使用GNRA/受体相互作用模块对DSL连接酶核酶进行合理优化。
Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules.
作者信息
Ishikawa Junya, Matsumura Shigeyoshi, Jaeger Luc, Inoue Tan, Furuta Hiroyuki, Ikawa Yoshiya
机构信息
Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan.
出版信息
Arch Biochem Biophys. 2009 Oct 15;490(2):163-70. doi: 10.1016/j.abb.2009.08.020. Epub 2009 Sep 1.
Abstract
The DSL ribozyme is a class of artificial ligase ribozymes with a highly modular architecture, which catalyzes template-directed RNA ligation on a helical substrate module that can be either covalently connected (cis-DSL) or physically separated (trans-DSL) from the catalytic module. Substrate recognition by the catalytic module is promoted by one or two sets of GNRA/receptor interactions acting as clamps in the cis or trans configurations, respectively. In this study, we have rationally designed and analyzed the catalytic and self-assembly properties of several trans-DSL ribozymes with different sets of natural and artificial GNRA-receptor clamps. Two variants newly designed in this study showed significantly enhanced catalytic properties with respect of the original trans-DSL construct. While this work allows dissection of the turnover and catalytic properties of the trans-DSL ribozyme, it also emphasizes the remarkable modularity of RNA tertiary structure for nano-construction of complex functions.
摘要
DSL核酶是一类具有高度模块化结构的人工连接酶核酶，它催化在螺旋底物模块上进行模板导向的RNA连接，该底物模块可以与催化模块共价连接（顺式DSL）或物理分离（反式DSL）。催化模块对底物的识别分别由一组或两组GNRA/受体相互作用促进，这些相互作用在顺式或反式构型中分别起夹子的作用。在本研究中，我们合理设计并分析了几种具有不同天然和人工GNRA-受体夹子组合的反式DSL核酶的催化和自组装特性。本研究新设计的两个变体相对于原始的反式DSL构建体显示出显著增强的催化特性。虽然这项工作有助于剖析反式DSL核酶的周转和催化特性，但它也强调了RNA三级结构在构建复杂功能纳米结构方面的显著模块化。
相似文献
1
Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules.使用GNRA/受体相互作用模块对DSL连接酶核酶进行合理优化。
Arch Biochem Biophys. 2009 Oct 15;490(2):163-70. doi: 10.1016/j.abb.2009.08.020. Epub 2009 Sep 1.
2
Coordinated control of a designed trans-acting ligase ribozyme by a loop-receptor interaction.通过环-受体相互作用对设计的反式作用连接酶核酶进行协同控制。
FEBS Lett. 2009 Sep 3;583(17):2819-26. doi: 10.1016/j.febslet.2009.07.036. Epub 2009 Jul 23.
3
Tailoring RNA modular units on a common scaffold: a modular ribozyme with a catalytic unit for beta-nicotinamide mononucleotide-activated RNA ligation.在通用支架上定制RNA模块化单元：一种具有催化单元的模块化核酶，用于β-烟酰胺单核苷酸激活的RNA连接。
RNA. 2009 May;15(5):877-88. doi: 10.1261/rna.1461309. Epub 2009 Mar 23.
4
Structural and biochemical characterization of DSL ribozyme.DSL核酶的结构与生化特性
Biochem Biophys Res Commun. 2006 Jan 6;339(1):115-21. doi: 10.1016/j.bbrc.2005.11.007. Epub 2005 Nov 9.
5
Concerted effects of two activator modules on the group I ribozyme reaction.两个激活模块对I组核酶反应的协同作用。
J Biochem. 2009 Apr;145(4):429-35. doi: 10.1093/jb/mvn183. Epub 2009 Jan 3.
6
Redesign of an artificial ligase ribozyme based on the analysis of its structural elements.基于结构元件分析的人工连接酶核酶的重新设计。
RNA Biol. 2005 Oct-Dec;2(4):137-42. doi: 10.4161/rna.2.4.2302. Epub 2005 Nov 9.
