Single-stranded DNA and RNA origami.
Single-stranded DNA and RNA origami.
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DOI：
10.1126/science.aao2648
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发表时间：
2017-12-15
期刊：
影响因子：
--
通讯作者：
Yin P
中科院分区：
文献类型：
--
作者：
Han D;Qi X;Myhrvold C;Wang B;Dai M;Jiang S;Bates M;Liu Y;An B;Zhang F;Yan H;Yin P
携带信息的聚合物的自折叠是生物学的基础，并且作为一种合成策略提供了诱人的潜力。虽然多组分自组装已经产生了复杂的合成纳米结构，但单分子折叠的进展有限。我们描述了一个框架来设计和合成单个DNA或RNA链，使其自我折叠成一个复杂但未结的结构，接近任意用户规定的形状。我们通过实验构建了多种多碱基单链结构，包括~10,000核苷酸（nt）的DNA结构和~ 6,000核苷酸（nt）的RNA结构。我们在体外和活细胞中证明了该链的易复制性。因此，本研究建立了单分子折叠作为构建复杂和可复制的核酸纳米结构的一般策略，并扩展了自下而上纳米技术的设计空间和材料可扩展性。DNA或RNA的折叠。(A)多个DNA链被设计成没有（左）或有（中）长支架链的自组装。在这里，我们将单个长的DNA或RNA链折叠成目标形状（右）。(B)单链DNA（上三行）和RNA（下一行）纳米结构的原理图和原子力显微镜图像。(C) ssOrigami与先前报道的单链核酸纳米结构的尺寸比较。将携带信息的聚合物自折叠成具有明确结构和功能的致密颗粒（例如，将多肽折叠成蛋白质）是生物学的基础，并且作为一种合成策略具有诱人的潜力。在过去的三十年里，核酸已被用于制造各种复杂的纳米级形状和器件。特别是，多个DNA链已经被设计成自组装成用户指定的结构，有或没有长支架链的帮助。近年来，RNA也作为一种独特的、可编程的材料出现，为分子自组装提供了明显的优势。另一方面，生物大分子，如蛋白质（或蛋白质结构域），通常从单一聚合物折叠成定义良好的致密结构。以类似的方式折叠从头设计的核酸纳米结构的能力将使单分子折叠成为可能，而不是多链组装，甚至可以复制这种结构。然而，在单链核酸折叠成用户指定形状的情况下，构建大[bbb1000个核苷酸（nt）]单链折纸（ssOrigami）的一般策略仍有待证明。构建紧凑单链结构的关键挑战是在保持链路由拓扑简单性的同时实现结构复杂性、可编程性和通用性（以避免假想的由结施加的动力学陷阱），从而确保平滑折叠。本研究的关键创新是利用部分互补的双链DNA或RNA和平行交叉内聚来构建这种结构复杂但无结的结构，可以从单链平滑折叠。在这里，我们展示了一个框架来设计和合成单个DNA或RNA链，以有效地自折叠成一个松散的紧凑的ssOrigami结构，接近任意用户规定的目标形状。通过构建18个多千碱基DNA和5个RNA纳米结构，验证了该方法的通用性，其中包括一个~10,000 nt的DNA结构（比以前最大的离散单链DNA纳米结构大37倍）和一个~ 6,000 nt的RNA结构（比以前最大的RNA结构大10倍）。ssOrigami的栅格填充特性允许在其表面上实验构建可编程的标记模式（例如，“笑脸”脸）和商品，其单链性使其在体外和活细胞中易于复制的演示成为可能，其可编程性使我们能够编写设计过程并开发基于web的自动化设计工具。本研究表明，单分子DNA或RNA折叠，类似于多组分自组装，是构建用户指定和可复制的核酸纳米结构的基本、通用和实际可处理的策略，并扩展了自下而上纳米技术的设计空间和材料可扩展性。
Self-folding of an information-carrying polymer into a defined structure is foundational to biology and offers attractive potential as a synthetic strategy. Although multicomponent self-assembly has produced complex synthetic nanostructures, unimolecular folding has seen limited progress. We describe a framework to design and synthesize a single DNA or RNA strand to self-fold into a complex yet unknotted structure that approximates an arbitrary user-prescribed shape. We experimentally construct diverse multikilobase single-stranded structures, including a ~10,000-nucleotide (nt) DNA structure and a ~6000-nt RNA structure. We demonstrate facile replication of the strand in vitro and in living cells. The work here thus establishes unimolecular folding as a general strategy for constructing complex and replicable nucleic acid nanostructures, and expands the design space and material scalability for bottom-up nanotechnology. Folding of DNA or RNA ssOrigami structures. (A) Multiple DNA strands have been designed to self-assemble without (left) or with (middle) a long scaffold strand. Here, we fold single long DNA or RNA strands into target shapes (right). (B) Schematics and atomic force microscopy images of single-stranded DNA (top three rows) and RNA (bottom row) nanostructures. (C) Size comparison between ssOrigami and previously reported single-stranded nucleic acid nanostructures. Self-folding of an information-carrying polymer into a compact particle with defined structure and function (for example, folding of a polypeptide into a protein) is foundational to biology and offers attractive potential as a synthetic strategy. Over the past three decades, nucleic acids have been used to create a variety of complex nanoscale shapes and devices. In particular, multiple DNA strands have been designed to self-assemble into user-specified structures, with or without the help of a long scaffold strand. In recent years, RNA has also emerged as a unique, programmable material, offering distinct advantages for molecular self-assembly. On the other hand, biological macromolecules, such as proteins (or protein domains), typically fold from a single polymer into a well-defined compact structure. The ability to fold de novo designed nucleic acid nanostructures in a similar manner would enable unimolecular folding instead of multistrand assembly and even replication of such structures. However, a general strategy to construct large [>1000 nucleotides (nt)] single-stranded origami (ssOrigami) remains to be demonstrated where a single-stranded nucleic acid folds into a user-specified shape. The key challenge for constructing a compact single-stranded structure is to achieve structural complexity, programmability, and generality while maintaining the topological simplicity of strand routing (to avoid putative kinetic traps imposed by knots) and hence ensuring smooth folding. The key innovation of our study is to use partially complemented double-stranded DNA or RNA and parallel crossover cohesion to construct such a structurally complex yet knot-free structure that can be folded smoothly from a single strand. Here, we demonstrate a framework to design and synthesize a single DNA or RNA strand to efficiently self-fold into an unknotted compact ssOrigami structure that approximates an arbitrary user-prescribed target shape. The generality of the method was validated by the construction of 18 multikilobase DNA and 5 RNA ssOrigami, including a ~10,000-nt DNA structure (37 times larger than the previous largest discrete single-stranded DNA nanostructure) and a ~6000-nt RNA structure (10 times larger than the previous largest RNA structure). The raster-filling nature of ssOrigami permitted the experimental construction of programmable patterns of markers (for example, a “smiley” face) and cargoes on its surface, its single-strandedness enabled the demonstration of facile replication of the strand in vitro and in living cells, and its programmability allowed us to codify the design process and develop a web-based automated design tool. The work here establishes that unimolecular DNA or RNA folding, similar to multicomponent self-assembly, is a fundamental, general, and practically tractable strategy for constructing user-specified and replicable nucleic acid nanostructures, and expands the design space and material scalability for bottom-up nanotechnology.
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