195 related articles for article (PubMed ID: 23748604)
1. RNA secondary structure prediction using high-throughput SHAPE.
Lusvarghi S; Sztuba-Solinska J; Purzycka KJ; Rausch JW; Le Grice SF
J Vis Exp; 2013 May; (75):e50243. PubMed ID: 23748604
[TBL] [Abstract][Full Text] [Related]
2. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution.
Wilkinson KA; Merino EJ; Weeks KM
Nat Protoc; 2006; 1(3):1610-6. PubMed ID: 17406453
[TBL] [Abstract][Full Text] [Related]
3. ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis.
Vasa SM; Guex N; Wilkinson KA; Weeks KM; Giddings MC
RNA; 2008 Oct; 14(10):1979-90. PubMed ID: 18772246
[TBL] [Abstract][Full Text] [Related]
4. Determination of RNA Structure with In Vitro SHAPE Experiments.
Baes R; Charlier D; Peeters E
Methods Mol Biol; 2022; 2516():259-290. PubMed ID: 35922631
[TBL] [Abstract][Full Text] [Related]
5. Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq).
Watters KE; Lucks JB
Methods Mol Biol; 2016; 1490():135-62. PubMed ID: 27665597
[TBL] [Abstract][Full Text] [Related]
6. Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.
Smola MJ; Rice GM; Busan S; Siegfried NA; Weeks KM
Nat Protoc; 2015 Nov; 10(11):1643-69. PubMed ID: 26426499
[TBL] [Abstract][Full Text] [Related]
7. RiboCAT: a new capillary electrophoresis data analysis tool for nucleic acid probing.
Cantara WA; Hatterschide J; Wu W; Musier-Forsyth K
RNA; 2017 Feb; 23(2):240-249. PubMed ID: 27821510
[TBL] [Abstract][Full Text] [Related]
8. Insights into secondary and tertiary interactions of dengue virus RNA by SHAPE.
Sztuba-Solinska J; Le Grice SF
Methods Mol Biol; 2014; 1138():225-39. PubMed ID: 24696340
[TBL] [Abstract][Full Text] [Related]
9. The mechanisms of RNA SHAPE chemistry.
McGinnis JL; Dunkle JA; Cate JH; Weeks KM
J Am Chem Soc; 2012 Apr; 134(15):6617-24. PubMed ID: 22475022
[TBL] [Abstract][Full Text] [Related]
10. QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis.
Karabiber F; McGinnis JL; Favorov OV; Weeks KM
RNA; 2013 Jan; 19(1):63-73. PubMed ID: 23188808
[TBL] [Abstract][Full Text] [Related]
11. Sequencing-based analysis of RNA structures in living cells with 2A3 via SHAPE-MaP.
Incarnato D
Methods Enzymol; 2023; 691():153-181. PubMed ID: 37914444
[TBL] [Abstract][Full Text] [Related]
12. A peak alignment algorithm with novel improvements in application to electropherogram analysis.
Karabiber F
J Bioinform Comput Biol; 2013 Oct; 11(5):1350011. PubMed ID: 24131055
[TBL] [Abstract][Full Text] [Related]
13. Analysis of the RNA backbone: structural analysis of riboswitches by in-line probing and selective 2'-hydroxyl acylation and primer extension.
Wakeman CA; Winkler WC
Methods Mol Biol; 2009; 540():173-91. PubMed ID: 19381560
[TBL] [Abstract][Full Text] [Related]
14. High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis.
Mitra S; Shcherbakova IV; Altman RB; Brenowitz M; Laederach A
Nucleic Acids Res; 2008 Jun; 36(11):e63. PubMed ID: 18477638
[TBL] [Abstract][Full Text] [Related]
15. SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing.
Loughrey D; Watters KE; Settle AH; Lucks JB
Nucleic Acids Res; 2014 Dec; 42(21):e165. PubMed ID: 25303992
[TBL] [Abstract][Full Text] [Related]
16. In-cell RNA structure probing with SHAPE-MaP.
Smola MJ; Weeks KM
Nat Protoc; 2018 Jun; 13(6):1181-1195. PubMed ID: 29725122
[TBL] [Abstract][Full Text] [Related]
17. SHAPE Profiling to Probe Group II Intron Conformational Dynamics During Splicing.
Wiryaman T; Toor N
Methods Mol Biol; 2021; 2167():171-182. PubMed ID: 32712920
[TBL] [Abstract][Full Text] [Related]
18. Exploring RNA structural codes with SHAPE chemistry.
Weeks KM; Mauger DM
Acc Chem Res; 2011 Dec; 44(12):1280-91. PubMed ID: 21615079
[TBL] [Abstract][Full Text] [Related]
19. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).
Lucks JB; Mortimer SA; Trapnell C; Luo S; Aviran S; Schroth GP; Pachter L; Doudna JA; Arkin AP
Proc Natl Acad Sci U S A; 2011 Jul; 108(27):11063-8. PubMed ID: 21642531
[TBL] [Abstract][Full Text] [Related]
20. Carbodiimide reagents for the chemical probing of RNA structure in cells.
Wang PY; Sexton AN; Culligan WJ; Simon MD
RNA; 2019 Jan; 25(1):135-146. PubMed ID: 30389828
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]