7
RNA-catalyzed RNA ligation on an external RNA template.在外部RNA模板上进行RNA催化的RNA连接反应。
Chem Biol. 2002 Mar;9(3):297-307. doi: 10.1016/s1074-5521(02)00110-2.
8
The antisense sequence of the HIV-1 TAR stem-loop structure covalently linked to the hairpin ribozyme enhances its catalytic activity against two artificial substrates.与发夹状核酶共价连接的HIV-1 TAR茎环结构的反义序列增强了其对两种人工底物的催化活性。
Antisense Nucleic Acid Drug Dev. 1999 Feb;9(1):33-42. doi: 10.1089/oli.1.1999.9.33.
9
Efficient RNA ligation by reverse-joined hairpin ribozymes and engineering of twin ribozymes consisting of conventional and reverse-joined hairpin ribozyme units.通过反向连接的发夹状核酶实现高效RNA连接以及由常规和反向连接的发夹状核酶单元组成的双核酶工程。
FEBS J. 2005 Sep;272(17):4464-74. doi: 10.1111/j.1742-4658.2005.04865.x.
10
Installation of orthogonality to the interface that assembles two modular domains in the Tetrahymena group I ribozyme.正交安装到接口上，组装四膜虫组 I 核酶的两个模块域。
J Biosci Bioeng. 2014 Apr;117(4):407-12. doi: 10.1016/j.jbiosc.2013.10.008. Epub 2013 Nov 8.
引用本文的文献
1
Minimizing amplification bias during reverse transcription for in vitro selections.最小化体外选择中逆转录时的扩增偏倚。
RNA. 2023 Aug;29(8):1301-1315. doi: 10.1261/rna.079650.123. Epub 2023 May 16.
2
In vitro selected GUAA tetraloop-binding receptors with structural plasticity and evolvability towards natural RNA structural modules.具有结构可塑性和对天然 RNA 结构模块的进化能力的体外选择 GUAA 四链体结合受体。
Nucleic Acids Res. 2021 Feb 26;49(4):2289-2305. doi: 10.1093/nar/gkab021.
3
Responsive self-assembly of tectoRNAs with loop-receptor interactions from the tetrahydrofolate (THF) riboswitch.四氢叶酸（THF）核糖开关中环受体相互作用的 tectoRNA 响应性自组装。
Nucleic Acids Res. 2019 Jul 9;47(12):6439-6451. doi: 10.1093/nar/gkz304.
4
Artificial RNA Motifs Expand the Programmable Assembly between RNA Modules of a Bimolecular Ribozyme Leading to Application to RNA Nanostructure Design.人工RNA基序扩展了双分子核酶RNA模块之间的可编程组装，从而应用于RNA纳米结构设计。
Biology (Basel). 2017 Oct 30;6(4):37. doi: 10.3390/biology6040037.
5
An in vitro-selected RNA receptor for the GAAC loop: modular receptor for non-GNRA-type tetraloop.一种体外选择的 GAAC 环 RNA 受体：非 GNRA 型四链体的模块化受体。
Nucleic Acids Res. 2013 Apr 1;41(6):3748-59. doi: 10.1093/nar/gkt040. Epub 2013 Feb 4.
6
Fixation and accumulation of thermotolerant catalytic competence of a pair of ligase ribozymes through complex formation and cross ligation.通过形成复合物和交叉连接固定和积累一对连接酶核酶的耐热催化能力。
J Mol Evol. 2013 Feb;76(1-2):48-58. doi: 10.1007/s00239-012-9536-x. Epub 2013 Jan 4.
7
Generation and development of RNA ligase ribozymes with modular architecture through "design and selection".通过“设计与选择”生成并开发具有模块化结构的 RNA 连接酶核酶
Molecules. 2010 Aug 26;15(9):5850-65. doi: 10.3390/molecules15095850.
8
Self-replication reactions dependent on tertiary interaction motifs in an RNA ligase ribozyme.依赖于 RNA 连接酶核酶中三级相互作用模体的自我复制反应。
J Mol Evol. 2011 Oct;73(3-4):221-9. doi: 10.1007/s00239-011-9471-2. Epub 2011 Nov 12.
