RNA折叠导致二级结构重排。
RNA folding causes secondary structure rearrangement.
作者信息
Wu M, Tinoco I
机构信息
Department of Chemistry, University of California, Berkeley, and Structural Biology Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-1460, USA.
出版信息
Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11555-60. doi: 10.1073/pnas.95.20.11555.
Abstract
The secondary structure of the P5abc subdomain (a 56-nt RNA) of the Tetrahymena thermophila group I intron ribozyme has been determined by NMR. Its base pairing in aqueous solution in the absence of magnesium ions is significantly different from the RNA in a crystal but is consistent with thermodynamic predictions. On addition of magnesium ions, the RNA folds into a tertiary structure with greatly changed base pairing consistent with the crystal structure: three Watson-Crick base pairs, three G.U base pairs, and an extra-stable tetraloop are lost. The common assumption that RNA folds by first forming secondary structure and then forming tertiary interactions from the unpaired bases is not always correct.
摘要
嗜热四膜虫I组内含子核酶的P5abc亚结构域（一种56个核苷酸的RNA）的二级结构已通过核磁共振确定。在没有镁离子的水溶液中，其碱基配对与晶体中的RNA有显著差异，但与热力学预测一致。加入镁离子后，RNA折叠成三级结构，碱基配对发生了很大变化，与晶体结构一致：三个沃森-克里克碱基对、三个G·U碱基对和一个超稳定四环消失。RNA先形成二级结构，然后从不配对的碱基形成三级相互作用的常见假设并不总是正确的。
相似文献
1
RNA folding causes secondary structure rearrangement.RNA折叠导致二级结构重排。
Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11555-60. doi: 10.1073/pnas.95.20.11555.
2
Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme.嗜热四膜虫核酶的单价离子介导折叠
J Mol Biol. 2004 Oct 1;342(5):1431-42. doi: 10.1016/j.jmb.2004.07.092.
3
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.
4
New pathways in folding of the Tetrahymena group I RNA enzyme.嗜热四膜虫I组RNA酶折叠的新途径。
J Mol Biol. 1999 Sep 3;291(5):1155-67. doi: 10.1006/jmbi.1999.3026.
5
Perturbation of the hierarchical folding of a large RNA by the destabilization of its Scaffold's tertiary structure.通过其支架三级结构的去稳定化对大型RNA的分层折叠进行扰动。
J Mol Biol. 2005 Nov 25;354(2):483-96. doi: 10.1016/j.jmb.2005.09.032. Epub 2005 Sep 30.
6
Hinge stiffness is a barrier to RNA folding.铰链刚度是RNA折叠的一个障碍。
J Mol Biol. 2008 Jun 13;379(4):859-70. doi: 10.1016/j.jmb.2008.04.013. Epub 2008 Apr 10.
7
Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group I ribozyme.P5abc中GNRA四环的形成会破坏嗜热四膜虫I组核酶中的结构域间相互作用。
Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):3695-700. doi: 10.1073/pnas.051608598.
8
Quantifying the energetic interplay of RNA tertiary and secondary structure interactions.量化RNA三级结构与二级结构相互作用之间的能量相互作用。
RNA. 1999 Dec;5(12):1665-74. doi: 10.1017/s1355838299991823.
9
Native secondary structure formation in RNA may be a slave to tertiary folding.RNA中天然二级结构的形成可能受三级折叠的支配。
Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11506-8. doi: 10.1073/pnas.95.20.11506.
10
Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme.I组核酶中异常稳定的RNA三级界面的组装。
Biochemistry. 1999 Mar 9;38(10):2982-90. doi: 10.1021/bi982113p.
引用本文的文献
1
Observation of SAM-VI Riboswitch Dynamics Using Single-Molecule FRET.利用单分子荧光共振能量转移观察SAM-VI核糖开关动力学
Biomolecules. 2025 Jun 9;15(6):841. doi: 10.3390/biom15060841.
2
The role of water in mediating DNA structures with epigenetic modifications, higher-order conformations and drug-DNA interactions.水在介导具有表观遗传修饰、高级构象及药物 -DNA 相互作用的 DNA 结构中的作用。
RSC Chem Biol. 2025 Mar 14;6(5):699-720. doi: 10.1039/d4cb00308j. eCollection 2025 May 8.
3
Origin of ribonucleotide recognition motifs through ligand mimicry at early earth.通过早期地球上的配体模拟识别核苷酸识别基序的起源。
RNA Biol. 2024 Jan;21(1):107-121. doi: 10.1080/15476286.2024.2423149. Epub 2024 Nov 11.
