使用化学试剂和酶探测RNA结构。
Probing RNA structure with chemical reagents and enzymes.
作者信息
Ziehler W A, Engelke D R
机构信息
University of Michigan, Ann Arbor, Michigan, USA.
出版信息
Curr Protoc Nucleic Acid Chem. 2001 May;Chapter 6:Unit 6.1. doi: 10.1002/0471142700.nc0601s00.
Abstract
This unit provides thorough coverage of the most useful chemical and enzyme probes that can be used to examine RNA secondary and tertiary structure. Footprinting methods are presented using dimethyl sulfate, diethyl pyrocarbonate, ethylnitrosourea, kethoxal, CMCT, and nucleases. For chemical probes, both strand scission and primer extension detection protocols are included.
摘要
本单元全面介绍了可用于检测RNA二级和三级结构的最有用的化学和酶探针。介绍了使用硫酸二甲酯、焦碳酸二乙酯、乙基亚硝基脲、乙二醛、CMCT和核酸酶的足迹法。对于化学探针，还包括链断裂和引物延伸检测方案。
相似文献
1
Probing RNA structure with chemical reagents and enzymes.使用化学试剂和酶探测RNA结构。
Curr Protoc Nucleic Acid Chem. 2001 May;Chapter 6:Unit 6.1. doi: 10.1002/0471142700.nc0601s00.
2
RNA Secondary Structure Study by Chemical Probing Methods Using DMS and CMCT.使用 DMS 和 CMCT 的化学探测方法研究 RNA 二级结构。
Methods Mol Biol. 2021;2300:241-250. doi: 10.1007/978-1-0716-1386-3_18.
3
The interplay between molecular flexibility and RNA chemical probing reactivities analyzed at the nucleotide level via an extensive molecular dynamics study.通过广泛的分子动力学研究，在核苷酸水平上分析分子柔性和 RNA 化学探测反应性之间的相互作用。
Methods. 2019 Jun 1;162-163:108-127. doi: 10.1016/j.ymeth.2019.05.021. Epub 2019 May 27.
4
5'-end labeling of RNA with [γ-32P]ATP and T4 polynucleotide kinase.使用[γ-32P]ATP和T4多核苷酸激酶对RNA进行5'末端标记。
Cold Spring Harb Protoc. 2014 Apr 1;2014(4):441-3. doi: 10.1101/pdb.prot080739.
5
RNA Remodeling by RNA Chaperones Monitored by RNA Structure Probing.通过RNA结构探测监测RNA伴侣介导的RNA重塑
Methods Mol Biol. 2020;2106:179-192. doi: 10.1007/978-1-0716-0231-7_11.
6
RNA Structure Analysis by Chemical Probing with DMS and CMCT.通过二甲基亚砜（DMS）和N-环己基-N′-（2-吗啉乙基）碳二亚胺对甲苯磺酸盐（CMCT）进行化学探针分析RNA结构
Methods Mol Biol. 2020;2106:209-223. doi: 10.1007/978-1-0716-0231-7_13.
7
Mapping RNA structure in vitro using nucleobase-specific probes.使用碱基特异性探针在体外绘制RNA结构
Methods Mol Biol. 2014;1086:79-94. doi: 10.1007/978-1-62703-667-2_5.
8
Efficient 5'-end labeling of oligonucleotides containing self-complementary sequences.含自身互补序列的寡核苷酸的高效5'末端标记
Biotechniques. 1997 Oct;23(4):658-60. doi: 10.2144/97234bm25.
9
RNA footprinting and modification interference analysis.RNA足迹法与修饰干扰分析。
Methods Mol Biol. 1999;118:73-91. doi: 10.1385/1-59259-676-2:73.
10
Quantification of DNA probes on nylon microarrays using T4 polynucleotide kinase labeling.使用T4多核苷酸激酶标记法对尼龙微阵列上的DNA探针进行定量分析。
Biotechniques. 2003 Aug;35(2):262-4, 266. doi: 10.2144/03352bm03.
引用本文的文献
1
Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments.研究RNA结构动力学与RNA化学探测实验之间的相互作用。
Nucleic Acids Res. 2025 Apr 10;53(7). doi: 10.1093/nar/gkaf290.
2
Bioorthogonal Cyclopropenones for Investigating RNA Structure.用于研究RNA结构的生物正交环丙烯酮
ACS Chem Biol. 2024 Dec 20;19(12):2406-2411. doi: 10.1021/acschembio.4c00633. Epub 2024 Dec 6.
3
Bioorthogonal cyclopropenones for investigating RNA structure.用于研究RNA结构的生物正交环丙烯酮
bioRxiv. 2024 Oct 24:2024.10.22.619649. doi: 10.1101/2024.10.22.619649.
