侧翼碱基对RNA金属结合的调控：GC、串联GU和串联GA位点的15N核磁共振评估
Modulation of RNA metal binding by flanking bases: 15N NMR evaluation of GC, tandem GU, and tandem GA sites.
作者信息
Wang Weimin, Zhao Jianwei, Han Qianwei, Wang Gang, Yang Gengcheng, Shallop Anthony J, Liu Jane, Gaffney Barbara L, Jones Roger A
机构信息
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
出版信息
Nucleosides Nucleotides Nucleic Acids. 2009 May;28(5):424-34. doi: 10.1080/15257770903044234.
Abstract
(15)N NMR chemical shift changes in the presence of Mg(H(2)O)(6)(2+), Zn(2+), Cd(2+), and Co(NH(3))(6)(3+) were used to probe the effect of flanking bases on metal binding sites in three different RNA motifs. We found that: for GC pairs, the presence of a flanking purine creates a site for the soft metals Zn(2+) and Cd(2+) only; a GG.UU motif selectively binds only Co(NH(3))(6)(3+), while a UG.GU motif binds none of these metals; a 3' guanosine flanking the adenosine of a sheared GA.AG pair creates an unusually strong binding site that precludes binding to the cross-strand stacked guanosines within the tandem pair.
摘要
利用在Mg(H₂O)₆²⁺、Zn²⁺、Cd²⁺和Co(NH₃)₆³⁺存在下的¹⁵N核磁共振化学位移变化，来探究侧翼碱基对三种不同RNA基序中金属结合位点的影响。我们发现：对于GC碱基对，侧翼嘌呤的存在仅为软金属Zn²⁺和Cd²⁺创造了一个位点；GG.UU基序仅选择性结合Co(NH₃)₆³⁺，而UG.GU基序不结合这些金属中的任何一种；剪切后的GA.AG对中腺苷侧翼的3'鸟苷创造了一个异常强的结合位点，该位点阻止了与串联对中跨链堆积鸟苷的结合。
相似文献
1
Modulation of RNA metal binding by flanking bases: 15N NMR evaluation of GC, tandem GU, and tandem GA sites.侧翼碱基对RNA金属结合的调控：GC、串联GU和串联GA位点的15N核磁共振评估
Nucleosides Nucleotides Nucleic Acids. 2009 May;28(5):424-34. doi: 10.1080/15257770903044234.
2
RNA GG x UU motif binds K+ but not Mg2+.RNA GG x UU 基序结合钾离子而非镁离子。
J Am Chem Soc. 2005 Dec 21;127(50):17588-9. doi: 10.1021/ja0555522.
3
2-Amino-1,3-benzothiazole-6-carboxamide Preferentially Binds the Tandem Mismatch Motif r(UY:GA).2-氨基-1,3-苯并噻唑-6-甲酰胺优先结合串联错配基序 r(UY:GA)。
Biochemistry. 2020 Sep 8;59(35):3225-3234. doi: 10.1021/acs.biochem.0c00369. Epub 2020 Aug 20.
4
Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs.RNA中局部结构的堆积效应：当侧翼GC对被异鸟嘌呤-异胞嘧啶对取代时串联GA对结构的变化。
J Phys Chem B. 2007 Jun 21;111(24):6718-27. doi: 10.1021/jp068732m. Epub 2007 Apr 6.
5
Solution structure of Cobalt(III)hexammine complexed to the GAAA tetraloop, and metal-ion binding to G.A mismatches.与GAAA四环体复合的六氨合钴（III）配合物的溶液结构以及金属离子与G.A错配的结合
J Mol Biol. 2000 Feb 4;295(5):1211-23. doi: 10.1006/jmbi.1999.3421.
6
Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair.与另一个非规范碱基对相邻的含鸟苷-鸟苷碱基对的RNA内部环的热力学
Biochemistry. 2001 Feb 27;40(8):2478-83. doi: 10.1021/bi0012181.
7
Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy.通过核磁共振光谱直接鉴定RNA非经典碱基对中的N-H...N氢键。
Nucleic Acids Res. 1999 Aug 1;27(15):3104-10. doi: 10.1093/nar/27.15.3104.
8
Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures.核磁共振揭示，侧翼内部环的 GU 碱基对可以采用多种结构。
Biochemistry. 2019 Feb 26;58(8):1094-1108. doi: 10.1021/acs.biochem.8b01027. Epub 2019 Jan 31.
9
Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2).核磁共振光谱和分子模型表明，G.U碱基对可能存在不同的氢键模式：在r(GGCGUGCC)(2)中每个G.U碱基对有一个氢键，而在r(GAGUGCUC)(2)中每个G.U碱基对有两个氢键。
Biochemistry. 2000 Aug 1;39(30):8970-82.
