Poblete Simón, Božič Anže, Kanduč Matej, Podgornik Rudolf, Guzman Horacio V
Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5091000, Chile.
Computational Biology Lab, Fundación Ciencia & Vida, Santiago 7780272, Chile.
ACS Omega. 2021 Nov 19;6(48):32823-32831. doi: 10.1021/acsomega.1c04774. eCollection 2021 Dec 7.
RNA is a functionally rich molecule with multilevel, hierarchical structures whose role in the adsorption to molecular substrates is only beginning to be elucidated. Here, we introduce a multiscale simulation approach that combines a tractable coarse-grained RNA structural model with an interaction potential of a structureless flat adsorbing substrate. Within this approach, we study the specific role of stem-hairpin and multibranch RNA secondary structure motifs on its adsorption phenomenology. Our findings identify a dual regime of adsorption for short RNA fragments with and without the secondary structure and underline the adsorption efficiency in both cases as a function of the surface interaction strength. The observed behavior results from an interplay between the number of contacts formed at the surface and the conformational entropy of the RNA molecule. The adsorption phenomenology of RNA seems to persist also for much longer RNAs as qualitatively observed by comparing the trends of our simulations with a theoretical approach based on an ideal semiflexible polymer chain.
RNA是一种功能丰富的分子,具有多层次的等级结构,其在吸附分子底物方面的作用才刚刚开始被阐明。在这里,我们引入了一种多尺度模拟方法,该方法将易于处理的粗粒度RNA结构模型与无结构的平面吸附底物的相互作用势相结合。在这种方法中,我们研究了茎环和多分支RNA二级结构基序在其吸附现象学中的具体作用。我们的研究结果确定了具有和不具有二级结构的短RNA片段的双重吸附机制,并强调了在这两种情况下吸附效率与表面相互作用强度的函数关系。观察到的行为是由表面形成的接触数量与RNA分子的构象熵之间的相互作用导致的。通过将我们的模拟趋势与基于理想半柔性聚合物链的理论方法进行比较定性观察,RNA的吸附现象似乎在更长的RNA中也持续存在。