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RNA Biology Volume 11, 2014 - Issue 5

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Research Paper

The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain

Senada Nozinovic Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute of Organic Chemistry and Chemical Biology

Anke Reining Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute of Organic Chemistry and Chemical Biology

Yong-Boum Kim Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute of Organic Chemistry and Chemical Biology

Jonas Noeske Department of Molecular and Cell Biology; University of California at Berkeley; Berkeley, CA USA

Kai Schlepckow Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute of Organic Chemistry and Chemical Biology

Jens Wöhnert Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute for Molecular Biosciences; Max-von-Laue-Strasse 9; Frankfurt, Germany

Harald Schwalbe Johann Wolfgang Goethe-University Frankfurt; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 7; Frankfurt, Germany; Institute of Organic Chemistry and Chemical BiologyCorrespondence[email protected]

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Pages 655-666 | Received 02 Apr 2014, Accepted 03 Jun 2014, Published online: 12 Jun 2014

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https://doi.org/10.4161/rna.29439
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Lin Wu, Dian Chen, Jienyu Ding & Yu Liu. (2021) A transient conformation facilitates ligand binding to the adenine riboswitch. iScience 24:12, pages 103512.
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Patrick St-Pierre, Euan Shaw, Samuel Jacques, Paul A Dalgarno, Cibran Perez-Gonzalez, Frédéric Picard-Jean, J Carlos Penedo & Daniel A Lafontaine. (2021) A structural intermediate pre-organizes the add adenine riboswitch for ligand recognition . Nucleic Acids Research 49:10, pages 5891-5904.
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Haley M. Wilt, Ping Yu, Kemin Tan, Yun-Xing Wang & Jason R. Stagno. (2021) Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation. Journal of Structural Biology 213:1, pages 107703.
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Jienv Ding, Monalisa Swain, Ping Yu, Jason R. Stagno & Yun-Xing Wang. (2019) Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser. Journal of Biomolecular NMR 73:8-9, pages 509-518.
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Christian A. Hanke & Holger Gohlke. (2017) Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch. PLOS ONE 12:6, pages e0179271.
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Christopher P. JonesAdrian R. Ferré-D'Amaré. (2017) Long-Range Interactions in Riboswitch Control of Gene Expression. Annual Review of Biophysics 46:1, pages 455-481.
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Sven Warhaut, Klara Rebecca Mertinkus, Philipp H?llthaler, Boris F?rtig, Mike Heilemann, Martin Hengesbach & Harald Schwalbe. (2017) Ligand-modulated folding of the full-length adenine riboswitch probed by NMR and single-molecule FRET spectroscopy. Nucleic Acids Research 45:9, pages 5512-5522.
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Sara Kališnik Verovšek & Alireza Mashaghi. (2016) Extended Topological Persistence and Contact Arrangements in Folded Linear Molecules. Frontiers in Applied Mathematics and Statistics 2.
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Asaminew H. Aytenfisu, Joseph A. Liberman, Joseph E. Wedekind & David H. Mathews. (2015) Molecular mechanism for preQ 1 -II riboswitch function revealed by molecular dynamics . RNA 21:11, pages 1898-1907.
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Fareed Aboul-ela, Wei Huang, Maaly Abd Elrahman, Vamsi Boyapati & Pan Li. (2015) Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design. Wiley Interdisciplinary Reviews: RNA 6:6, pages 631-650.
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Emmanuelle Fiore, Eric Dausse, Herv? Dubouchaud, Eric Peyrin & Corinne Ravelet. (2015) Ultrafast capillary electrophoresis isolation of DNA aptamer for the PCR amplification-based small analyte sensing. Frontiers in Chemistry 3.
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Joan G. Marcano-Velázquez & Robert T. Batey. (2015) Structure-guided Mutational Analysis of Gene Regulation by the Bacillus subtilis pbuE Adenine-responsive Riboswitch in a Cellular Context. Journal of Biological Chemistry 290:7, pages 4464-4475.
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Boris Fürtig, Senada Nozinovic, Anke Reining & Harald Schwalbe. (2015) Multiple conformational states of riboswitches fine-tune gene regulation. Current Opinion in Structural Biology 30, pages 112-124.
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Karen M. Ruff & Scott A. Strobel. (2014) Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy. RNA 20:11, pages 1775-1788.
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The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain

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The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain

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