Center for Soft Matter Research, Physics Department, New York University, 4 Washington Place, New York, New York 10003, USA.
J Am Chem Soc. 2010 Feb 17;132(6):1903-13. doi: 10.1021/ja907919j.
Surface functionalization with complementary single-stranded DNA sticky ends is increasingly used for guiding the self-assembly of nano- and micrometer-sized particles into larger scale ordered structures. Here we present measurements, formulas, and graphs that allow one to quantitatively predict the association behavior of DNA-coated particles from readily available Web-based data. From experiments it appears that the suspension behavior is very sensitive to the grafting details, such as the length and flexibility of the tether constructs and the particles' surface coverage. Thus, if one wants to control the interactions and assembly processes, insight is needed into the structural and dynamical features of the DNA coatings. We demonstrate how a straightforward measurement of the particles' association-dissociation kinetics during selected temperature cycles, combined with a simple quantitative model, can reveal the relevant properties. We used this method in a systematic study where we varied the temperature cycle, the bead concentration, the particles' surface coverage, and the DNA construct. Among other things, we find that the backbone that tethers the sticky ends to the surface can have a significant impact on the particles' dissociation properties, as it affects the total number of interparticle bonds and the configurational entropy cost associated with these bonds. We further find that, independent of the tether backbone, self-complementary "palindromic" sticky ends readily form intraparticle hairpins and loops, which greatly affect the particles' association behavior. Such secondary structure formation is increasingly important in faster temperature quenches, at lower particle concentration, and at lower surface coverage. The latter observations are especially useful for the design of so-called self-protected DNA-mediated interactions, which we pioneered recently and for which we expect to find an increasing use, as they enable more versatile assembly schemes.
表面功能化与互补的单链 DNA 粘性末端越来越多地用于指导纳米和微米级颗粒自组装成更大规模的有序结构。在这里，我们提供了可以从现成的基于网络的数据定量预测 DNA 包覆颗粒的结合行为的测量、公式和图表。实验表明，悬浮行为对嫁接细节非常敏感，例如系链结构的长度和灵活性以及颗粒的表面覆盖率。因此，如果要控制相互作用和组装过程，就需要深入了解 DNA 涂层的结构和动态特性。我们展示了如何通过在选定的温度循环期间对颗粒的结合-解离动力学进行简单的测量，并结合简单的定量模型，来揭示相关特性。我们在系统研究中使用了这种方法，其中我们改变了温度循环、珠粒浓度、颗粒的表面覆盖率和 DNA 结构。除其他外，我们发现将粘性末端系在表面上的主链会对颗粒的解离特性产生重大影响，因为它会影响颗粒之间的总键数以及与这些键相关的构象熵成本。我们还发现，无论系链主链如何，自我互补的“回文”粘性末端都容易形成颗粒内发夹和环，这会极大地影响颗粒的结合行为。这种二级结构形成在更快的温度淬火、更低的颗粒浓度和更低的表面覆盖率下变得越来越重要。后一种观察结果对于所谓的自我保护 DNA 介导相互作用的设计尤其有用，我们最近率先提出了这种相互作用，预计它的应用会越来越广泛，因为它们可以实现更通用的组装方案。
