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.

doi:10.1038/s41467-018-06942-3

Title: Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif

Journal Article · Wed Oct 31 00:00:00 EDT 2018 · Nature Communications

DOI:https://doi.org/10.1038/s41467-018-06942-3· OSTI ID:1481292

Shelke, Sandip A. ^[1]; Shao, Yaming ^[1]; Laski, Artur ^[1]; Koirala, Deepak ^[1]; Weissman, Benjamin P. ^[1];

^[1]; Tan, Xiaohong ^[2]; Constantin, Tudor P. ^[2];

^[2];

^[2]; Armitage, Bruce A. ^[2];

^[1]

Univ. of Chicago, IL (United States)
Carnegie Mellon Univ., Pittsburgh, PA (United States)

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-SO₃ 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-SO₃ fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO₃, 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.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-06CH11357; AC02-05CH11231

OSTI ID:: 1481292

Journal Information:: Nature Communications, Vol. 9, Issue 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

Citation Metrics:

Cited by: 25 works

Citation information provided by
Web of Science

References (62)

Fluorophore-binding RNA aptamers and their applications: Fluorophore-binding RNA aptamers Dolgosheina, Elena V.; Unrau, Peter J. Wiley Interdisciplinary Reviews: RNA, Vol. 7, Issue 6 https://doi.org/10.1002/wrna.1383	journal	August 2016
Laser-mediated, site-specific inactivation of RNA transcripts Grate, D.; Wilson, C. Proceedings of the National Academy of Sciences, Vol. 96, Issue 11 https://doi.org/10.1073/pnas.96.11.6131	journal	May 1999
Synthesis of New Fluorogenic Cyanine Dyes and Incorporation into RNA Fluoromodules Constantin, Tudor P.; Silva, Gloria L.; Robertson, Kelly L. Organic Letters, Vol. 10, Issue 8 https://doi.org/10.1021/ol702920e	journal	April 2008
RNA Fluorescence with Light-Up Aptamers Ouellet, Jonathan Frontiers in Chemistry, Vol. 4 https://doi.org/10.3389/fchem.2016.00029	journal	June 2016
RNA aptamers that bind flavin and nicotinamide redox cofactors Lauhon, Charles T.; Szostak, Jack W. Journal of the American Chemical Society, Vol. 117, Issue 4 https://doi.org/10.1021/ja00109a008	journal	February 1995
Isolation of RNA Aptamers for Biological Cofactors by In Vitro Selection Burgstaller, Petra; Famulok, Michael Angewandte Chemie International Edition in English, Vol. 33, Issue 10 https://doi.org/10.1002/anie.199410841	journal	June 1994
Contact-Mediated Quenching for RNA Imaging in Bacteria with a Fluorophore-Binding Aptamer Sunbul, Murat; Jäschke, Andres Angewandte Chemie International Edition, Vol. 52, Issue 50 https://doi.org/10.1002/anie.201306622	journal	October 2013
SRB-2: a promiscuous rainbow aptamer for live-cell RNA imaging Sunbul, Murat; Jäschke, Andres Nucleic Acids Research, Vol. 46, Issue 18 https://doi.org/10.1093/nar/gky543	journal	June 2018
Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: a blue fluorescent RNA Sando, Shinsuke; Narita, Atsushi; Hayami, Masayoshi Chemical Communications, Issue 33 https://doi.org/10.1039/b808449a	journal	January 2008
Small-molecule fluorescent probes for specific RNA targets Murata, Asako; Sato, Shin-ichi; Kawazoe, Yoshinori Chemical Communications, Vol. 47, Issue 16 https://doi.org/10.1039/c1cc10393h	journal	January 2011
Live-Cell Imaging of Endogenous mRNAs with a Small Molecule Sato, Shin-ichi; Watanabe, Mizuki; Katsuda, Yousuke Angewandte Chemie International Edition, Vol. 54, Issue 6 https://doi.org/10.1002/anie.201410339	journal	December 2014
RNA Mimics of Green Fluorescent Protein Paige, J. S.; Wu, K. Y.; Jaffrey, S. R. Science, Vol. 333, Issue 6042 https://doi.org/10.1126/science.1207339	journal	July 2011
