Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
Phys Chem Chem Phys. 2023 Dec 21;26(1):241-248. doi: 10.1039/d3cp04704k.
Förster resonant energy transfer (FRET) can be utilized in the study of tertiary structures of RNA aptamers, which bind specific fluorophoric ligands to form a fluorogenic aptamer complex. By introducing the emissive nucleobase analog 4-cyanoindole into the fluorogenic Chili RNA aptamer a FRET pair was established. The interpretation of studies aiming to investigate those tertiary structures using FRET, however, relies on prior knowledge about conformational properties of the nucleobase, which govern exciton transfer capabilities. Herein we employed classical molecular dynamics combined with Förster exciton theory to elucidate the preferred orientation relative to proximate bases and the influence on exciton transfer efficiency in multiple substitution sites. We did this by comparing the chromophoric distances emergent from MD simulations with experimental FRET data based on structural data of the native aptamer. We present the outlined methodology as a means to reliably evaluate future nucleobase analogue candidates in terms of their structural behavior and emergent exciton transfer properties as exemplified in the study of the preferred orientation of 4-cyanoindole in the Chili RNA aptamer.
Förster 共振能量转移 (FRET) 可用于研究 RNA 适体的三级结构，RNA 适体可以与特定的荧光配体结合形成荧光适体复合物。通过将发荧光的核苷类似物 4-氰基吲哚引入到 Chili RNA 适体中，建立了一个 FRET 对。然而，为了利用 FRET 研究这些三级结构的研究结果，需要依赖于对核苷构象特性的先验知识，而核苷构象特性决定了激子转移能力。在这里，我们采用经典分子动力学结合 Förster 激子理论，阐明了与邻近碱基的相对取向以及在多个取代位置上对激子转移效率的影响。我们通过将 MD 模拟产生的发色团距离与基于天然适体结构数据的实验 FRET 数据进行比较来实现这一点。我们提出了这种方法，以可靠地评估未来核苷类似物候选物的结构行为和出现的激子转移特性，如在 Chili RNA 适体中 4-氰基吲哚的优先取向研究中所示。
