Effects of magnesium ions on the stabilization of RNA oligomers of defined structures
Effects of magnesium ions on the stabilization of RNA oligomers of defined structures
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DOI：
10.1017/s1355838202024226
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发表时间：
2002-03-01
期刊：
影响因子：
4.5
通讯作者：
Westhof, E
中科院分区：
文献类型：
--
作者：
Serra, MJ;Baird, JD;Westhof, E
采用光学熔融法测定了11种具有明确二级结构的小RNA寡聚物的稳定性与镁离子浓度的关系。这些低聚物包括由沃森-克里克碱基对、GA串联碱基对、GU串联碱基对和环E基序组成的螺旋（真核生物和真核生物都有）。用两个简单的模型解释了镁离子浓度对稳定性的影响。第一种假设金属离子在双相形成时被吸收。第二种假设金属离子对RNA低聚物具有非特异性静电吸引力。对于除真细菌环E外的所有低聚物，数据可以最好地解释为金属离子与rna的非特异性结合。镁离子对真细菌环E稳定性的影响在两个方面不同于其他低聚物。首先，镁离子的稳定程度（通过熔化温度或自由能的变化来测量）是其他螺旋低聚物的三倍。其次，镁离子的存在使熔化转变的焓增加了一倍。这些结果表明，镁离子通过特异性螯合RNA来稳定真细菌环E序列。此外，在一个相当小的系统上的这些结果揭示了在像I族内含子这样的大rna热展开时观察到的大焓变。这表明，在rna折叠中观察到的这些大的焓变化的部分可能归因于某些特定结合的镁离子的水合状态和配位原子类型的变化，以及由于这些镁离子的结合将两个茎偶联在一起而观察到的折叠转变的协同性的增加。为了可视化金属离子结合位点而进行的布朗动态模拟显示，除真细菌环E外，所有低聚物的离子密度都相当偏域，其中精确定位的离子密度是先前计算出来的。
Optical melting was used to determine the stabilities of 11 small RNA oligomers of defined secondary structure as a function of magnesium ion concentration. The oligomers included helices composed of Watson-Crick base pairs, GA tandem base pairs, GU tandem base pairs, and loop E motifs (both eubacterial and eukaryotic). The effect of magnesium ion concentration on stability was interpreted in terms of two simple models. The first assumes an uptake of metal ion upon duplex formation. The second assumes nonspecific electrostatic attraction of metal ions to the RNA oligomer. For all oligomers, except the eubacterial loop E, the data could best be interpreted as nonspecific binding of metal ions to the RNAs. The effect of magnesium ions on the stability of the eubacterial loop E was distinct from that seen with the other oligomers in two ways. First, the extent of stabilization by magnesium ions (as measured by either change in melting temperature or free energy) was three times greater than that observed for the other helical oligomers. Second, the presence of magnesium ions produces a doubling of the enthalpy for the melting transition. These results indicate that magnesium ion stabilizes the eubacterial loop E sequence by chelating the RNA specifically. Further, these results on a rather small system shed light on the large enthalpy changes observed upon thermal unfolding of large RNAs like group I introns. It is suggested that parts of those large enthalpy changes observed in the folding of RNAs may be assigned to variations in the hydration states and types of coordinating atoms in some specifically bound magnesium ions and to an increase in the observed cooperativity of the folding transition due to the binding of those magnesium ions coupling the two stems together. Brownian dynamic simulations, carried out to visualize the metal ion binding sites, reveal rather delocalized ionic densities in all oligomers, except for the eubacterial loop E, in which precisely located ion densities were previously calculated.