Imaging RNA polymerase III transcription using a photostable RNA–fluorophore complex Song, Wenjiao; Filonov, Grigory S.; Kim, Hyaeyeong Nature Chemical Biology, Vol. 13, Issue 11 https://doi.org/10.1038/nchembio.2477	journal	September 2017
A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat–containing RNA Strack, Rita L.; Disney, Matthew D.; Jaffrey, Samie R. Nature Methods, Vol. 10, Issue 12 https://doi.org/10.1038/nmeth.2701	journal	October 2013
Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution Filonov, Grigory S.; Moon, Jared D.; Svensen, Nina Journal of the American Chemical Society, Vol. 136, Issue 46 https://doi.org/10.1021/ja508478x	journal	November 2014
RNA Mango Aptamer-Fluorophore: A Bright, High-Affinity Complex for RNA Labeling and Tracking Dolgosheina, Elena V.; Jeng, Sunny C. Y.; Panchapakesan, Shanker Shyam S. ACS Chemical Biology, Vol. 9, Issue 10 https://doi.org/10.1021/cb500499x	journal	August 2014
Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells Autour, Alexis; C. Y. Jeng, Sunny; D. Cawte, Adam Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-02993-8	journal	February 2018
Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells Zhang, Jichuan; Fei, Jingyi; Leslie, Benjamin J. Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep17295	journal	November 2015
RNA Signal Amplifier Circuit with Integrated Fluorescence Output Akter, Farhima; Yokobayashi, Yohei ACS Synthetic Biology, Vol. 4, Issue 5 https://doi.org/10.1021/sb500314r	journal	September 2014
Green fluorescent protein as a marker for gene expression Chalfie, M.; Tu, Y.; Euskirchen, G. Science, Vol. 263, Issue 5148 https://doi.org/10.1126/science.8303295	journal	February 1994
Imaging metabolite dynamics in living cells using a Spinach-based riboswitch You, Mingxu; Litke, Jacob L.; Jaffrey, Samie R. Proceedings of the National Academy of Sciences, Vol. 112, Issue 21 https://doi.org/10.1073/pnas.1504354112	journal	May 2015
RNA-Based Fluorescent Biosensors for Live Cell Imaging of Second Messengers Cyclic di-GMP and Cyclic AMP-GMP Kellenberger, Colleen A.; Wilson, Stephen C.; Sales-Lee, Jade Journal of the American Chemical Society, Vol. 135, Issue 13 https://doi.org/10.1021/ja311960g	journal	March 2013
Fluorescence Imaging of Cellular Metabolites with RNA Paige, Jeremy S.; Nguyen-Duc, Thinh; Song, Wenjiao Science, Vol. 335, Issue 6073 https://doi.org/10.1126/science.1218298	journal	March 2012
Imaging bacterial protein expression using genetically encoded RNA sensors Song, Wenjiao; Strack, Rita L.; Jaffrey, Samie R. Nature Methods, Vol. 10, Issue 9 https://doi.org/10.1038/nmeth.2568	journal	July 2013
A Spinach molecular beacon triggered by strand displacement Bhadra, Sanchita; Ellington, Andrew D. RNA, Vol. 20, Issue 8 https://doi.org/10.1261/rna.045047.114	journal	June 2014
Understanding the Photophysics of the Spinach–DFHBI RNA Aptamer–Fluorogen Complex To Improve Live-Cell RNA Imaging Han, Kyu Young; Leslie, Benjamin J.; Fei, Jingyi Journal of the American Chemical Society, Vol. 135, Issue 50 https://doi.org/10.1021/ja411060p	journal	December 2013
Photochemical properties of Spinach and its use in selective imaging Wang, Pengcheng; Querard, Jérôme; Maurin, Sylvie Chemical Science, Vol. 4, Issue 7 https://doi.org/10.1039/c3sc50729g	journal	January 2013
Quadruplex DNA: sequence, topology and structure Burge, Sarah; Parkinson, Gary N.; Hazel, Pascale Nucleic Acids Research, Vol. 34, Issue 19 https://doi.org/10.1093/nar/gkl655	journal	September 2006
G-quadruplexes in RNA biology: G-quadruplexes in RNA biology Millevoi, Stefania; Moine, Hervé; Vagner, Stéphan Wiley Interdisciplinary Reviews: RNA, Vol. 3, Issue 4 https://doi.org/10.1002/wrna.1113	journal	April 2012
