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 <s...

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 border="0" cellpadding="0" cellspacing="0" width="919">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Name of Material/ Equipment</td>
			<td style="width:183px;">Company</td>
			<td style="width:119px;">Catalog Number</td>
			<td style="width:401px;">Comments/Description</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">DNA Strands&#160;</td>
			<td style="width:183px;">Integrated DNA Technology</td>
			<td style="width:119px;"></td>
			<td>Section 3.1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">SYBR Safe DNA gel stain</td>
			<td style="width:183px;">Invitrogen</td>
			<td style="width:119px;">S33102</td>
			<td>Section 3.4.2</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Freeze&#39;N Squeeze DNA Gel Extraction Spin Columns</td>
			<td style="width:183px;">BIO-RAD</td>
			<td style="width:119px;">731-6166</td>
			<td>Section 3.6</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Bruker&#39;s Sharp Nitride Lever Probes</td>
			<td style="width:183px;">Bruker AFM Probes</td>
			<td style="width:119px;">SNL10</td>
			<td>Section 4.3</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Safe Imager 2.0 Blue Light Transilluminator</td>
			<td style="width:183px;">Invitrogen</td>
			<td style="width:119px;">G6600</td>
			<td>Section 3.6</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Centrifuge 5430R</td>
			<td style="width:183px;">Eppendorf</td>
			<td style="width:119px;">5428 000.414</td>
			<td>Section 3.6</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Transmission Electron Microscope&#160;</td>
			<td style="width:183px;">Jeol</td>
			<td style="width:119px;">Jem 1400</td>
			<td>Section 7.4</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Multimode 8</td>
			<td style="width:183px;">Veeco</td>
			<td style="width:119px;"></td>
			<td>Section 4</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Typhoon FLA 9000 Laser Scanner</td>
			<td style="width:183px;">GE Heathcare Life Sciences</td>
			<td style="width:119px;">28-9558-08</td>
			<td>Section 3.5</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Ultrapure Distilled water</td>
			<td style="width:183px;">Invitrogen</td>
			<td style="width:119px;">10977-023</td>
			<td>Section 3.7.1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Mica disk</td>
			<td style="width:183px;">SPI Supplies</td>
			<td style="width:119px;">12001-26-2</td>
			<td>Section 4.1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Steel mounting disk</td>
			<td style="width:183px;">Ted Pella, Inc.</td>
			<td style="width:119px;">16218</td>
			<td>Section 4.1</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">carbon coated copper grid for TEM</td>
			<td style="width:183px;">Electron Microscopy Sciences</td>
			<td style="width:119px;">FCF400-Cu</td>
			<td>Section 7.2</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">tweezers</td>
			<td style="width:183px;">Dumont</td>
			<td>0203-N5AC-PO</td>
			<td>Section 7.31</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">glow discharge system</td>
			<td style="width:183px;">Quorum Technologies</td>
			<td style="width:119px;">K100X</td>
			<td>Section 7.2</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">DNA Engine Tetrad 2 Peltier Thermal Cycler</td>
			<td style="width:183px;">BIO-RAD</td>
			<td>PTC&#8211;0240G</td>
			<td>Section 3.3</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Owl Easycast B2 Mini Gel Electrophoresis Systems</td>
			<td style="width:183px;">ThermoScientific</td>
			<td>B2</td>
			<td>Section 3.4.3</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Seekam LE Agarose 500G</td>
			<td style="width:183px;">Lonza</td>
			<td style="width:119px;">50004</td>
			<td>Section 3.4.1</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">GeneRuler 1kb Plus DNA Ladder, Ready-To-Use 75-20000bp</td>
			<td style="width:183px;">ThermoScientific</td>
			<td style="width:119px;">SM1333</td>
			<td>Section 3.4.4</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Nanodrop 2000c UV-vis Spectrophotometer</td>
			<td style="width:183px;">ThermoScientific</td>
			<td style="width:119px;"></td>
			<td>Section 3.7</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">0.2 um filter</td>
			<td style="width:183px;">Corning Inc.</td>
			<td style="width:119px;">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?...

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

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Chemistry

11.5K 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 ...

