Simultaneous binding of molecules by multiple binding partners is known to strongly reduce the apparent dissociation constant of the corresponding molecular complexes, and can be used to achieve strong, non-covalent molecular interactions. Based on this principle, efficient binding of proteins to DNA nanostructures has been achieved previously by placing several aptamers in close proximity to each other onto DNA scaffolds. Here, we develop an approach for exploring design parameters, such as the geometric arrangement or the nanomechanical properties of the binding sites, that use two-dimensional DNA origami-based nanocavities that bear aptamers with known mechanical properties at defined distances and orientations. The origami structures are labelled with barcodes, which enables large numbers of binding cavities to be investigated in parallel and under identical conditions, and facilitates a direct and reliable quantitative comparison of their binding yields. We demonstrate that binding geometry and mechanical properties have a dramatic effect on origami-based multivalent binding sites, and that optimization of linker spacings and flexibilities can improve the effective binding strength of the sites substantially.

已知通过多个结合配偶体同时结合分子会大大降低相应分子复合物的表观解离常数，并可用于实现强的非共价分子相互作用。基于该原理，先前已经通过将几个适体彼此紧邻放置在DNA支架上来实现蛋白质与DNA纳米结构的有效结合。在这里，我们开发了一种方法，用于探索设计参数，例如结合位点的几何排列或纳米机械性能，这些方法使用二维基于DNA折纸的纳米腔，这些纳米腔在定义的距离和方向上具有具有已知机械特性的适体。折纸结构标有条形码，这样可以在相同条件下平行研究大量的结合腔，并有助于对其结合产量进行直接可靠的定量比较。我们证明，结合的几何形状和机械性能对基于折纸的多价结合位点具有戏剧性的影响，并且接头间隔和柔性的优化可以显着提高位点的有效结合强度。