The influence of monovalent cation size on the stability of RNA tertiary structures.
The influence of monovalent cation size on the stability of RNA tertiary structures.
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DOI：
10.1016/j.jmb.2009.04.083
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发表时间：
2009-07-24
影响因子：
5.6
通讯作者：
Draper, David E.
中科院分区：
文献类型：
--
作者：
Lambert, Dominic;Leipply, Desirae;Shiman, Ross;Draper, David E.
许多RNA三级结构在单价离子单独存在下是稳定的。为了评估在这种RNA的表面处或附近的离子对稳定性的贡献程度，用五种I族阳离子中的每一种测量了各种RNA结构的盐依赖性稳定性。发夹二级结构和假结三级结构的稳定性对离子的身份不敏感，但其他两种RNA的三级结构，腺嘌呤核糖开关和接吻环复合物，随着离子尺寸的减小而变得更稳定2-3 kcal/mol。这种“默认”趋势归因于较小离子更接近RNA表面的能力。亲吻环复合物周围的阳离子积累的程度也成反比的离子半径，也许是因为存在的空间限制的口袋，可以访问只有较小的离子。含有四环受体基序的RNA显示出对Na+或K+的强烈偏好（高达103 kcal/mol），而不是其他I族离子，这与在某些晶体结构中该基序对K+的螯合作用一致。当形成螯合位点的一部分的碱基突变时，这种RNA恢复到对离子大小的“默认”依赖性。最后，最初在高LiCl浓度存在下选择的用于cobinamide的RNA适体在Li+存在下比其他单价离子更强地结合配体。基于这些趋势，在RNA的稳定性与组I离子的大小，有人认为，RNA的三级结构的两个功能可能会促进强相互作用的离子或附近的RNA表面：负电荷密度，高于二级结构中发现的，和偶尔存在的螯合位点，电负性口袋，选择性地结合离子的最佳尺寸。
Many RNA tertiary structures are stable in the presence of monovalent ions alone. To evaluate the degree to which ions at or near the surfaces of such RNAs contribute to stability, the salt-dependent stabilities of a variety of RNA structures were measured with each of the five group I cations. The stabilities of hairpin secondary structures and a pseudoknot tertiary structure are insensitive to the ion identity, but the tertiary structures of two other RNAs, an adenine riboswitch and a kissing loop complex, become more stable by 2-3 kcal/mol as ion size decreases. This “default” trend is attributed to the ability of smaller ions to approach the RNA surface more closely. The degree of cation accumulation around the kissing loop complex was also inversely proportional to ion radius, perhaps because of the presence of sterically restricted pockets that can be accessed only by smaller ions. An RNA containing the tetraloop-receptor motif shows a strong (up to ∼3 kcal/mol) preference for Na+ or K+ over other group I ions, consistent with the chelation of K+ by this motif in some crystal structures. This RNA reverts to the “default” dependence on ion size when a base forming part of the chelation site is mutated. Lastly, an RNA aptamer for cobinamide, which was originally selected in the presence of high LiCl concentrations, binds ligand more strongly in the presence of Li+ than other monovalent ions. Based on these trends in RNA stability with group I ion size, it is argued that two features of RNA tertiary structures may promote strong interactions with ions at or near the RNA surface: negative charge densities that are higher than found in secondary structures, and the occasional presence of chelation sites, electronegative pockets that selectively bind ions of an optimum size.
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影响因子：
2.9
作者：
Downey, CD;Fiore, JL;Pardi, A
通讯作者：
Pardi, A
影响因子：
5.6
作者：
Chang, KY;Tinoco, I
通讯作者：
Tinoco, I
影响因子：
5.6
作者：
Batey, RT;Sagar, MB;Doudna, JA
通讯作者：
Doudna, JA
影响因子：
5.6
作者：
Conn, GL;Gittis, AG;Draper, DE
通讯作者：
Draper, DE
影响因子：
2.9
作者：
Batey, RT;Doudna, JA
通讯作者：
Doudna, JA