Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, Trieste 34136, Italy.
Department of Mathematics and Geosciences, University of Trieste, Trieste 34127, Italy.
J Chem Theory Comput. 2023 Jun 27;19(12):3672-3685. doi: 10.1021/acs.jctc.3c00084. Epub 2023 Jun 8.
Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules. In this work, we use atomistic molecular dynamics simulations to test the hypothesis that binding of RNA with SHAPE reagents is affected by cooperative effects leading to an observed reactivity that is dependent on the reagent concentration. We develop a general technique that enables the calculation of the affinity for arbitrary molecules as a function of their concentration in the grand-canonical ensemble. Our simulations of an RNA structural motif suggest that, at the concentration typically used in SHAPE experiments, cooperative binding would lead to a measurable concentration-dependent reactivity. We also provide a qualitative validation of this statement by analyzing a new set of experiments collected at different reagent concentrations.
化学探测实验，如 SHAPE，通常用于探测 RNA 分子。在这项工作中，我们使用原子分子动力学模拟来检验以下假设：即 RNA 与 SHAPE 试剂的结合受到协同效应的影响，从而导致观察到的反应性依赖于试剂浓度。我们开发了一种通用技术，可以计算任意分子在巨正则系综中的浓度作为其亲和力的函数。我们对 RNA 结构基序的模拟表明，在 SHAPE 实验中通常使用的浓度下，协同结合会导致可测量的浓度依赖性反应性。我们还通过分析在不同试剂浓度下收集的一组新实验，对这一说法进行了定性验证。