10
NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs.r(GCAGGCGUGC)2的核磁共振结构及单个鸟嘌呤-鸟嘌呤碱基对的稳定性决定因素
Biochemistry. 2000 Sep 26;39(38):11748-62. doi: 10.1021/bi000720i.
引用本文的文献
1
Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.RNA 螺旋折叠热力学的最近邻规则：改进的末端效应。
Nucleic Acids Res. 2022 May 20;50(9):5251-5262. doi: 10.1093/nar/gkac261.
2
RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources.RPocket：一个直观的 RNA 口袋拓扑结构信息数据库，包含 RNA-配体数据资源。
BMC Bioinformatics. 2021 Sep 8;22(1):428. doi: 10.1186/s12859-021-04349-4.
3
Deflating the RNA Mg bubble. Stereochemistry to the rescue!消除RNA镁泡。立体化学来帮忙！
RNA. 2020 Dec 2;27(3):243-52. doi: 10.1261/rna.076067.120.
4
Evaluation of N-detected H-N correlation experiments on increasingly large RNAs.对越来越大的RNA进行氮检测氢-氮相关实验的评估。
J Biomol NMR. 2017 Sep;69(1):31-44. doi: 10.1007/s10858-017-0132-7. Epub 2017 Sep 6.
5
Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters.测试规范 RNA 碱基对的最近邻模型：GU 参数修订。
Biochemistry. 2012 Apr 24;51(16):3508-22. doi: 10.1021/bi3002709. Epub 2012 Apr 10.
本文引用的文献
1
Nitrogen-15 NMR spectroscopy of N-metallated nucleic acids: insights into 15N NMR parameters and N-metal bonds.N-金属化核酸的氮-15核磁共振光谱：对15N核磁共振参数和N-金属键的见解
Dalton Trans. 2008 Oct 7(37):4965-74. doi: 10.1039/b803510p. Epub 2008 Jul 9.
2
RNA dynamics: it is about time.RNA动力学：时机已到。
Curr Opin Struct Biol. 2008 Jun;18(3):321-9. doi: 10.1016/j.sbi.2008.04.004. Epub 2008 Jun 9.
3
Crystal structure of a self-spliced group II intron.一种自我剪接的II类内含子的晶体结构。
Science. 2008 Apr 4;320(5872):77-82. doi: 10.1126/science.1153803.
4
Tertiary contacts distant from the active site prime a ribozyme for catalysis.远离活性位点的三级接触为核酶的催化作用做好准备。
Cell. 2006 Jul 28;126(2):309-20. doi: 10.1016/j.cell.2006.06.036. Epub 2006 Jul 20.
5
RNA GG x UU motif binds K+ but not Mg2+.RNA GG x UU 基序结合钾离子而非镁离子。
J Am Chem Soc. 2005 Dec 21;127(50):17588-9. doi: 10.1021/ja0555522.
6
Metal ions and RNA folding: a highly charged topic with a dynamic future.金属离子与RNA折叠：一个充满活力且前景广阔的热门话题。
Curr Opin Chem Biol. 2005 Apr;9(2):104-9. doi: 10.1016/j.cbpa.2005.02.004.
7
Differential binding of Mg2+, Zn2+, and Cd2+ at two sites in a hammerhead ribozyme motif, determined by 15N NMR.通过15N核磁共振确定锤头状核酶基序中两个位点上Mg2+、Zn2+和Cd2+的差异结合。
J Am Chem Soc. 2004 Jul 28;126(29):8908-9. doi: 10.1021/ja049804v.
8
Use of 13C as an indirect tag in 15N specifically labeled nucleosides. Syntheses of [8-13C-1,7,NH2-15N3]adenosine, -guanosine, and their deoxy analogues.将¹³C用作¹⁵N特异性标记核苷中的间接标记。[8-¹³C-1,7,NH₂-¹⁵N₃]腺苷、鸟苷及其脱氧类似物的合成。
J Org Chem. 2003 Oct 31;68(22):8657-61. doi: 10.1021/jo0345446.
9
Two decades of RNA catalysis.RNA催化的二十年。
Chem Biol. 2002 Sep;9(9):961-9. doi: 10.1016/s1074-5521(02)00217-x.
10
Metal ions in the structure and function of RNA.RNA结构与功能中的金属离子
J Biol Inorg Chem. 2002 Sep;7(7-8):679-90. doi: 10.1007/s00775-002-0387-6. Epub 2002 Jul 18.
Zotero 插件