4
Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time.一次一个分子观察由能量和拓扑约束引起的核酶折叠和错误折叠的离子驱动动力学。
Nucleic Acids Res. 2023 Oct 27;51(19):10737-10751. doi: 10.1093/nar/gkad755.
5
A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript.一个功能性 SNP 通过动态重塑与启动子相关的非编码 RNA 转录本的 3D 结构来调节 E-钙黏蛋白的表达。
Nucleic Acids Res. 2022 Oct 28;50(19):11331-11343. doi: 10.1093/nar/gkac875.
6
Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts.由于电荷密度变化导致的离子与RNA结合模式的差异解释了RNA在单价盐中的稳定性。
Sci Adv. 2022 Jul 22;8(29):eabo1190. doi: 10.1126/sciadv.abo1190. Epub 2022 Jul 20.
7
Magnetization Transfer to Enhance NOE Cross-Peaks among Labile Protons: Applications to Imino-Imino Sequential Walks in SARS-CoV-2-Derived RNAs.利用磁化转移增强不稳定质子间的核欧沃豪斯效应交叉峰：应用于严重急性呼吸综合征冠状病毒2（SARS-CoV-2）衍生RNA中的亚氨基-亚氨基序列步移
Angew Chem Weinheim Bergstr Ger. 2021 May 17;133(21):11991-11998. doi: 10.1002/ange.202015948. Epub 2021 May 1.
8
3D Heteronuclear Magnetization Transfers for the Establishment of Secondary Structures in SARS-CoV-2-Derived RNAs.3D 异核磁化转移在 SARS-CoV-2 衍生 RNA 二级结构建立中的应用。
J Am Chem Soc. 2021 Apr 7;143(13):4942-4948. doi: 10.1021/jacs.1c01914. Epub 2021 Mar 30.
9
Magnetization Transfer to Enhance NOE Cross-Peaks among Labile Protons: Applications to Imino-Imino Sequential Walks in SARS-CoV-2-Derived RNAs.磁化转移增强不稳定质子之间的 NOE 交叉峰：在 SARS-CoV-2 衍生 RNA 中的亚氨基-亚氨基顺序行走中的应用。
Angew Chem Int Ed Engl. 2021 May 17;60(21):11884-11891. doi: 10.1002/anie.202015948. Epub 2021 May 4.
10
Different views of the dynamic landscape covered by the 5'-hairpin of the 7SK small nuclear RNA.7SK 小核 RNA 5’-发夹结构覆盖的动态景观的不同视角。
RNA. 2020 Sep;26(9):1184-1197. doi: 10.1261/rna.074955.120. Epub 2020 May 19.
本文引用的文献
1
RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting.通过同步加速器羟基自由基足迹法以毫秒间隔进行RNA折叠
Science. 1998 Mar 20;279(5358):1940-3. doi: 10.1126/science.279.5358.1940.
2
Solution structure of a GAAA tetraloop receptor RNA.一种GAAA四环受体RNA的溶液结构
EMBO J. 1997 Dec 15;16(24):7490-9. doi: 10.1093/emboj/16.24.7490.
3
Solution conformation of a five-nucleotide RNA bulge loop from a group I intron.来自I组内含子的一个五核苷酸RNA凸起环的溶液构象。
Biochemistry. 1997 Aug 19;36(33):10246-55. doi: 10.1021/bi9701540.
4
A magnesium ion core at the heart of a ribozyme domain.位于核酶结构域核心的镁离子。
Nat Struct Biol. 1997 Jul;4(7):553-8. doi: 10.1038/nsb0797-553.
5
The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement.HIV TAR发夹环与其互补序列形成的RNA“亲吻”发夹复合物的结构。
J Mol Biol. 1997 May 30;269(1):52-66. doi: 10.1006/jmbi.1997.1021.
6
The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core.P4 - P6结构域指导嗜热四膜虫核酶核心的高级折叠。
Biochemistry. 1997 Mar 18;36(11):3159-69. doi: 10.1021/bi962428+.
7
Metal-binding sites in the major groove of a large ribozyme domain.一个大型核酶结构域大沟中的金属结合位点。
Structure. 1996 Oct 15;4(10):1221-9. doi: 10.1016/s0969-2126(96)00129-3.
8
RNA tertiary structure mediation by adenosine platforms.腺苷平台介导的RNA三级结构
Science. 1996 Sep 20;273(5282):1696-9. doi: 10.1126/science.273.5282.1696.
9
Crystal structure of a group I ribozyme domain: principles of RNA packing.I类核酶结构域的晶体结构：RNA堆积原理
Science. 1996 Sep 20;273(5282):1678-85. doi: 10.1126/science.273.5282.1678.
Zotero 插件