来自 R2 反转录转座子的 4x4 核苷酸 RNA 内部环的 NMR 结构：鉴定出三嘌呤-嘌呤剪切对基序，并与 MC-SYM 预测进行比较。
NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.
机构信息
Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.
出版信息
RNA. 2011 Sep;17(9):1664-77. doi: 10.1261/rna.2641911. Epub 2011 Jul 21.
Abstract
The NMR solution structure is reported of a duplex, 5'GUGAAGCCCGU/3'UCACAGGAGGC, containing a 4 × 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine-purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 5'GAA/3'AGG, 5'GAG/3'AGG, 5'GAA/3'AAG, and 5'AAG/3'AGG. The structural information is compared with predictions made with the MC-Sym program.
摘要
本文报道了来自 R2 反转录转座子 RNA 的一个 4×4 核苷酸内部环的双链体 5'GUGAAGCCCGU/3'UCACAGGAGGC 的 NMR 溶液结构。该环包含三个剪接嘌呤-嘌呤对，并揭示了在其他 RNA 中发现的结构元件，我们将其称为 3RRs 基序。双链体热力学的光学熔解测量表明，内部环在 37°C 时比预测的稳定 1.6 kcal/mol。结果表明，3RRs 基序是一个常见的结构元件，可以促进 3D 结构的预测。已知的例子包括具有配对的内部环：5'GAA/3'AGG、5'GAG/3'AGG、5'GAA/3'AAG 和 5'AAG/3'AGG。结构信息与使用 MC-Sym 程序进行的预测进行了比较。
相似文献
1
NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.来自 R2 反转录转座子的 4x4 核苷酸 RNA 内部环的 NMR 结构：鉴定出三嘌呤-嘌呤剪切对基序，并与 MC-SYM 预测进行比较。
RNA. 2011 Sep;17(9):1664-77. doi: 10.1261/rna.2641911. Epub 2011 Jul 21.
2
Molecular recognition in purine-rich internal loops: thermodynamic, structural, and dynamic consequences of purine for adenine substitutions in 5'(rGGCAAGCCU)2.富含嘌呤的内环中的分子识别：5'(rGGCAAGCCU)2中嘌呤对腺嘌呤取代的热力学、结构和动力学影响
Biochemistry. 2002 Dec 17;41(50):14978-87. doi: 10.1021/bi0203278.
3
An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA.RNA中一个交替剪切的AA对以及一个被剪切的GA对侧翼包围的单个剪切嘌呤-嘌呤对的稳定性元素。
Biochemistry. 2006 Jun 6;45(22):6889-903. doi: 10.1021/bi0524464.
4
Consecutive GA pairs stabilize medium-size RNA internal loops.连续的GA碱基对稳定中等大小的RNA内部环。
Biochemistry. 2006 Mar 28;45(12):4025-43. doi: 10.1021/bi052060t.
5
Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions.一侧由三对沃森-克里克碱基对环绕的8×8核苷酸RNA内部环的核磁共振结构及其与三维预测结果的比较
Biochemistry. 2017 Jul 25;56(29):3733-3744. doi: 10.1021/acs.biochem.7b00201. Epub 2017 Jul 12.
6
Solution structure of an RNA internal loop with three consecutive sheared GA pairs.具有三个连续剪切GA对的RNA内部环的溶液结构
Biochemistry. 2005 Mar 1;44(8):2845-56. doi: 10.1021/bi048079y.
7
Factors affecting thermodynamic stabilities of RNA 3 x 3 internal loops.影响RNA 3×3内部环热力学稳定性的因素。
Biochemistry. 2004 Oct 12;43(40):12865-76. doi: 10.1021/bi049168d.
8
Structural studies of symmetric DNA undecamers containing non-symmetrical sheared (PuGAPu):(PyGAPy) motifs.含有非对称剪切（嘌呤-鸟嘌呤-嘌呤）：（嘧啶-鸟嘌呤-嘧啶）基序的对称DNA十一聚体的结构研究
J Biomol NMR. 1999 Jun;14(2):157-67. doi: 10.1023/a:1008351213029.
9
A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops.与剪切的GA或AA对相邻的CA(+)对可稳定大小对称的RNA内部环。
Biochemistry. 2009 Jun 23;48(24):5738-52. doi: 10.1021/bi8019405.
10
Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron.卡氏肺孢子虫I组内含子中J4/5环的热力学稳定性和结构特征
Biochemistry. 2003 Dec 9;42(48):14184-96. doi: 10.1021/bi0301587.
引用本文的文献
1
Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA.用小角度 X 射线散射法对发夹结发夹 RNA 进行 RNA 力场的细化。
J Phys Chem Lett. 2022 Apr 21;13(15):3400-3408. doi: 10.1021/acs.jpclett.2c00359. Epub 2022 Apr 11.
