RNA构象开关的动力学
Kinetics of an RNA conformational switch.
作者信息
LeCuyer K A, Crothers D M
机构信息
Department of Chemistry, Yale University, New Haven, CT 06511.
出版信息
Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3373-7. doi: 10.1073/pnas.91.8.3373.
Abstract
The spliced leader RNA from Leptomonas collosoma has two competing secondary structures of nearly equal free energy. Short, complementary oligonucleotides can drive the structure from one form of the other. We report stopped-flow rapid-mixing and temperature-jump measurements of the kinetics of the structural switch. At high concentrations of oligonucleotide, the rate of binding becomes limited by the rate of the structural switch, which occurs on a time scale of a fraction of a second. The low activation energy observed for the process implies a branch migration type of mechanism in which portions of the two competing helices transiently coexist.
摘要
来自巨大细滴虫的剪接前导RNA具有两种自由能几乎相等的相互竞争的二级结构。短的互补寡核苷酸可以促使结构从一种形式转变为另一种形式。我们报告了对结构转换动力学的停流快速混合和温度跃变测量。在高浓度寡核苷酸条件下，结合速率受结构转换速率的限制，结构转换发生在几分之一秒的时间尺度上。该过程观察到的低活化能意味着一种分支迁移类型的机制，即两个相互竞争的螺旋部分会短暂共存。
相似文献
1
Kinetics of an RNA conformational switch.RNA构象开关的动力学
Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3373-7. doi: 10.1073/pnas.91.8.3373.
2
The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms.粗短细滴虫剪接前导RNA可在两种交替的结构形式之间转换。
Biochemistry. 1993 May 25;32(20):5301-11. doi: 10.1021/bi00071a004.
3
4
5
RNA folding pathways and kinetics using 2D energy landscapes.利用二维能量景观的RNA折叠途径与动力学
J Math Biol. 2015 Jan;70(1-2):173-96. doi: 10.1007/s00285-014-0760-4. Epub 2014 Feb 12.
6
Stable transfection in the monogenetic trypanosomatid Leptomonas collosoma--transcription barrier of heterologous trypanosomatid SL RNA genes and expression of a chimeric SL RNA molecule.单基因锥虫Leptomonas collosoma中的稳定转染——异源锥虫SL RNA基因的转录障碍及嵌合SL RNA分子的表达
Exp Parasitol. 1996 Oct;84(1):28-41. doi: 10.1006/expr.1996.0087.
7
A family of target site-specific retrotransposons interrupts spliced leader RNA genes in trypanosomatids.一类靶位点特异性逆转座子打断了锥虫中的剪接前导RNA基因。
J Parasitol. 1993 Oct;79(5):645-51.
8
The spliced leader RNA gene of Leptomonas collosoma.巨大细滴虫的剪接前导RNA基因。
Exp Parasitol. 1995 Mar;80(2):333-8. doi: 10.1006/expr.1995.1041.
9
Sequence and structural characterization of the spliced leader genes and transcripts in Phytomonas.植滴虫中剪接前导基因和转录本的序列及结构特征
Mol Biochem Parasitol. 1995 Nov;74(2):233-7. doi: 10.1016/0166-6851(95)02496-4.
10
Structure-function analysis of the trypanosomatid spliced leader RNA.锥虫剪接前导RNA的结构-功能分析
Nucleic Acids Res. 1998 May 1;26(9):2200-7. doi: 10.1093/nar/26.9.2200.
引用本文的文献
1
A transient intermediate RNA structure underlies the regulatory function of the TPP translational riboswitch.一种瞬时中间 RNA 结构为 TPP 翻译核糖体开关的调控功能提供了基础。
RNA. 2023 Nov;29(11):1658-1672. doi: 10.1261/rna.079427.122. Epub 2023 Jul 7.
2
Tuning strand displacement kinetics enables programmable ZTP riboswitch dynamic range in vivo.调控链位移动力学使可编程 ZTP 核糖开关在体内具有动态范围。
Nucleic Acids Res. 2023 Apr 11;51(6):2891-2903. doi: 10.1093/nar/gkad110.
3
IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations.IndelsRNAmute：预测有害的多点取代和插入缺失突变。
BMC Bioinformatics. 2022 Oct 14;23(Suppl 8):424. doi: 10.1186/s12859-022-04943-0.
4
How does RNA fold dynamically?RNA 如何动态折叠？
J Mol Biol. 2022 Sep 30;434(18):167665. doi: 10.1016/j.jmb.2022.167665. Epub 2022 Jun 1.
