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Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif
The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization mod...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208384/ https://www.ncbi.nlm.nih.gov/pubmed/30382099 http://dx.doi.org/10.1038/s41467-018-06942-3 |
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author | Shelke, Sandip A. Shao, Yaming Laski, Artur Koirala, Deepak Weissman, Benjamin P. Fuller, James R. Tan, Xiaohong Constantin, Tudor P. Waggoner, Alan S. Bruchez, Marcel P. Armitage, Bruce A. Piccirilli, Joseph A. |
author_facet | Shelke, Sandip A. Shao, Yaming Laski, Artur Koirala, Deepak Weissman, Benjamin P. Fuller, James R. Tan, Xiaohong Constantin, Tudor P. Waggoner, Alan S. Bruchez, Marcel P. Armitage, Bruce A. Piccirilli, Joseph A. |
author_sort | Shelke, Sandip A. |
collection | PubMed |
description | The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO(3) bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO(3) fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO(3,) and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure. |
format | Online Article Text |
id | pubmed-6208384 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-62083842018-10-31 Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif Shelke, Sandip A. Shao, Yaming Laski, Artur Koirala, Deepak Weissman, Benjamin P. Fuller, James R. Tan, Xiaohong Constantin, Tudor P. Waggoner, Alan S. Bruchez, Marcel P. Armitage, Bruce A. Piccirilli, Joseph A. Nat Commun Article The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO(3) bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO(3) fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO(3,) and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure. Nature Publishing Group UK 2018-10-31 /pmc/articles/PMC6208384/ /pubmed/30382099 http://dx.doi.org/10.1038/s41467-018-06942-3 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Shelke, Sandip A. Shao, Yaming Laski, Artur Koirala, Deepak Weissman, Benjamin P. Fuller, James R. Tan, Xiaohong Constantin, Tudor P. Waggoner, Alan S. Bruchez, Marcel P. Armitage, Bruce A. Piccirilli, Joseph A. Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif |
title | Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif |
title_full | Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif |
title_fullStr | Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif |
title_full_unstemmed | Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif |
title_short | Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif |
title_sort | structural basis for activation of fluorogenic dyes by an rna aptamer lacking a g-quadruplex motif |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208384/ https://www.ncbi.nlm.nih.gov/pubmed/30382099 http://dx.doi.org/10.1038/s41467-018-06942-3 |
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