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Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease.
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Template switching enables chemical probing of native RNA structures.
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Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).
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Substrate recognition and catalysis by the exoribonuclease RNase R.
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SHAPE to Probe RNA Structure and RNA-Protein Interactions In Vitro.
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Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation.
Nucleic Acids Res. 2021 May 7;49(8):4738-4749. doi: 10.1093/nar/gkab202.
2
The chemistry and applications of RNA 2'-OH acylation.
Nat Rev Chem. 2020 Jan;4(1):22-37. doi: 10.1038/s41570-019-0147-6. Epub 2019 Nov 19.
3
DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data.
Bioinformatics. 2019 Dec 15;35(24):5103-5112. doi: 10.1093/bioinformatics/btz449.
4
High-throughput determination of RNA structures.
Nat Rev Genet. 2018 Oct;19(10):615-634. doi: 10.1038/s41576-018-0034-x.
5
Single-molecule FRET studies on the cotranscriptional folding of a thiamine pyrophosphate riboswitch.
Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):331-336. doi: 10.1073/pnas.1712983115. Epub 2017 Dec 26.
6
Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism.
RNA. 2017 Oct;23(10):1539-1551. doi: 10.1261/rna.061796.117. Epub 2017 Jul 12.
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Long-Range Interactions in Riboswitch Control of Gene Expression.
Annu Rev Biophys. 2017 May 22;46:455-481. doi: 10.1146/annurev-biophys-070816-034042. Epub 2017 Mar 30.
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Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells.
Methods Enzymol. 2016;572:315-33. doi: 10.1016/bs.mie.2016.03.021. Epub 2016 Apr 19.
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The RNA Domain Vc1 Regulates Downstream Gene Expression in Response to Cyclic Diguanylate in Vibrio cholerae.
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本文引用的文献

2
The ligand-free state of the TPP riboswitch: a partially folded RNA structure.
J Mol Biol. 2010 Feb 12;396(1):153-65. doi: 10.1016/j.jmb.2009.11.030. Epub 2009 Nov 17.
3
Architecture and secondary structure of an entire HIV-1 RNA genome.
Nature. 2009 Aug 6;460(7256):711-6. doi: 10.1038/nature08237.
5
Determination of key residues for catalysis and RNA cleavage specificity: one mutation turns RNase II into a "SUPER-ENZYME".
J Biol Chem. 2009 Jul 31;284(31):20486-98. doi: 10.1074/jbc.M109.020693. Epub 2009 May 19.
6
Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA.
RNA. 2009 Jul;15(7):1314-21. doi: 10.1261/rna.1536209. Epub 2009 May 20.
7
Insights into how RNase R degrades structured RNA: analysis of the nuclease domain.
J Mol Biol. 2009 Apr 3;387(3):570-83. doi: 10.1016/j.jmb.2009.01.068. Epub 2009 Feb 10.
8
Accurate SHAPE-directed RNA structure determination.
Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):97-102. doi: 10.1073/pnas.0806929106. Epub 2008 Dec 24.
9
Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA.
J Am Chem Soc. 2008 Sep 17;130(37):12244-5. doi: 10.1021/ja804541s. Epub 2008 Aug 19.

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