Synthesis of a Water-soluble Metal&#8211;Organic Complex Array

We demonstrate a method for the synthesis of a water-soluble multimetallic peptidic array containing a predetermined sequence of metal centers such as Ru(II), Pt(II), and Rh(III). The compound, named as a water-soluble metal-organic complex array (WSMOCA), is obtained through 1) the conventional solution-chemistry-based preparation of the corresponding metal complex monomers having a 9-fluorenylmethyloxycarbonyl (Fmoc)-protected amino acid moiety and 2) their sequential coupling together with other water-soluble organic building units on the surface-functionalized polymeric resin by following the procedures originally developed for the solid-phase synthesis of polypeptides, with proper modifications. Traces of reactions determined by mass spectrometric analysis at the representative coupling steps in stage 2 confirm the selective construction of a predetermined sequence of metal centers along with the peptide backbone. The WSMOCA cleaved from the resin at the end of stage 2 has a certain level of solubility in aqueous media dependent on the pH value and/or salt content, which is useful for the purification of the compound.

Synthesis of a Water-soluble Metal&amp;#8211;Organic Complex Array

A potential general method for the synthesis of water-soluble multimetallic peptidic arrays containing a predetermined sequence of metal centers is presented.

一个水溶性金属 - 有机络合物阵列合成

We demonstrate a method for the synthesis of a water-soluble multimetallic peptidic array containing a predetermined sequence of metal centers such as ...

Grafting Multiwalled Carbon Nanotubes with Polystyrene to Enable Self-Assembly and Anisotropic Patchiness

We demonstrate a straightforward protocol to graft pristine multiwalled carbon nanotubes (MWCNTs) with polystyrene (PS) chains at the sidewalls through a free-radical polymerization strategy to enable the modulation of the nanotube surface properties and produce supramolecular self-assembly of the nanostructures. First, a selective hydroxylation of the pristine nanotubes through a biphasic catalytically mediated oxidation reaction creates superficially distributed reactive sites at the sidewalls. The latter reactive sites are subsequently modified with methacrylic moieties using a silylated methacrylic precursor to create polymerizable sites. Those polymerizable groups can address further polymerization of styrene to produce a hybrid nanomaterial containing PS chains grafted to the nanotube sidewalls. The polymer-graft content, amount of silylated methacrylic moieties introduced and hydroxylation modification of the nanotubes are identified and quantified by Thermogravimetric Analysis (TGA). The presence of reactive functional groups hydroxyl and silylated methacrylate are confirmed by Fourier Transform Infrared Spectroscopy (FT-IR). Polystyrene-grafted carbon nanotube solutions in tetrahydrofuran (THF) provide wall-to-wall collinearly self-assembled nanotubes when cast samples are analyzed by transmission electron microscopy (TEM). Those self-assemblies are not obtained when suitable blanks are similarly cast from analogous solutions containing non-grafted counterparts. Therefore, this method enables the modification of the nanotube anisotropic patchiness at the sidewalls which results into spontaneous auto-organization at the nanoscale.

A procedure for the synthesis of polystyrene-grafted multiwalled carbon nanotubes using successive chemical modification steps to selectively introduce the polymer chains to the sidewalls and their self-assembly via anisotropic patchiness is presented.

用聚苯乙烯接枝多壁纳米碳纳米管使自组装和各向异性斑块

We demonstrate a straightforward protocol to graft pristine multiwalled carbon nanotubes (MWCNTs) with polystyrene (PS) chains at the sidewalls through a ...

Liquid-cell Transmission Electron Microscopy for Tracking Self-assembly of Nanoparticles

Drying a nanoparticle dispersion is a versatile way to create self-assembled structures of nanoparticles, but the mechanism of this process is not fully understood. We have traced the trajectories of individual nanoparticles using liquid-cell transmission electron microscopy (TEM) to investigate the mechanism of the assembly process. Herein, we present the protocols used for liquid-cell TEM studies of the self-assembly mechanism. First, we introduce the detailed synthetic protocols used to produce uniformly sized platinum and lead selenide nanoparticles. Next, we present the microfabrication processes used to produce liquid cells with silicon nitride or silicon windows and then describe the loading and imaging procedures of the liquid-cell TEM technique. Several notes are included to provide helpful tips for the entire process, including how to manage the fragile cell windows. The individual motions of nanoparticles tracked by liquid-cell TEM revealed that changes in the solvent boundaries caused by evaporation affected the self-assembly process of nanoparticles. The solvent boundaries drove nanoparticles to primarily form amorphous aggregates, followed by flattening of the aggregates to produce a 2-dimensional (2D) self-assembled structure. These behaviors are also observed for different nanoparticle types and different liquid-cell compositions.

Here we introduce experimental protocols for the real-time observation of a self-assembly process using liquid-cell transmission electron microscopy.

用于跟踪纳米粒子自组装的液体细胞透射电子显微镜

Drying a nanoparticle dispersion is a versatile way to create self-assembled structures of nanoparticles, but the mechanism of this process is not fully ...