2
Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3'-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides.核磁共振显示流感 A 病毒 7 段 mRNA 3' 剪接位点附近存在一种双发夹平衡，这种平衡可以通过寡核苷酸进行改变。
RNA. 2022 Apr;28(4):508-522. doi: 10.1261/rna.078951.121. Epub 2022 Jan 4.
3
Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs.非canonical 碱基配对对 RNA 折叠的影响：G·A 对的结构上下文和空间排列。
Biochemistry. 2019 May 21;58(20):2474-2487. doi: 10.1021/acs.biochem.9b00122. Epub 2019 May 8.
4
Blind prediction of noncanonical RNA structure at atomic accuracy.原子精度的非规范 RNA 结构的盲预测。
Sci Adv. 2018 May 25;4(5):eaar5316. doi: 10.1126/sciadv.aar5316. eCollection 2018 May.
5
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.分子模拟捕捉到的 RNA 结构动力学：全面概述。
Chem Rev. 2018 Apr 25;118(8):4177-4338. doi: 10.1021/acs.chemrev.7b00427. Epub 2018 Jan 3.
6
Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions.一侧由三对沃森-克里克碱基对环绕的8×8核苷酸RNA内部环的核磁共振结构及其与三维预测结果的比较
Biochemistry. 2017 Jul 25;56(29):3733-3744. doi: 10.1021/acs.biochem.7b00201. Epub 2017 Jul 12.
7
Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server.使用罗塞塔FARFAR服务器对小型非规范RNA基序进行建模。
Methods Mol Biol. 2016;1490:187-98. doi: 10.1007/978-1-4939-6433-8_12.
8
Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus.甲型流感病毒8号基因组裸片段RNA的自我折叠
PLoS One. 2016 Feb 5;11(2):e0148281. doi: 10.1371/journal.pone.0148281. eCollection 2016.
9
RNA Structures as Mediators of Neurological Diseases and as Drug Targets.RNA结构作为神经疾病的介质及药物靶点
Neuron. 2015 Jul 1;87(1):28-46. doi: 10.1016/j.neuron.2015.06.012.
10
Structural features of a 3' splice site in influenza a.甲型流感病毒3'剪接位点的结构特征。
Biochemistry. 2015 Jun 2;54(21):3269-85. doi: 10.1021/acs.biochem.5b00012. Epub 2015 May 21.
本文引用的文献
1
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.用于RNA模拟的分子力学力场的性能：UUCG和GNRA发夹的稳定性
J Chem Theory Comput. 2010 Dec 14;6(12):3836-3849. doi: 10.1021/ct100481h. Epub 2010 Nov 9.
2
YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models.YUP：用于粗粒度和多尺度模型的分子模拟程序。
J Chem Theory Comput. 2006 May 1;2(3):529-540. doi: 10.1021/ct050323r. Epub 2006 Mar 18.
3
Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints.基于二级结构和低分辨率限制条件的自动化RNA三级结构预测
J Comput Chem. 2011 Jul 30;32(10):2232-44. doi: 10.1002/jcc.21806. Epub 2011 Apr 21.
4
Optical melting measurements of nucleic acid thermodynamics.核酸热力学的光学熔解测量
Methods Enzymol. 2009;468:371-87. doi: 10.1016/S0076-6879(09)68017-4. Epub 2009 Nov 17.
5
Analysis of (1)H chemical shifts in DNA: Assessment of the reliability of (1)H chemical shift calculations for use in structure refinement.分析 DNA 中的（1）H 化学位移：评估（1）H 化学位移计算在结构精修中的可靠性。
J Biomol NMR. 1997 Dec;10(4):337-50. doi: 10.1023/A:1018348123074.
6
HiRE-RNA: a high resolution coarse-grained energy model for RNA.HiRE-RNA：一种用于 RNA 的高分辨率粗粒度能量模型。
J Phys Chem B. 2010 Sep 23;114(37):11957-66. doi: 10.1021/jp102497y.
7
Folding and finding RNA secondary structure.折叠和发现 RNA 二级结构。
Cold Spring Harb Perspect Biol. 2010 Dec;2(12):a003665. doi: 10.1101/cshperspect.a003665. Epub 2010 Aug 4.
8
RNA structure determination using SAXS data.使用 SAXS 数据进行 RNA 结构测定。
J Phys Chem B. 2010 Aug 12;114(31):10039-48. doi: 10.1021/jp1057308.
9
Turning limited experimental information into 3D models of RNA.将有限的实验信息转化为 RNA 的 3D 模型。
RNA. 2010 Sep;16(9):1769-78. doi: 10.1261/rna.2112110. Epub 2010 Jul 22.
10
Predicting and modeling RNA architecture.预测和建模 RNA 结构。
Cold Spring Harb Perspect Biol. 2011 Feb 1;3(2):a003632. doi: 10.1101/cshperspect.a003632.
Zotero 插件