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首页> 外文期刊>Biochemistry >Denaturation of RNA secondary and tertiary structure by urea: Simple unfolded state models and free energy parameters account for measured m -values
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Denaturation of RNA secondary and tertiary structure by urea: Simple unfolded state models and free energy parameters account for measured m -values

机译：尿素使RNA二级和三级结构变性：简单的展开状态模型和自由能参数说明了测得的m值

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摘要

To investigate the mechanism by which urea destabilizes RNA structure, urea-induced unfolding of four different RNA secondary and tertiary structures was quantified in terms of an m-value, the rate at which the free energy of unfolding changes with urea molality. From literature data and our osmometric study of a backbone analogue, we derived average interaction potentials (per square angstrom of solvent accessible surface) between urea and three kinds of RNA surfaces: phosphate, ribose, and base. Estimates of the increases in solvent accessible surface areas upon RNA denaturation were based on a simple model of unfolded RNA as a combination of helical and single-strand segments. These estimates, combined with the three interaction potentials and a term to account for interactions of urea with released ions, yield calculated m-values that are in good agreement with experimental values (200 mm monovalent salt). Agreement was obtained only if single-stranded RNAs were modeled in a highly stacked, A-form conformation. The primary driving force for urea-induced denaturation is the strong interaction of urea with the large surface areas of bases that become exposed upon denaturation of either RNA secondary or tertiary structure, though interactions of urea with backbone and released ions may account for up to a third of the m-value. Urea m-values for all four RNAs are salt-dependent, which we attribute to an increased extension (or decreased charge density) of unfolded RNAs with an increased urea concentration. The sensitivity of the urea m-value to base surface exposure makes it a potentially useful probe of the conformations of RNA unfolded states.
机译：为了研究尿素使RNA结构不稳定的机理，根据m值对尿素诱导的四个不同RNA二级和三级结构的展开进行了定量，该值的展开自由能随尿素摩尔浓度的变化而变化。从文献数据和我们对骨架类似物的渗透压研究中，我们得出了尿素与三种RNA表面（磷酸盐，核糖和碱基）之间的平均相互作用势（溶剂可及表面的每平方埃）。 RNA变性后，溶剂可及表面积增加的估计是基于未折叠RNA的简单模型（螺旋和单链片段的组合）得出的。这些估计值与三个相互作用电位以及一个解释尿素与释放离子相互作用的术语结合，得出计算出的m值与实验值（200毫米单价盐）非常吻合。仅当以高度堆叠的A型构象对单链RNA进行建模时，才能获得协议。尿素诱导的变性的主要驱动力是尿素与较大的碱基表面积的强相互作用，该碱基在RNA二级或三级结构变性时暴露出来，尽管尿素与主链和释放的离子的相互作用最多可导致m值的三分之一。所有四个RNA的尿素m值都是盐依赖性的，这归因于尿素浓度增加的未折叠RNA的延伸性增加（或电荷密度降低）。尿素m值对基本表面暴露的敏感性使其成为RNA折叠状态构象的潜在有用探针。

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