Name: self-assembly of complex two-dimensional shapes from single-stranded dna tiles
Uploaded: 2015-05-08T13:00:00
Description: Watch this Scientific Journal Video about Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles at JoVE.com

Este trabalho foi financiado pelo Escritório do Programa de Pesquisa Naval Young Investigator Award N000141110914, o Office of Naval Research Grant N000141010827, NSF Prémio Carreira CCF1054898, do NIH Director New Innovator Award 1DP2OD007292 e um Instituto Wyss para Biologicamente Inspirada Fundo Startup Faculdade de Engenharia (para PY) e Centro de Ciências da Vida Fundo de inicialização (para PC) Tsinghua-Pequim.

1. DNA Sequence projeto <ol><li> Use software UNIQUIMER 27 para projetar uma estrutura SST-finito, especificando o número de hélices duplas, comprimentos de hélice superior e inferior para cada dupla hélice, eo padrão cruzado para criar um 24H × lona 28T. Depois de definir estes parâmetros, a arquitetura geral (vertente composição eo arranjo complementaridade) é ilustrado graficamente no programa. </li><li> Gerar sequências para os fios da estrutura especificada para atender o arranjo complementa...

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No passo de formação da estrutura, é importante manter uma concentração de catiões de magnésio apropriado (por exemplo., 15 mM) na mistura cadeia de ADN para nanoestruturas de DNA auto-montar. Do mesmo modo, no passo de caracterização em gel de agarose / purificação, é importante manter uma concentração de catiões de magnésio apropriado (por exemplo., 10 mM) em gel e o tampão de gel de corrida para reter as nanoestruturas de ADN durante a electroforese. Para a estrutura 24H × 28T rect...

Anterior ácido nucleico de auto-montagem 1-25 trabalho levou à bem sucedida da construção de uma variedade de estruturas complexas, incluindo ADN 2 - 5,8,10 - 13,17,23 ou RNA 7,22 3,4,7 periódica, 22 e algorítmica 5 bidimensionais treliças, fitas 10,12 e tubos de 4,12,13, cristais 3D 17, poliedros 11 e finitos, 2D formas 7,8. Um método particularmente eficaz é o scaffold origami de DNA, em que uma cadeia simples de andaime é dobrado por muitos fios auxiliares curtas descontínuas, para formar uma forma complexa 9,14 - 16,18 - 21,25. Recentemente, relatou um método para a construção de nanoestruturas discretos com formas 2D prescritas utilizando azulejos de cadeia simples (SST), e demonstraram as estruturas com complexidade comparável à origami de ADN 26. Este article é uma adaptação do nosso trabalho anterior 26 e descreve os protocolos detalhados para organizar SSTs individualmente endereçáveis ​​em formas 2D finitos sofisticados, com dimensões precisamente prescritos (larguras e comprimentos) e morfologias. Uma das principais vantagens do método de SST é a sua modularidade. Cada componente SST de uma estrutura serve como uma unidade de construção modular na assembléia, e diferentes subconjuntos destes SSTs produzir formas distintas. Assim, estabelecemos uma plataforma geral para construir nanoestruturas com tamanhos e formas prescritas, de filamentos de DNA sintéticas curtas. TSMs conter quatro domínios, cada um de 10 ou 11 nucleótidos de comprimento (Figura 1A). As SSTs vincular tal que as suas hélices paralelas criar uma estrutura de DNA realizada em conjunto por ligações de crossover. Cada passagem é o fosfato entre os domínios 2 e 3. O fosfato é esticado artificialmente nos diagramas para claridade visual. Os crossovers são espaçados duas voltas helicoidais (21 bases) de distância (&lt;forte&gt; Figura 1B). Os retângulos compostos são referidos por suas dimensões do número de hélices e voltas helicoidais. Por exemplo, um rectângulo que é de seis hélices de largura e oito helicoidal gira tempo é referida como um 6H × T8 rectângulo. SSTs pode ser deixado de fora, adicionado, ou de outra forma reorganizados para criar estruturas de formas e tamanhos (Figura 1C) arbitrárias. Por exemplo, um formato rectangular pode ser enrolada em forma de tubo com um comprimento desejado e um raio (Figura 1D). Alternativamente, a estrutura rectangular SST pode ser visto como uma tela molecular constituído por SST pixels, cada um de 3 nm de 7 nm. Neste estudo, utilizamos uma lona molecular de 310 full-length SSTs internos, 24 SSTs-metragens que compõem os limites esquerdo e direito, e 28 SSTs metade do comprimento, formando os limites superior e inferior. A tela tem 24 hélices duplas ligações por cruzamentos e cada hélice contém 28 voltas helicoidais (294 bases) e, por conseguinte, é designado porum 24H × 28T lona retangular. O 24H × tela 28T tem um peso molecular semelhante ao de uma estrutura origami de DNA criado a partir de um fago M13 andaime.

<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.

A auto-montagem de SST (Figura 1) vai produzir uma 24H × 28T rectângulo, conforme ilustrado na Figura 2. As sequências de ADN para as diferentes SST pode ser modificada / optimizado para permitir rotulagem estreptavidina (Figura 3 e 4), a transformação de um retângulo para dentro de um tubo (Figura 5), a auto-montagem de SST programável para formar tubos e rectângulos de diversos tamanhos (Figura 10), e a constr...

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.

A auto-montagem de formas bidimensionais complexos de ADN de cadeia simples Azulejos

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

Origami Inspirado Auto-montagem de Partículas estampados e Reconfigurável

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

Química

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

Formação de Estruturas Biomoleculares Ordenadas pela Automontagem de Peptídeos Pequenos

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

Dobragem e Caracterização de um Robô Bioresponsivo a partir de 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 ...

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

Enxertia de nanotubos de carbono de Multiwalled com poliestireno para habilitar auto-montagem e anisotrópica Patchiness

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

Microscopia eletrônica de transmissão de líquido-celular para rastreamento auto-montagem de nanopartículas

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

Fabricação de nanocristais micélica esférico e em forma de verme, combinando Electrospray, auto-montagem e controle de estrutura de base solvente

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

Fabricação aditiva negativa do complexo em forma de carbonetos de boro

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

Sal fundido síntese de nanopartículas de óxido metálico complexo

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

Esfoliação e análise da grande-área, bidimensionais materiais sensíveis ao ar

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

Motivos de DNA estável, 1D e 2D nanoestruturas construídas a partir de moléculas de DNA Circular pequeno

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