Design principles for rapid folding of knotted DNA nanostructures.
Design principles for rapid folding of knotted DNA nanostructures.
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DOI：
10.1038/ncomms10803
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发表时间：
2016-02-18
影响因子：
16.6
通讯作者：
Jerala R
中科院分区：
文献类型：
--
作者：
Kočar V;Schreck JS;Čeru S;Gradišar H;Bašić N;Pisanski T;Doye JPK;Jerala R
纽结是自然界中最显著的拓扑特征之一。打结聚合物的自组装而不破坏或形成共价键是具有挑战性的，因为链需要以精确定义的顺序穿过先前形成的环。在这里，我们描述的原则，以指导高度打结的单链DNA纳米结构的折叠上展示了纳米尺寸的正方形金字塔。折叠的结编码的不同稳定性的模块的安排，根据派生的拓扑和动力学规则。在由相同模块组成并编码相同拓扑结构的DNA设计中，只有具有根据“自由端”规则设计的折叠途径的DNA设计有效地折叠成目标结构。除了在缓慢退火下的高折叠产率之外，该设计还在温度淬火和化学变性剂稀释下快速折叠。这种策略可以用于设计其他打结的可编程聚合物（如RNA或蛋白质）的折叠。 在互补碱基配对的驱动下，如果能够实现适当的折叠途径，人工单链DNA能够形成复杂的3D结构。在这里，作者描述了快速折叠结构的设计原理，通过制造纳米级的正方形金字塔来举例说明。
Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded through previously formed loops in an exactly defined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology, only the one with the folding pathway designed according to the ‘free-end' rule folds efficiently into the target structure. Besides high folding yield on slow annealing, this design also folds rapidly on temperature quenching and dilution from chemical denaturant. This strategy could be used to design folding of other knotted programmable polymers such as RNA or proteins. Driven by complementary base pairing, artificial single-chain DNA is capable of forming complex 3D architectures if an appropriate folding pathway can be realised. Here, the authors describe the design principles for rapidly folding structures, exemplified through fabrication of a nanosized square pyramid.