Williams D J, Hall K B
Department of Biochemistry, Washington University School of Medicine, St Louis, MO 63110, USA.
J Mol Biol. 2000 Apr 14;297(5):1045-61. doi: 10.1006/jmbi.2000.3623.
In prokaryotic ribosomal RNAs, most UUCG tetraloops are closed by a C-G base-pair. However, this preference is greatly reduced in eukaryotic rRNA species where many UUCG tetraloops are closed by G-C base-pairs. Here, biophysical properties of the C[UUCG]G and G[UUCG]C tetraloops are compared, using experimental and computational methods. Thermal denaturation experiments are used to derive thermodynamic parameters for the wild-type G[UUCG]C tetraloop and variants containing single deoxy substitutions in the loop. A comparison with analogous experiments on the C[UUCG]G motif shows that the two RNA species exhibit similar patterns in response to the substitutions, suggesting that their loop structures are similar. This conclusion is supported by NMR data that suggest that the essential UUCG loop structure is maintained in both tetraloops. However, NMR results show that the G[UUCG]C loop structure is disrupted prior to melting of the stem; this behavior is in contrast to the two-state behavior of the C[UUCG]G molecule. Stochastic dynamics simulations using the GB/SA continuum solvation model, run as a function of temperature, show rare conformational transitions in several G[UUCG]C simulations. These results lead to the conclusion that substitution of a G-C for a C-G closing base-pair increases the intrinsic flexibility of the UUCG loop.
在原核生物核糖体RNA中，大多数UUCG四环由C-G碱基对封闭。然而，在真核生物rRNA种类中，这种偏好性大大降低，其中许多UUCG四环由G-C碱基对封闭。在此，使用实验和计算方法比较了C[UUCG]G和G[UUCG]C四环的生物物理性质。热变性实验用于推导野生型G[UUCG]C四环以及环中含有单个脱氧取代的变体的热力学参数。与C[UUCG]G基序的类似实验进行比较表明，这两种RNA种类在对取代的响应中表现出相似的模式，表明它们的环结构相似。这一结论得到了核磁共振数据的支持，该数据表明两种四环中都维持了基本的UUCG环结构。然而，核磁共振结果表明，G[UUCG]C环结构在茎干解链之前就被破坏了；这种行为与C[UUCG]G分子的双态行为形成对比。使用GB/SA连续介质溶剂化模型进行的随机动力学模拟作为温度的函数运行，结果显示在几个G[UUCG]C模拟中出现了罕见的构象转变。这些结果得出这样的结论：用G-C取代C-G封闭碱基对会增加UUCG环的内在灵活性。