9
Computational generation and screening of RNA motifs in large nucleotide sequence pools.在大型核苷酸序列库中计算生成和筛选 RNA 基序。
Nucleic Acids Res. 2010 Jul;38(13):e139. doi: 10.1093/nar/gkq282. Epub 2010 May 6.
10
Evolutionary optimization of a modular ligase ribozyme: a small catalytic unit and a hairpin motif masking an element that could form an inactive structure.模块化连接酶核酶的进化优化：一个小的催化单元和一个发夹基序掩盖了一个可能形成无活性结构的元件。
Nucleic Acids Res. 2010 Jun;38(10):3328-39. doi: 10.1093/nar/gkq018. Epub 2010 Jan 27.
本文引用的文献
1
Coordinated control of a designed trans-acting ligase ribozyme by a loop-receptor interaction.通过环-受体相互作用对设计的反式作用连接酶核酶进行协同控制。
FEBS Lett. 2009 Sep 3;583(17):2819-26. doi: 10.1016/j.febslet.2009.07.036. Epub 2009 Jul 23.
2
Tailoring RNA modular units on a common scaffold: a modular ribozyme with a catalytic unit for beta-nicotinamide mononucleotide-activated RNA ligation.在通用支架上定制RNA模块化单元：一种具有催化单元的模块化核酶，用于β-烟酰胺单核苷酸激活的RNA连接。
RNA. 2009 May;15(5):877-88. doi: 10.1261/rna.1461309. Epub 2009 Mar 23.
3
Square-shaped RNA particles from different RNA folds.来自不同RNA折叠结构的方形RNA颗粒。
Nano Lett. 2009 Mar;9(3):1270-7. doi: 10.1021/nl900261h.
4
A designed RNA selection: establishment of a stable complex between a target and selectant RNA via two coordinated interactions.一种设计的RNA筛选：通过两种协同相互作用在靶标RNA和选择剂RNA之间建立稳定复合物。
Nucleic Acids Res. 2009 Feb;37(3):e23. doi: 10.1093/nar/gkn1012. Epub 2009 Jan 9.
5
The UA_handle: a versatile submotif in stable RNA architectures.UA_handle：稳定RNA结构中的一种通用亚基序。
Nucleic Acids Res. 2009 Jan;37(1):215-30. doi: 10.1093/nar/gkn911. Epub 2008 Nov 26.
6
Evolutionary origins and directed evolution of RNA.RNA的进化起源与定向进化
Int J Biochem Cell Biol. 2009 Feb;41(2):254-65. doi: 10.1016/j.biocel.2008.08.015. Epub 2008 Aug 19.
7
Synthetic biology with RNA motifs.具有RNA基序的合成生物学。
Int J Biochem Cell Biol. 2009 Feb;41(2):398-404. doi: 10.1016/j.biocel.2008.08.017. Epub 2008 Aug 19.
8
Selection of a novel class of RNA-RNA interaction motifs based on the ligase ribozyme with defined modular architecture.基于具有明确模块化结构的连接酶核酶，筛选一类新型的RNA-RNA相互作用基序。
Nucleic Acids Res. 2008 Jun;36(11):3600-7. doi: 10.1093/nar/gkn206. Epub 2008 May 6.
9
Facile syntheses of BODIPY derivatives for fluorescent labeling of the 3' and 5' ends of RNAs.用于RNA 3'和5'末端荧光标记的BODIPY衍生物的简便合成方法。
Anal Biochem. 2008 Jul 15;378(2):166-70. doi: 10.1016/j.ab.2008.03.054. Epub 2008 Apr 12.
10
Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors.天然及体外筛选的GNRA四环结合受体的综合特征
Nucleic Acids Res. 2008 Mar;36(4):1138-52. doi: 10.1093/nar/gkm1048. Epub 2007 Dec 23.
Zotero 插件