Department of Applied Experimental Biophysics, Johannes Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria.
Department of Chemistry, University College London, Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom.
Nano Lett. 2023 May 24;23(10):4439-4447. doi: 10.1021/acs.nanolett.3c00743. Epub 2023 May 11.
The binding of ligands to receptors within a nanoscale small space is relevant in biology, biosensing, and affinity filtration. Binding in confinement can be studied with biological systems but under the limitation that essential parameters cannot be easily controlled including receptor type and position within the confinement and its dimensions. Here we study molecular recognition with a synthetic confined nanopore with controllable pore dimension and molecular DNA receptors at different depth positions within the channel. Binding of a complementary DNA strand is studied at the single-molecule level with atomic force microscopy. Following the analysis, kinetic association rates are lower for receptors positioned deeper inside the pore lumen while dissociation is faster and requires less force. The phenomena are explained by the steric constraints on molecular interactions in confinement. Our study is the first to explore recognition in DNA nanostructures with atomic force microscopy and lays out new tools to further quantify the effect of nanoconfinement on molecular interactions.
配体与纳米级小空间内受体的结合在生物学、生物传感和亲和过滤中具有重要意义。可以使用生物系统研究受限条件下的结合，但存在的限制是，包括受体类型和在受限环境中的位置及其尺寸等基本参数不容易控制。在这里，我们使用具有可控孔径的合成受限纳米孔和不同深度位置的分子 DNA 受体来研究分子识别。使用原子力显微镜在单分子水平上研究互补 DNA 链的结合。通过分析发现，位于孔腔内更深位置的受体的结合动力学速率较低，而解离更快且需要的力更小。这些现象可以用分子在受限环境中的空间位阻来解释。我们的研究首次使用原子力显微镜探索 DNA 纳米结构中的识别，并为进一步量化纳米受限对分子相互作用的影响提供了新的工具。
