新型三维DNA纳米骨架的组装及其在生物和材料学中的应用

The aim of nanotechnology is to put specific atomic and molecular species where we want them, when we want them there. Achieving such precise control will have a major impact on a variety of applications, including circuit design, programmable chemical synthesis, biological structure determination and novel materials discovery.. The applicant will utilize DNA nanotechnology to engineer a universal three-dimensional (3D) DNA scaffold (crystal) that can serve as a template to precisely organize biological molecules. The 3D DNA crystal self-assembles with well-structured branched DNA motifs tailed by short single-stranded cohesive segments (sticky ends) to direct intermolecular associations. DNA sticky ends are well-defined and programmable, so that both molecular affinity (Watson-Crick base pairing) and the local product structure (B-form DNA) can be predicted.. A century-old design technique using interlocking mortise and tenon joints has been continuously used by cabinetmakers to join rails to legs for the manufacture of sturdy tables and chairs. Inspired by this simple design, the applicant built a mechanically interlocking DNA motif, analogous to a table corner, consisting of three triple crossover DNA molecules directed along the orthogonal X Y Z vectors. This unit cell can self-assemble a 3D crystal in a cubic lattice with a minimum cavity of 5000 cubic nanometers, large enough to accommodate most molecules. Moreover, the cavity is tunable to accommodate larger molecules. . Initial demonstration of the DNA crystal’s utility will involve lnc RNA crystallization. RNA can be organized by this 3D DNA scaffold via DNA/RNA hybridization. Besides biological structure determination, the applicant will also assemble nanoparticles on the DNA scaffold to create novel nanomaterials. Such a 3D DNA crystal would be a major milestone in DNA nanotechnology and could potentially benefit many different areas, ranging from biological science to materials science.

纳米技术的目标旨在能随时随地的在分子水平上操控物质，做到这一点可以极大地促进自然科学的发展。在本项目里，申请人将致力于利用DNA纳米技术实现在分子水平上精确地操控物质。受木匠使用的榫和榫头的技术的启发，申请人利用DNA自组装了一个三维正交且在每个维度都互相锁住的三维结点。该结点具备通过末端互补的sticky ends自组装成三维立方晶体（骨架）的潜力。该晶体单个晶格的最小容量在5000立方纳米左右，足够容纳大部分生物分子，而且它的容量可以调整以适应容纳更大尺寸的生物分子。RNA分子可以通过RNA/DNA的互补杂化与三维DNA晶体骨架关联起来。申请人将首先利用此三维DNA骨架辅助解析某些难以自我结晶的长链非编码RNA的结构；此外还将利用DNA结点和骨架组装纳米金属粒子制备新型复合纳米材料。这样的一个三维DNA骨架不仅会成为纳米技术的一个重要突破，而且也会使得生物、材料等学科受益。

脱氧核糖核酸（DNA）不仅是生物界的遗传物质，还是纳米级世界中强大的建筑材料。DNA已成为工程自组装材料中使用最广泛的分子构件之一。利用DNA分子作为通用聚合物，编程性组装定义明确的纳米结构，用于合成新材料和构建功能性纳米器件，这一技术我们称之为DNA纳米技术。近三十年来，随着这一领域的迅速发展，科学家们已能够合成成百上千种不同规模和尺寸的各种框架型纳米结构（Framework Nucleic Acids）。由于其可寻址性、可编程性以及空间构架等特点，DNA纳米结构一直被人们寄望用于在纳米尺寸上的物质精确排布，而实现三维空间内有效的纳米排布需要使用具有足够刚性和尺寸的三维骨架。针对这一研究领域的空缺，我们借鉴宏观世界中木工常用的“榫”和“榫头的”相互嵌套，通过计算机模拟和实验相结合的方式成功构建了三维正交DNA结点。结点的每条臂上有三个DNA螺旋绑在一起，三条臂互相锁定形成较为稳定的结构，并且其还可以实现在三维空间三个维度六个正交方向的延伸，方便进一步构建层次更复杂的框架结构，例如长方形、长方体、正方体、拥有一个封闭面的正方体以及连体正方体三维线框结构等。经过一系列参数的优化和改进，并采取多种表征手段对这些框架结构进行验证，我们证明了以该新型三维结点为单元在空间内构建多层次立体网格结构具备可行性。该工作为构建坚固耐用的三维框架核酸提供了一种新策略，有望为下游的应用（如依托框架核酸进一步组装其他物质）提供保障。