FOM Institute AMOLF, Amsterdam, The Netherlands.
J Chem Phys. 2011 Feb 28;134(8):084702. doi: 10.1063/1.3557794.
DNA-coated colloids have great potential for the design of complex self-assembling materials. In order to predict the structures that will form, knowledge of the interactions between DNA-functionalized particles is crucial. Here, we report results from Monte Carlo simulations of the pair-interaction between particles coated with single-stranded DNA sticky ends that are connected to the surface by relatively short and stiff surface tethers. We complement our calculations with a study of the interaction between two planar surfaces coated with the same DNA. Based on our simulations we propose analytical expressions for the interaction potentials. These analytical expressions describe the DNA-mediated interactions well for particle sizes ranging from tens of nanometers to a few micrometers and for a wide range of grafting densities. We find that important contributions to both the repulsive and attractive parts of the free energy come from purely entropic effects of the discrete tethered sticky ends. Per bond, these entropic contributions have a magnitude similar to the hybridization free energy of a free pair of sticky ends in solution and they can thus considerably change the effective sticky-end binding strength. Based on the calculated interaction potentials, we expect that stable gas-liquid separation only occurs for particles with radii smaller than a few tens of nanometers, which suggests that nanoparticles and micrometer-sized colloids will follow different routes to crystallization. Finally, we note that the natural statistical nonuniformities in the surface distribution of sticky ends lead to large variations in the binding strength. This phenomenon may compromise the reliability of tests that aim to detect specific DNA targets in diagnostics. In addition to guiding the design of novel self-assembling materials and gene-detection assays, the insights presented here could also shed more light on (multivalent) interactions in other systems with tethered binding groups, for instance in the areas of supramolecular chemistry or ligand-receptor mediated biorecognition.
DNA 包覆胶体在设计复杂自组装材料方面具有巨大的潜力。为了预测将形成的结构，了解 DNA 功能化颗粒之间的相互作用至关重要。在这里，我们报告了单链 DNA 粘性末端包覆的颗粒之间的对相互作用的蒙特卡罗模拟结果，这些粘性末端通过相对较短且刚性的表面系链连接到表面。我们通过研究具有相同 DNA 涂层的两个平面之间的相互作用来补充我们的计算。基于我们的模拟，我们提出了相互作用势的解析表达式。这些解析表达式很好地描述了粒径从数十纳米到数微米以及接枝密度范围很宽的 DNA 介导相互作用。我们发现，离散系链粘性末端的纯熵效应对自由能的排斥和吸引部分都有重要贡献。对于每一个键，这些熵贡献的大小与溶液中自由对粘性末端的杂交自由能相似，因此它们可以显著改变有效粘性末端结合强度。基于计算出的相互作用势，我们预计只有当颗粒半径小于数十纳米时才会发生稳定的气-液分离，这表明纳米颗粒和微米胶体将遵循不同的结晶途径。最后，我们注意到，粘性末端表面分布的自然统计非均匀性会导致结合强度的巨大变化。这种现象可能会影响旨在诊断中检测特定 DNA 靶标的测试的可靠性。除了指导新型自组装材料和基因检测分析的设计之外，这里提出的见解还可以更深入地了解其他带有系链结合基团的系统中的（多价）相互作用，例如在超分子化学或配体-受体介导的生物识别领域。