5
Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.转录共转录 RNA 链交换是嘌呤感应转录核糖开关基因调控机制的基础。
Nucleic Acids Res. 2022 Nov 28;50(21):12001-12018. doi: 10.1093/nar/gkac102.
6
Simulation of Folding Kinetics for Aligned RNAs.模拟 RNA 有序折叠的动力学。
Genes (Basel). 2021 Feb 26;12(3):347. doi: 10.3390/genes12030347.
7
Requirements for efficient ligand-gated co-transcriptional switching in designed variants of the B. subtilis pbuE adenine-responsive riboswitch in E. coli.在大肠杆菌中设计的枯草芽孢杆菌 pbuE 腺嘌呤响应型核糖开关的有效配体门控共转录开关的要求。
PLoS One. 2020 Dec 1;15(12):e0243155. doi: 10.1371/journal.pone.0243155. eCollection 2020.
8
How to measure and evaluate binding affinities.如何测量和评估结合亲和力。
Elife. 2020 Aug 6;9:e57264. doi: 10.7554/eLife.57264.
9
A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control.ZTP 核糖开关转录调控的配体门控链置换机制。
Nat Chem Biol. 2019 Nov;15(11):1067-1076. doi: 10.1038/s41589-019-0382-7. Epub 2019 Oct 21.
10
Probing RNA structure and interaction dynamics at the single molecule level.在单分子水平上探测 RNA 结构和相互作用动力学。
Methods. 2019 Jun 1;162-163:3-11. doi: 10.1016/j.ymeth.2019.04.002. Epub 2019 Apr 3.
本文引用的文献
1
THE KINETICS OF DOUBLE HELIX FORMATION FROM POLYRIBOADENYLIC ACID AND POLYRIBOURIDYLIC ACID.聚腺苷酸与聚尿苷酸形成双螺旋的动力学
Proc Natl Acad Sci U S A. 1960 Oct;46(10):1360-5. doi: 10.1073/pnas.46.10.1360.
2
The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms.粗短细滴虫剪接前导RNA可在两种交替的结构形式之间转换。
Biochemistry. 1993 May 25;32(20):5301-11. doi: 10.1021/bi00071a004.
3
Reconstitution of Bacillus subtilis trp attenuation in vitro with TRAP, the trp RNA-binding attenuation protein.利用色氨酸 RNA 结合衰减蛋白（TRAP）在体外重建枯草芽孢杆菌色氨酸衰减调控机制。
Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):133-7. doi: 10.1073/pnas.90.1.133.
4
Escherichia coli phenylalanyl-tRNA synthetase operon region. Evidence for an attenuation mechanism. Identification of the gene for the ribosomal protein L20.大肠杆菌苯丙氨酰 - tRNA合成酶操纵子区域。衰减机制的证据。核糖体蛋白L20基因的鉴定。
J Mol Biol. 1983 Dec 15;171(3):239-61. doi: 10.1016/0022-2836(83)90092-x.
5
Relaxation kinetics of dimer formation by self complementary oligonucleotides.自互补寡核苷酸形成二聚体的弛豫动力学
J Mol Biol. 1971 Dec 14;62(2):383-401. doi: 10.1016/0022-2836(71)90434-7.
6
Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic--oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH.协同非酶碱基识别。3. 酸性pH条件下，寡聚核糖尿苷酸-寡聚核糖腺苷酸系统及单独的寡聚核糖腺苷酸螺旋-卷曲转变的动力学。
J Mol Biol. 1971 Dec 14;62(2):361-81. doi: 10.1016/0022-2836(71)90433-5.
7
Conformational changes of transfer ribonucleic acid. Relaxation kinetics of the early melting transition of methionine transfer ribonucleic acid (Escherichia coli).转移核糖核酸的构象变化。甲硫氨酸转移核糖核酸（大肠杆菌）早期解链转变的弛豫动力学。
Biochemistry. 1972 Nov 7;11(23):4368-74. doi: 10.1021/bi00773a025.
8
Identification of a novel Y branch structure as an intermediate in trypanosome mRNA processing: evidence for trans splicing.鉴定一种新型Y分支结构作为锥虫mRNA加工过程中的中间体：反式剪接的证据。
Cell. 1986 Nov 21;47(4):517-25. doi: 10.1016/0092-8674(86)90616-1.
9
Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates.使用T7 RNA聚合酶和合成DNA模板进行寡核糖核苷酸合成。
Nucleic Acids Res. 1987 Nov 11;15(21):8783-98. doi: 10.1093/nar/15.21.8783.
10
Evidence for trans splicing in trypanosomes.锥虫中反式剪接的证据。
Cell. 1986 Nov 21;47(4):527-35. doi: 10.1016/0092-8674(86)90617-3.
Zotero 插件