A G-quadruplex–containing RNA activates fluorescence in a GFP-like fluorophore Huang, Hao; Suslov, Nikolai B.; Li, Nan-Sheng Nature Chemical Biology, Vol. 10, Issue 8 https://doi.org/10.1038/nchembio.1561	journal	June 2014
Structural basis for activity of highly efficient RNA mimics of green fluorescent protein Warner, Katherine Deigan; Chen, Michael C.; Song, Wenjiao Nature Structural & Molecular Biology, Vol. 21, Issue 8 https://doi.org/10.1038/nsmb.2865	journal	July 2014
A homodimer interface without base pairs in an RNA mimic of red fluorescent protein Warner, Katherine Deigan; Sjekloća, Ljiljana; Song, Wenjiao Nature Chemical Biology, Vol. 13, Issue 11 https://doi.org/10.1038/nchembio.2475	journal	September 2017
Structural basis for high-affinity fluorophore binding and activation by RNA Mango Trachman, Robert J.; Demeshkina, Natalia A.; Lau, Matthew W. L. Nature Chemical Biology, Vol. 13, Issue 7 https://doi.org/10.1038/nchembio.2392	journal	May 2017
RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria Guo, J. U.; Bartel, D. P. Science, Vol. 353, Issue 6306 https://doi.org/10.1126/science.aaf5371	journal	September 2016
A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells Braselmann, Esther; Wierzba, Aleksandra J.; Polaski, Jacob T. Nature Chemical Biology, Vol. 14, Issue 10 https://doi.org/10.1038/s41589-018-0103-7	journal	July 2018
Fluoromodules Consisting of a Promiscuous RNA Aptamer and Red or Blue Fluorogenic Cyanine Dyes: Selection, Characterization, and Bioimaging Tan, Xiaohong; Constantin, Tudor P.; Sloane, Kelly L. Journal of the American Chemical Society, Vol. 139, Issue 26 https://doi.org/10.1021/jacs.7b04211	journal	June 2017
In vitro selection of RNA molecules that bind specific ligands Ellington, Andrew D.; Szostak, Jack W. Nature, Vol. 346, Issue 6287 https://doi.org/10.1038/346818a0	journal	August 1990
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Tuerk, C.; Gold, L. Science, Vol. 249, Issue 4968 https://doi.org/10.1126/science.2200121	journal	August 1990
A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination Koldobskaya, Yelena; Duguid, Erica M.; Shechner, David M. Nature Structural & Molecular Biology, Vol. 18, Issue 1 https://doi.org/10.1038/nsmb.1945	journal	December 2010
A class I ligase ribozyme with reduced Mg2+ dependence: Selection, sequence analysis, and identification of functional tertiary interactions Bagby, S. C.; Bergman, N. H.; Shechner, D. M. RNA, Vol. 15, Issue 12 https://doi.org/10.1261/rna.1912509	journal	November 2009
Structurally complex and highly active RNA ligases derived from random RNA sequences Ekland, E.; Szostak, J.; Bartel, D. Science, Vol. 269, Issue 5222 https://doi.org/10.1126/science.7618102	journal	July 1995
The non-Watson-Crick base pairs and their associated isostericity matrices Leontis, N. B. Nucleic Acids Research, Vol. 30, Issue 16 https://doi.org/10.1093/nar/gkf481	journal	August 2002
A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs Leontis, Neocles B.; Westhof, Eric Journal of Molecular Biology, Vol. 283, Issue 3 https://doi.org/10.1006/jmbi.1998.2106	journal	October 1998
Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label ç Shelke, Sandip A.; Sigurdsson, Snorri Th. Nucleic Acids Research, Vol. 40, Issue 8 https://doi.org/10.1093/nar/gkr1210	journal	December 2011
Recognition of Planar and Nonplanar Ligands in the Malachite Green-RNA Aptamer Complex Flinders, Jeremy; DeFina, Steven C.; Brackett, David M. ChemBioChem, Vol. 5, Issue 1 https://doi.org/10.1002/cbic.200300701	journal	December 2003
2.8 Å crystal structure of the malachite green aptamer 1 1Edited by J. A. Doudna Baugh, Christopher; Grate, Dilârâ; Wilson, Charles Journal of Molecular Biology, Vol. 301, Issue 1 https://doi.org/10.1006/jmbi.2000.3951	journal	August 2000