Fabrication of Spherical and Worm-shaped Micellar Nanocrystals by Combining Electrospray, Self-assembly, and Solvent-based Structure Control

Micellar nanocrystals (micelles with encapsulated nanocrystals) have become an emerging major class of nanobiomaterials. We describe a method of fabricating micellar nanocrystals based on combining top-down electrospray, bottom-up self-assembly, and solvent-based structure control. This method involves first using electrospray to generate uniform ultrafine liquid droplets, each of which functions as a micro-reactor in which self-assembly reaction occurs forming micellar nanocrystals, with the structures (micelle shape and nanocrystal encapsulation) controlled by the organic solvent used. This method is largely continuous and produces high quality micellar nanocrystal products with an inexpensive structure control approach. By using a water-miscible organic solvent tetrahydrofuran (THF), worm-shaped micellar nanocrystals can be produced due to solvent-induced/facilitated micelle fusion. Compared with the common spherical micellar nanocrystals, worm-shaped micellar nanocrystals can offer minimized non-specific cellular uptake, thus enhancing biological targeting. By co-encapsulating multiple nanocrystals into each micelle, multifunctional or synergistic effects can be achieved. Current limitations of this fabrication method, which will be part of the future work, primarily include imperfect encapsulation in the micellar nanocrystal product and the incompletely continuous nature of the process.

The present work describes a method to fabricate micellar nanocrystals, an emerging major class of nanobiomaterials. This method combines top-down electrospray, bottom-up self-assembly, and solvent-based structure control. The fabrication method is largely continuous, can produce high quality products, and possesses an inexpensive means of structure control.

结合电喷雾、自组装和溶剂型结构控制制备球形和蜗杆状胶束纳米晶

Micellar nanocrystals (micelles with encapsulated nanocrystals) have become an emerging major class of nanobiomaterials. We describe a method of ...

Negative Additive Manufacturing of Complex Shaped Boron Carbides

Boron carbide (B4C) is one of the hardest materials in existence. However, this attractive property also limits its machineability into complex shapes for high wear, high hardness, and lightweight material applications such as armors. To overcome this challenge, negative additive manufacturing (AM) is employed to produce complex geometries of boron carbides at various length scales. Negative AM first involves gelcasting a suspension into a 3D-printed plastic mold. The mold is then dissolved away, leaving behind a green body as a negative copy. Resorcinol-formaldehyde (RF) is used as a novel gelling agent because unlike traditional hydrogels, there is little to no shrinkage, which allows for extremely complex molds to be used. Furthermore, this gelling agent can be pyrolyzed to leave behind ~50 wt% carbon, which is a highly effective sintering aid for B4C. Due to this highly homogenous distribution of in situ carbon within the B4C matrix, less than 2% porosity can be achieved after sintering. This protocol highlights in detail the methodology for creating near fully dense boron carbide parts with highly complex geometries.

A method called negative additive manufacturing is used to produce near fully dense complex shaped boron carbide parts of various length scales. This technique is possible via the formulation of a novel suspension involving resorcinol-formaldehyde as a unique gelling agent that leaves behind a homogenous carbon sintering aid after pyrolysis.

复合型碳化硼的负添加剂制造

Boron carbide (B4C) is one of the hardest materials in existence. However, this attractive property also limits its machineability into complex shapes for ...

Exfoliation and Analysis of Large-area, Air-Sensitive Two-Dimensional Materials

We describe methods for producing and analyzing large, thin flakes of air-sensitive two-dimensional materials. Thin flakes of layered or van der Waals crystals are produced using mechanical exfoliation, in which layers are peeled off a bulk crystal using adhesive tape. This method produces high-quality flakes, but they are often small and can be hard to find, particularly for materials with relatively high cleavage energies such as black phosphorus. By heating the substrate and the tape, two-dimensional material adhesion to the substrate is promoted, and the flake yield can be increased by up to a factor of ten. After exfoliation, it is necessary to image or otherwise analyze these flakes but some two-dimensional materials are sensitive to oxygen or water and will degrade when exposed air. We have designed and tested a hermetic transfer cell to temporarily maintain the inert environment of a glovebox so that air-sensitive flakes can be imaged and analyzed with minimal degradation. The compact design of the transfer cell is such that optical analysis of sensitive materials can be performed outside of a glovebox without specialized equipment or modifications to existing equipment.

A method for exfoliating large thin flakes of air sensitive two-dimensional materials and safely transporting them for analysis outside of a glovebox is presented.

大面积空气敏感二维材料的去角质与分析

We describe methods for producing and analyzing large, thin flakes of air-sensitive two-dimensional materials. Thin flakes of layered or van der Waals ...

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 ...