Influence of dimethylsulfoxide on RNA structure and ligand binding.
Influence of dimethylsulfoxide on RNA structure and ligand binding.
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DOI：
10.1021/ac402038t
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发表时间：
2013-10-15
影响因子：
7.4
通讯作者：
Al-Hashimi, Hashim M.
中科院分区：
文献类型：
--
作者：
Lee, Janghyun;Vogt, Catherine E.;McBrairty, Mitchell;Al-Hashimi, Hashim M.
二甲基亚砜（DMSO）被广泛用作助溶剂，以溶解RNA-配体结合试验中的疏水化合物。尽管已知高浓度的DMSO（>75%）可显著影响RNA结构和折叠能量学，但尚未对结合测定中通常使用的较低浓度（<10%）的DMSO如何影响RNA结构和配体结合进行彻底分析。在这里，我们使用NMR和2-氨基嘌呤荧光光谱检查DMSO如何影响两个灵活的发夹RNA的结构，动力学和配体结合特性;来自HIV-1和细菌核糖体A位点的反式激活反应元件。在这两种情况下，5%-10%DMSO降低了堆积相互作用，增加了凸起和环内非典型残基的局部无序，并导致不同小分子的实测结合亲和力降低0.3-4倍，其中观察到非特异性结合RNA的嵌入化合物的降低最大。我们的研究结果表明，通过竞争疏水相互作用，DMSO可以对RNA结构和配体结合产生微小但显著的影响。在开发配体结合试验和高通量筛选时应考虑这些影响。
Dimethyl sulfoxide (DMSO) is widely used as a cosolvent to solubilize hydrophobic compounds in RNA-ligand binding assays. Although it is known that high concentrations of DMSO (>75%) can significantly affect RNA structure and folding energetics, a thorough analysis of how lower concentrations (<10%) of DMSO typically used in binding assays affects RNA structure and ligand binding has not been undertaken. Here, we use NMR and 2-aminopurine fluorescence spectroscopy to examine how DMSO affects the structure, dynamics, and ligand binding properties of two flexible hairpin RNAs; the transactivation response element from HIV-1 and bacterial ribosomal A-site. In both cases, 5%-10% DMSO decreased stacking interactions and increased local disorder in non-canonical residues within bulges and loops and resulted in 0.3–4 fold reduction in the measured binding affinities for different small molecules, with the greatest reduction observed for an intercalating compound that binds RNA non-specifically. Our results suggest that by competing for hydrophobic interactions, DMSO can have a small but significant effect on RNA structure and ligand binding. These effects should be considered when developing ligand binding assays and high throughput screens.
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影响因子：
64.5
作者：
Cooper TA;Wan L;Dreyfuss G
通讯作者：
Dreyfuss G
影响因子：
15
作者：
Hansen, Alexandar L.;Al-Hashimi, Hashim M.
通讯作者：
Al-Hashimi, Hashim M.
氨基糖苷与解码位点寡核苷酸之间的复合物的晶体结构：环数和正电荷在特定结合中导致错误编码的作用。
影响因子：
14.9
作者：
François, B;Russell, RJM;Murray, JB;Aboul-ela, F;Masquida, B;Vicens, Q;Westhof, E
通讯作者：
Westhof, E
DOI：
10.1073/pnas.95.17.9819
发表时间：
1998-08-18
影响因子：
11.1
作者：
Ippolito, JA;Steitz, TA
通讯作者：
Steitz, TA
影响因子：
2.7
作者：
DELAGLIO, F;GRZESIEK, S;BAX, A
通讯作者：
BAX, A