DMREF: Self Assembly with DNA-Labeled Colloidal Particles and DNA Nanostructures

非技术和创造能够自我组装的材料和设备长期以来一直是材料科学的圣杯，因为它将从质量上引入制造纳米级结构和材料的新方法。DNA纳米技术领域在创造完全由DNA制成的坚固而动态的材料方面取得了惊人的进展，但DNA作为一种材料本身的用途比它可以与其他材料结合在一起时要有限得多。胶体组装和DNA纳米技术的结合可能会带来巨大的协同效应。人们可以使用溶液中更复杂和潜在的动态DNA纳米结构来控制这些相互作用，而不是通过使用DNA连接物来调节粒子之间的相互作用(这是目前的技术水平)。这个项目试图对(动态的)DNA纳米结构如何控制和编程胶体自组装有一个基本的理解。通过将这一概念建立在坚实的基础上，将有可能通过设计DNA反应网络来最大限度地利用这一概念，从而解决使胶体自组装成为实用材料制造平台的基本挑战。构建块之间可能相互作用的集合是如此之大，以至于只有在理论、数值模拟和实验的联合攻击下才能系统地探索这个设计空间。该项目旨在发现DNA颗粒-纳米结构相互作用的基本原理，并创造从等离子体分子到超流的新材料，并立即产生技术影响。该项目还将让哈佛本科生参与市中心中学的设计课程，哈佛应用计算科学研究所的暑期软件开发项目，以及参加国际基因工程机器竞赛的团队。技术总结研究人员将努力了解和利用从颗粒和DNA纳米结构制造新的周期性和非周期性胶体结构的不同方法。几种类型的DNA纳米结构可以用来控制胶体自组装。最简单类型的中介DNA纳米结构包括溶液中的单链DNA(SsDNA)。初步实验表明，自由DNA链通过链置换反应对组装和融化的控制达到了前所未有的水平。研究人员还将开发中介DNA纳米结构，即使在颗粒均匀覆盖单链DNA的情况下，也能有效地实现颗粒间的相互作用。Valence为强健的自组装创造了许多新的方向，从建造大型结构到设计在有限浓度下在浴缸中自发形成的结构。最后，他们将研究DNA发夹如何导致非平衡相互作用。这为理论和实验开辟了新的前景，包括设计自复制胶体簇和开发动力学校对方案，以显著提高超过平衡极限的相互作用的保真度。对于每一种类型的DNA介导的相互作用，研究小组将使用理论和模拟--在某些情况下需要开发新的方法--来列举可以组装的可能性。这些将与实验结合使用，以实现模拟中描述的组件，这些实验将为理论和模拟的改进提供信息。最终，他们将得出每个中介纳米结构可以组装成什么的整体观点。

NON-TECHNICAL SUMMARYCreating materials and devices that can assemble themselves has long been a holy grail in materials science, since it would introduce qualitatively new ways of making nano-scale structures and materials. The field of DNA nanotechnology has exploded with striking advances in creating robust and dynamic materials made entirely out of DNA, but the uses of DNA as a material on its own are much more limited than if it could be combined with other materials. A potentially vast synergy lies in the combination of colloidal assembly and DNA nanotechnology. Instead of mediating the interactions between particles by using DNA linkers (the current state of the art), one could control these interactions using more complex and potentially dynamic DNA nanostructures in solution. This project seeks to develop a fundamental understanding of how (dynamic) DNA nanostructures can control and program colloidal self-assembly. By putting this concept on a strong fundamental footing, it will be possible to exploit it to maximum effect through the design of DNA reaction networks that solve essential challenges to making colloidal self-assembly a practical materials fabrication platform. The set of possible interactions between building blocks is so large that this design space can only be systematically explored with a combined attack from theory, numerical simulation, and experiment. The project aims both to discover the fundamental principles underlying DNA particle-nanostructure interactions and to create new materials from plasmonic molecules to metafluids with immediate technological impact. The project will also involve Harvard undergraduates in a design curriculum for inner city middle schools, in a summer software development project through Harvard's Institute for Applied Computational Science, and in teams that participate in the International Genetically Engineered Machines competition.TECHNICAL SUMMARYThe investigators will work to understand and harness the different ways of making novel periodic and aperiodic colloidal structures out of particles and DNA nanostructures. Several types of DNA nanostructures can be used to control colloidal self-assembly. The simplest type of mediating DNA nanostructure involves single strands of DNA (ssDNA) in solution. Preliminary experiments show that free DNA strands give an unprecedented level of control over assembly and melting through strand displacement reactions. The investigators will also develop mediating DNA nanostructures that give an effective valence to inter-particle interactions, even when the particles are uniformly coated with ssDNA. Valence creates many new directions for robust self-assembly, from building large structures to designing structures that form spontaneously in a bath at finite concentration. Finally, they will investigate how DNA hairpins can lead to non-equilibrium interactions. This opens up new vistas for theory and experiments, including the design of self-replicating colloidal clusters and the development of kinetic proofreading schemes for significantly increasing the fidelity of the interactions over the equilibrium limit. For each type of DNA-mediated interaction, the team will use theory and simulation--which in some cases requires developing new methods--to enumerate the possibilities of what can be assembled. These will be used in conjunction with experiment to realize the assemblies described in the simulations, and these experiments will inform refinements of theory and simulations. Ultimately, they will arrive at a holistic view of what can be assembled with each mediating nanostructure.