Name: self-assembly of complex two-dimensional shapes from single-stranded dna tiles
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Description: Watch this Scientific Journal Video about Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles at JoVE.com

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DN...

<ol>
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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>
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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 ...

Research

JoVE Journal

Chemistry

Origami Inspired Self-assembly of Patterned and Reconfigurable Particles

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

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

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 ...

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

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

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

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

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 ...

Molten-Salt Synthesis of Complex Metal Oxide Nanoparticles

复合金属氧化物纳米粒子的熔融盐合成

The development of feasible synthesis methods is critical for the successful exploration of novel properties and potential applications of nanomaterials. ...

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

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

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 ...