Variable helix elongation as a tool to modulate RNA alignment and motional couplings.
Variable helix elongation as a tool to modulate RNA alignment and motional couplings.
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可变螺旋伸长作为调节RNA比对和运动耦合的工具。
DOI：
10.1016/j.jmr.2009.09.022
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发表时间：
2010-01
期刊：
影响因子：
--
通讯作者：
Al-Hashimi HM
中科院分区：
文献类型：
--
作者：
Dethoff EA;Hansen AL;Zhang Q;Al-Hashimi HM
剩余偶极耦合（RDC）在RNA结构和动力学研究中的应用可能会因集体螺旋运动和整体对齐之间存在耦合以及无法通过改变有序介质来调节分子的整体对齐而变得复杂。在这里，我们显示了一个27-nt的TAR RNA构建体，可变水平的螺旋延伸可以用来改变整体对齐和耦合集体螺旋运动在一个半可预测的方式。在不存在延伸的情况下，与六个碱基对的螺旋I相比，由UUCG顶端环封端的四个碱基对的螺旋II表现出更高的有序度（cDNAI/cDNAII = 0.56±0.1）。主Szz方向几乎平行于螺旋II的轴，但相对于螺旋I的轴偏离0.40 °。将螺旋I延长三个碱基对使两个螺旋的排列相等，并将RNA推入运动偶联极限，使得两个螺旋具有可比的有序度（α I/α II = 0.92±0.04）和相对于Szz的取向（α 17°）。将延伸长度进一步增加到22个碱基对，将RNA推向运动解耦极限，在该极限中，螺旋I主导排列（螺旋II/螺旋I = 0.45±0.05），Szz几乎平行于其螺旋轴。许多这些趋势可以合理化使用PALES模拟，采用先前提出的三态动态合奏TAR。我们的研究结果提供了新的见解运动耦合，提供评估其程度的指导方针，并表明，不同程度的螺旋延伸可以允许访问独立的集的RDC表征RNA结构动力学。
The application of residual dipolar couplings (RDCs) in studies of RNA structure and dynamics can be complicated by the presence of couplings between collective helix motions and overall alignment and by the inability to modulate overall alignment of the molecule by changing the ordering medium. Here, we show for a 27-nt TAR RNA construct that variable levels of helix elongation can be used to alter both overall alignment and couplings to collective helix motions in a semi-predictable manner. In the absence of elongation, a four base-pair helix II capped by a UUCG apical loop exhibits a higher degree of order compared to a six base-pair helix I (ϑI/ϑII = 0.56±0.1). The principal Szz direction is nearly parallel to the axis of helix II but deviates by ∼40° relative to the axis of helix I. Elongating helix I by three base-pairs equalizes the alignment of the two helices and pushes the RNA into the motional coupling limit such that the two helices have comparable degrees of order (ϑI/ϑII = 0.92±0.04) and orientations relative to Szz (∼17°). Increasing the length of elongation further to twenty-two base-pairs pushes the RNA into the motional decoupling limit in which helix I dominates alignment (ϑII/ϑI = 0.45±0.05), with Szz orientated nearly parallel to its helix axis. Many of these trends can be rationalized using PALES simulations that employ a previously proposed three-state dynamic ensemble of TAR. Our results provide new insights into motional couplings, offer guidelines for assessing their extent, and suggest that variable degrees of helix elongation can allow access to independent sets of RDCs for characterizing RNA structural dynamics.
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影响因子：
2.2
作者：
Al-Hashimi, HM;Valafar, H;Prestegard, JH
通讯作者：
Prestegard, JH
影响因子：
15
作者：
Rückert, M;Otting, G
通讯作者：
Otting, G
影响因子：
15
作者：
Meiler, J;Prompers, JJ;Brüschweiler, R
通讯作者：
Brüschweiler, R
影响因子：
5.6
作者：
Al-Hashimi, HM;Gosser, Y;Patel, DJ
通讯作者：
Patel, DJ
影响因子：
15
作者：
Ramirez, BE;Bax, A
通讯作者：
Bax, A