每个图像为150nm×在区域150纳米。有100个独特的形状。包括10个阿拉伯数字，拉丁字母的26个大写字母，23个标点符号和keyboaRD符号，表情符号10，9星象符号，6中国文字，和一些其它符号。这个数字已被修改从先前公布的数字26。 <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/52486/52486fig8large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图9" src="/files/ftp_upload/52486/52486fig9.jpg" /> 图9.机器人自动化流程图。该图描绘了用于自动混合过程的工作流程。首先，自定义MATLAB程序用于设计所需形状。再次，深蓝色矩形表示的股线被包括在混合物中。设计完成之后，程序输出用于所述机器人液体处理程序的一组吸液指令。该机器人移液器适当链对于一个特定的形状正确的浓度成高原Ë很好。该混合物然后进行一锅退火，接着将所得的形状的原子力显微镜成像。 （这个数字已经被修改以前出版的图26）。 <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/52486/52486fig9large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图10" src="/files/ftp_upload/52486/52486fig10.jpg" /> 图10.自组装和矩形管跨不同尺度的。 （A）中的SST矩形的原子力显微镜图像与下列设计尺寸（从左至右）:4H×4T，6H×7T，10H×10T，12H×14T，18H×20T，24H×28T和36H×34T（ B）中的结构的分子量对数刻度。星号表示一个典型的M13 DNA的折纸结构作为参考的重量。（C）的 TEM图像SST的管与下列设计尺寸（从左至右）:8H×28T，8H×55T，8H×84T，24H×28T和12H×177T。所有比例尺显示100纳米。这个数字已被修改从先前公布的数字26。 <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/52486/52486fig10highres.jpg" target="_blank">请点击此处查看该图的放大版本。</a>

Watch this Scientific Journal Video about Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles at JoVE.com

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

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 ...

self-assembly-complex-two-dimensional-shapes-from-single-stranded-dna

Nanyang Technological University

Research

JoVE Journal

Chemistry

11.6K 次观看.  Tsinghua University. 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.

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

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

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control self-assembly and mimicking this process in vitro will bring about major advances in the areas of materials science and nanotechnology. Among the available biological building blocks, peptides have several advantages as they present substantial diversity, their synthesis in large scale is straightforward, and they can easily be modified with biological and chemical entities1,2. Several classes of designed peptides such as cyclic peptides, amphiphile peptides and peptide-conjugates self-assemble into ordered structures in solution. Homoaromatic dipeptides, are a class of short self-assembled peptides that contain all the molecular information needed to form ordered structures such as nanotubes, spheres and fibrils3-8. A large variety of these peptides is commercially available.
This paper presents a procedure that leads to the formation of ordered structures by the self-assembly of homoaromatic peptides. The protocol requires only commercial reagents and basic laboratory equipment. In addition, the paper describes some of the methods available for the characterization of peptide-based assemblies. These methods include electron and atomic force microscopy and Fourier-Transform Infrared Spectroscopy (FT-IR). Moreover, the manuscript demonstrates the blending of peptides (coassembly) and the formation of a &#34;beads on a string&#34;-like structure by this process.9 The protocols presented here can be adapted to other classes of peptides or biological building blocks and can potentially lead to the discovery of new peptide-based structures and to better control of their assembly.

This paper describes the formation of highly ordered peptide-based structures by the spontaneous process of self-assembly. The method utilizes commercially available peptides and common lab equipment. This technique can be applied to a large variety of peptides and may lead to the discovery of new peptide-based assemblies.

生物分子有序结构由短肽的自组装形成

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control ...

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

The DNA nanorobot is a hollow hexagonal nanometric device, designed to open in response to specific stimuli and present cargo sequestered inside. Both stimuli and cargo can be tailored according to specific needs. Here we describe the DNA nanorobot fabrication protocol, with the use of the DNA origami technique. The procedure initiates by mixing short single-strand DNA staples into a stock mixture which is then added to a long, circular, single-strand DNA scaffold in presence of a folding buffer. A standard thermo cycler is programmed to gradually lower the mixing reaction temperature to facilitate the staples-to-scaffold annealing, which is the guiding force behind the folding of the nanorobot. Once the 60 hr folding reaction is complete, excess staples are discarded using a centrifugal filter, followed by visualization via agarose-gel electrophoresis (AGE). Finally, successful fabrication of the nanorobot is verified by transmission electron microscopy (TEM), with the use of uranyl-formate as negative stain.

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 ...

