Kinetics and Thermodynamics of Watson-Crick Base Pairing Driven DNA Origami Dimerization
Kinetics and Thermodynamics of Watson-Crick Base Pairing Driven DNA Origami Dimerization
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DOI：
10.1021/jacs.5b10502
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发表时间：
2016-03-16
影响因子：
15
通讯作者：
Schulman, Rebecca
中科院分区：
文献类型：
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作者：
Zenk, John;Tuntivate, Chanon;Schulman, Rebecca
我们调查的动力学和热力学的DNA折纸二聚体使用扁平矩形折纸组件和不同的沃森-克里克互补单链DNA（“粘性末端”）连接策略的架构。我们系统地改变连接器的数量，连接器上的粘性末端的长度，和连接器的架构，并通过荧光猝灭测定测量相应的产量以及正向和反向反应速率常数。使用原子力显微镜进一步验证产率。我们计算各种接口设计的H度和δ S度的值，并找到非线性范的霍夫行为，最好的描述两个线性方程，这表明不同的制度之间的二聚化和那些没有良好的接口。我们发现，自组装反应可以通过操纵界面结构来调节，而不会损失产率，即使产率很高，类似于7.5- 80%。我们发现，二级正向反应速率常数（k（on））取决于连接体结构和所用连接体的数量，典型值约为10（5）-10（5）（M.s）（-1），与小互补DNA链的双分子缔合相似。K（上）值通常是非阿耳忒弥斯的，倾向于随着温度的降低而增加。最后，我们使用动力学和热力学信息的最佳连接架构扩展到一个无限的系统，两个组件的重复晶格系统，并表明我们可以形成微米尺寸的晶格，良好的结构高达8 μ m（2）。
We investigate the kinetics and thermodynamics of DNA origami dimerization using flat rectangle origami components and different architectures of Watson-Crick complementary single-stranded DNA ("sticky end") linking strategies. We systematically vary the number of linkers, the length of the sticky ends on the linker, and linker architecture and measure the corresponding yields as well as forward and reverse reaction rate constants through fluorescence quenching assays. Yields were further verified using atomic force microscopy. We calculate values of H degrees and Delta S degrees for various interface designs and find nonlinear van't Hoff behavior, best described by two linear equations, suggesting distinct regimes of dimerization between those with and those without well formed interfaces. We find that self-assembly reactions can be tuned by manipulating the interface architecture without suffering a loss in yield, even when yield is high, similar to 7.5-80%. We show that the second-order forward reaction rate constant (k(on)) depends on both linker architecture and number of linkers used, with typical values on the order of 10(5)-10(5) (M.s)(-1), values that are similar to those of bimolecular association of small, complementary DNA strands. The k(on). values are generally non-Arrhenius, tending to increase with decreasing temperature. Finally, we use kinetic and thermodynamic information about the optimal linking architecture to extend the system to an infinite, two-component repeating lattice system and show that we can form micron-sized lattices, with well-formed structures up to 8 mu m(2).