Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling.
Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling.
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DOI：
10.1021/ja805759z
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发表时间：
2008-12-10
影响因子：
15
通讯作者：
Hoogstraten, Charles G.
中科院分区：
文献类型：
--
作者：
Johnson, James E., Jr.;Hoogstraten, Charles G.
构象动力学在蛋白质和核酸的性质和功能中起着关键作用。异核磁共振自旋弛豫是一种独特而强大的蛋白质动力学位点特异性探针，已发现越来越多的应用于核苷酸碱基侧链和RNA的端粒位点。然而，在均匀13c标记的样品中，环碳之间的强磁偶联阻碍了核酸核糖骨架的应用。在这项工作中，我们应用了最近开发的代谢定向同位素标记方案，该方案将13C高效率和特异性地放置在核苷酸核糖C2 ‘和C4 ’位点上。我们利用这一方案来探索已被充分研究的GCAA RNA四环的骨干动力学。利用CPMG （carr - pur细胞- meiboomm - gill）和R1ρ弛豫色散光谱的结合来探索微秒到毫秒时间尺度上的交换过程，我们发现了一个广泛的动态转变模式，连接了一组相对明确的构象。在许多情况下，观察到的转变似乎与相应核苷酸的C3 ' -末端/C2 ' -末端糖折叠转变有关，并且也可能在四环内的多个核苷酸之间相关。这些结果证明了基于替代位点同位素标记的核磁共振自旋弛豫的力量，为RNA中核糖主干基团的动态特性打开了一个新的窗口。
Conformational dynamics play a key role in the properties and functions of proteins and nucleic acids. Heteronuclear NMR spin relaxation is a uniquely powerful site-specific probe of dynamics in proteins and has found increasing applications to nucleotide base side chains and anomeric sites in RNA. Applications to the nucleic acid ribose backbone, however, have been hampered by strong magnetic coupling among ring carbons in uniformly 13C-labeled samples. In this work, we apply a recently-developed, metabolically-directed isotope labeling scheme that places 13C with high efficiency and specificity at the nucleotide ribose C2’ and C4’ sites. We take advantage of this scheme to explore backbone dynamics in the well-studied GCAA RNA tetraloop. Using a combination of CPMG (Carr-Purcell-Meiboom-Gill) and R1ρ relaxation dispersion spectroscopy to explore exchange processes on the microsecond to millisecond timescale, we find an extensive pattern of dynamic transitions connecting a set of relatively well-defined conformations. In many cases, the observed transitions appear to be linked to C3’-endo/C2’-endo sugar pucker transitions of the corresponding nucleotides, and may also be correlated across multiple nucleotides within the tetraloop. These results demonstrate the power of NMR spin relaxation based on alternate-site isotope labeling to open a new window into the dynamic properties of ribose backbone groups in RNA.
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影响因子：
1.7
作者：
DEVERELL, C;MORGAN, RE;STRANGE, JH
通讯作者：
STRANGE, JH
影响因子：
14.9
作者：
BATEY, RT;INADA, M;WILLIAMSON, JR
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WILLIAMSON, JR
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2.7
作者：
Boisbouvier, J;Wu, ZR;Bax, A
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Bax, A
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作者：
Clerte, C;Hall, KB
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Hall, KB
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作者：
Dayie, KT;Brodsky, AS;Williamson, JR
通讯作者：
Williamson, JR