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

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

This article presents a detailed protocol for synthesis of small circular DNA molecules, annealing of circular DNA motifs, and construction of 1D and 2D DNA nanostructures. Over decades, the rapid development of DNA nanotechnology is attributed to the use of linear DNAs as the source materials. For example, the DAO (double crossover, antiparallel, odd half-turns) tile is well-known as a building block for construction of 2D DNA lattices; the core structure of DAO is made from two linear single-stranded (ss) oligonucleotides, like two ropes making a right hand granny&#160;knot. Herein, a new type of DNA tiles called cDAO (coupled DAO) are built using a small circular ss-DNA of c64nt or c84nt (circular 64 or 84 nucleotides) as the scaffold strand and several linear ss-DNAs as the staple strands. Perfect 1D and 2D nanostructures are assembled from cDAO tiles: infinite nanowires, nanospirals, nanotubes, nanoribbons; and finite nano-rectangles. Detailed protocols are described: 1) preparation by T4 ligase and purification by denaturing PAGE (polyacrylamide gel electrophoresis) of small circular oligonucleotides, 2) annealing of stable circular tiles, followed by native PAGE analysis, 3) assembling of infinite 1D nanowires, nanorings, nanospirals, infinite 2D lattices of nanotubes and nanoribbons, and finite 2D nano-rectangles, followed by AFM (Atomic Force Microscopy) imaging. The method is simple, robust, and affordable for most labs.

This article presents a detailed protocol for T4 ligation and denaturing PAGE purification of small circular DNA molecules, annealing and native PAGE analysis of circular tiles, assembling and AFM imaging of 1D and 2D DNA nanostructures, as well as agarose gel electrophoresis and centrifugation purification of finite DNA nanostructures.

由小圆形 DNA 分子构建的稳定 DNA 分子、一维和二维纳米结构

This article presents a detailed protocol for synthesis of small circular DNA molecules, annealing of circular DNA motifs, and construction of 1D and 2D ...

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 ...

Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly

This protocol presents the use of Lewis acidic multi-role reagents to circumvent kinetic trapping observed during the self-assembly of information-encoded oligomeric strands mediated by paired dynamic covalent interactions in a manner mimicking the thermal cycling commonly employed for the self-assembly of complementary nucleic acid sequences. Primary amine monomers bearing aldehyde and amine pendant moieties are functionalized with orthogonal protecting groups for use as dynamic covalent reactant pairs. Using a modified automated peptide synthesizer, the primary amine monomers are encoded into oligo(peptoid) strands through solid-phase submonomer synthesis. Upon purification by high-performance liquid chromatography (HPLC) and characterization by electrospray ionization mass spectrometry (ESI-MS), sequence-specific oligomers are subjected to high-loading of a Lewis acidic rare-earth metal triflate which both deprotects the aldehyde moieties and affects the reactant pair equilibrium such that strands completely dissociate. Subsequently, a fraction of the Lewis acid is extracted, enabling annealing of complementary sequence-specific strands to form information-encoded molecular ladders characterized by matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). The simple procedure outlined in this report circumvents kinetic traps commonly experienced in the field of dynamic covalent assembly and serves as a platform for the future design of robust, complex architectures.

A protocol is presented for the synthesis of information-encoded peptoid oligomers and for the sequence-directed self-assembly of these peptoids into molecular ladders using amines and aldehydes as dynamic covalent reactant pairs and Lewis acidic rare-earth metal triflates as multi-role reagents.

信息承载Peptoids及其序列定向动态共价自组装的合成

This protocol presents the use of Lewis acidic multi-role reagents to circumvent kinetic trapping observed during the self-assembly of information-encoded ...

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 ...

Self-Assembly of Gamma-Modified Peptide Nucleic Acids into Complex Nanostructures in Organic Solvent Mixtures

Current strategies in DNA and RNA nanotechnology enable the self-assembly of a variety of nucleic acid nanostructures in aqueous or substantially hydrated media. In this article, we describe detailed protocols that enable the construction of nanofiber architectures in organic solvent mixtures through the self-assembly of uniquely addressable, single-stranded, gamma-modified peptide nucleic acid (&#947;PNA) tiles. Each single-stranded tile (SST) is a 12-base &#947;PNA oligomer composed of two concatenated modular domains of 6 bases each. Each domain can bind to a mutually complimentary domain present on neighboring strands using programmed complementarity to form nanofibers that can grow to microns in length. The SST motif is made of 9 total oligomers to enable the formation of 3-helix nanofibers. In contrast with analogous DNA nanostructures, which form diameter-monodisperse structures, these &#947;PNA systems form nanofibers that bundle along their widths during self-assembly in organic solvent mixtures. Self-assembly protocols described here therefore also include a conventional surfactant, Sodium Dodecyl Sulfate (SDS), to reduce bundling effects.

This article provides protocols for the design and self-assembly of nanostructures from gamma-modified peptide nucleic acid oligomers in organic solvent mixtures.

将伽马改性肽核酸自组装成有机溶剂混合物中复杂的纳米结构

Current strategies in DNA and RNA nanotechnology enable the self-assembly of a variety of nucleic acid nanostructures in aqueous or substantially hydrated ...