4
RNA structural probing of guanine and uracil nucleotides in yeast.酵母中鸟嘌呤和尿嘧啶核苷酸的 RNA 结构探测。
PLoS One. 2023 Jul 7;18(7):e0288070. doi: 10.1371/journal.pone.0288070. eCollection 2023.
5
The RNA interactome in the Hallmarks of Cancer.癌症的标志性特征中的 RNA 相互作用组。
Wiley Interdiscip Rev RNA. 2023 Sep-Oct;14(5):e1786. doi: 10.1002/wrna.1786. Epub 2023 Apr 12.
6
Secondary Structure of Subgenomic RNA M of SARS-CoV-2.SARS-CoV-2 的亚基因组 RNA M 的二级结构。
Viruses. 2022 Feb 4;14(2):322. doi: 10.3390/v14020322.
7
Structural characterization of a new subclass of panicum mosaic virus-like 3' cap-independent translation enhancer.一种新型 panicum mosaic virus-like 3' 帽非依赖性翻译增强子的结构特征。
Nucleic Acids Res. 2022 Feb 22;50(3):1601-1619. doi: 10.1093/nar/gkac007.
8
Universal and strain specific structure features of segment 8 genomic RNA of influenza A virus-application of 4-thiouridine photocrosslinking.甲型流感病毒 8 节段基因组 RNA 的通用和株特异性结构特征-4-硫代尿嘧啶光交联技术的应用。
J Biol Chem. 2021 Dec;297(6):101245. doi: 10.1016/j.jbc.2021.101245. Epub 2021 Oct 22.
9
Decoding LncRNAs.长链非编码核糖核酸的解码
Cancers (Basel). 2021 May 27;13(11):2643. doi: 10.3390/cancers13112643.
10
RNA G-quadruplexes (rG4s): genomics and biological functions.RNA 四链体 (rG4s)：基因组学与生物学功能。
Nucleic Acids Res. 2021 Jun 4;49(10):5426-5450. doi: 10.1093/nar/gkab187.
本文引用的文献
1
Purification of oligonucleotides using denaturing polyacrylamide gel electrophoresis.使用变性聚丙烯酰胺凝胶电泳纯化寡核苷酸。
Curr Protoc Mol Biol. 2001 May;Chapter 2:Unit2.12. doi: 10.1002/0471142727.mb0212s42.
2
Finding the most significant common sequence and structure motifs in a set of RNA sequences.在一组RNA序列中寻找最显著的共同序列和结构基序。
Nucleic Acids Res. 1997 Sep 15;25(18):3724-32. doi: 10.1093/nar/25.18.3724.
3
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.螺旋的同轴堆积增强了寡核糖核苷酸的结合，并改善了RNA折叠的预测。
Proc Natl Acad Sci U S A. 1994 Sep 27;91(20):9218-22. doi: 10.1073/pnas.91.20.9218.
4
Chemical probes for higher-order structure in RNA.用于研究RNA高阶结构的化学探针。
Proc Natl Acad Sci U S A. 1980 Aug;77(8):4679-82. doi: 10.1073/pnas.77.8.4679.
5
Specific labeling of 3' termini of RNA with T4 RNA ligase.利用T4 RNA连接酶对RNA的3'末端进行特异性标记。
Methods Enzymol. 1980;65(1):65-74. doi: 10.1016/s0076-6879(80)65011-3.
6
A guide for probing native small nuclear RNA and ribonucleoprotein structures.探测天然小核RNA和核糖核蛋白结构的指南。
Methods Enzymol. 1989;180:212-27. doi: 10.1016/0076-6879(89)80103-x.
7
Synthesis of small RNAs using T7 RNA polymerase.使用T7 RNA聚合酶合成小RNA。
Methods Enzymol. 1989;180:51-62. doi: 10.1016/0076-6879(89)80091-6.
8
Enzymatic approaches to probing of RNA secondary and tertiary structure.用于探测RNA二级和三级结构的酶学方法。
Methods Enzymol. 1989;180:192-212. doi: 10.1016/0076-6879(89)80102-8.
9
On finding all suboptimal foldings of an RNA molecule.关于寻找RNA分子的所有次优折叠结构。
Science. 1989 Apr 7;244(4900):48-52. doi: 10.1126/science.2468181.
10
The combination of symbolic and numerical computation for three-dimensional modeling of RNA.用于RNA三维建模的符号计算与数值计算相结合的方法
Science. 1991 Sep 13;253(5025):1255-60. doi: 10.1126/science.1716375.
Zotero 插件