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首页> 外文期刊>The Journal of Chemical Physics >An asymmetric mesoscopic model for single bulges in RNA
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An asymmetric mesoscopic model for single bulges in RNA

机译：RNA中单凸起的非对称介观模型

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摘要

Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here we derived the conditions for the Peyrard-Bishop mesoscopic model to overcome these limitations and applied it to the calculation of single bulges, the smallest and simplest of these asymmetric structures. We found that these theoretical conditions can indeed be applied to any situation where stacking asymmetry needs to be considered. The full set of parameters for group I RNA bulges was determined from experimental melting temperatures using an optimization procedure, and we also calculated average opening profiles for several RNA sequences. We found that guanosine bulges show the strongest perturbation on their neighboring base pairs, considerably reducing the on-site interactions of their neighboring base pairs. Published by AIP Publishing.
机译：简单的一维DNA或RNA介观模型对于它们的计算效率感兴趣，同时保留分子相互作用的关键元件。然而，它们仅处理完美形成的DNA或RNA双螺旋，并考虑两条链中的链中相互作用。这使得难以描述诸如凸起和环的高度不对称结构，并且例如防止介面镜片模型的应用来确定RNA二级结构。在这里，我们衍生出幽灵 - 主教介绍模型的条件，以克服这些限制并将其应用于单一凸起的计算，最小，最简单的这些不对称结构。我们发现这些理论条件确实适用于需要考虑堆叠不对称的任何情况。通过使用优化程序从实验熔化温度确定基团I RNA凸起的全套参数，并且我们还计算了几个RNA序列的平均开口曲线。我们发现鸟苷凸起在其邻近的基对上显示出最强的扰动，大大减少了邻近碱基对的现场相互作用。通过AIP发布发布。

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