A Simple and Efficient Method to Transcribe RNAs with Reduced 3′ Heterogeneity Kao, Cheng; Rüdisser, Simon; Zheng, Minxue Methods, Vol. 23, Issue 3 https://doi.org/10.1006/meth.2000.1131	journal	March 2001
PRODRG : a tool for high-throughput crystallography of protein–ligand complexes Schüttelkopf, Alexander W.; van Aalten, Daan M. F. Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 8 https://doi.org/10.1107/S0907444904011679	journal	July 2004
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
Automated acquisition and analysis of small angle X-ray scattering data Franke, Daniel; Kikhney, Alexey G.; Svergun, Dmitri I. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 689 https://doi.org/10.1016/j.nima.2012.06.008	journal	October 2012
Crystal structure of the Varkud satellite ribozyme Suslov, Nikolai B.; DasGupta, Saurja; Huang, Hao Nature Chemical Biology, Vol. 11, Issue 11 https://doi.org/10.1038/nchembio.1929	journal	September 2015
ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis Petoukhov, Maxim V.; Konarev, Peter V.; Kikhney, Alexey G. Journal of Applied Crystallography, Vol. 40, Issue s1 https://doi.org/10.1107/S0021889807002853	journal	April 2007
Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A. Biophysical Journal, Vol. 105, Issue 4 https://doi.org/10.1016/j.bpj.2013.07.020	journal	August 2013
PRIMUS: a Windows PC-based system for small-angle scattering data analysis Konarev, Petr V.; Volkov, Vladimir V.; Sokolova, Anna V. Journal of Applied Crystallography, Vol. 36, Issue 5, p. 1277-1282 https://doi.org/10.1107/S0021889803012779	journal	September 2003
Contact-Mediated Quenching for RNA Imaging in Bacteria with a Fluorophore-Binding Aptamer Sunbul, Murat; Jäschke, Andres Angewandte Chemie, Vol. 125, Issue 50 https://doi.org/10.1002/ange.201306622	journal	October 2013
Isolation and characterization of fluorophore-binding RNA aptamers Holeman, Leslie A.; Robinson, Sara L.; Szostak, Jack W. Folding and Design, Vol. 3, Issue 6 https://doi.org/10.1016/s1359-0278(98)00059-5	journal	November 1998
Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion Benton, Donald J.; Wrobel, Antoni G.; Xu, Pengqi Nature, Vol. 588, Issue 7837 https://doi.org/10.1038/s41586-020-2772-0	journal	September 2020
Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments Zanotti, Kimberly J.; Silva, Gloria L.; Creeger, Yehuda Org. Biomol. Chem., Vol. 9, Issue 4 https://doi.org/10.1039/c0ob00444h	journal	January 2011
Spinach RNA aptamer detects lead( ii ) with high selectivity DasGupta, Saurja; Shelke, Sandip A.; Li, Nan-sheng Chemical Communications, Vol. 51, Issue 43 https://doi.org/10.1039/c5cc01526j	journal	January 2015
Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers Arora, Ankita; Sunbul, Murat; Jäschke, Andres Nucleic Acids Research https://doi.org/10.1093/nar/gkv718	journal	July 2015
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/s0021889807021206	journal	July 2007
ATSAS 2.8 : a comprehensive data analysis suite for small-angle scattering from macromolecular solutions Franke, D.; Petoukhov, M. V.; Konarev, P. V. Journal of Applied Crystallography, Vol. 50, Issue 4 https://doi.org/10.1107/s1600576717007786	journal	June 2017

Similar Records

A Variable Light Domain Fluorogen Activating Protein Homodimerizes To Activate Dimethylindole Red

Journal Article · Wed Jul 11 00:00:00 EDT 2012 · Biochemistry (Eaton) · OSTI ID:1481292

Senutovitch, Nina; Stanfield, Robyn L; Bhattacharyya, Shantanu; +5 more

Structure and functional reselection of the Mango-III fluorogenic RNA aptamer

Journal Article · Mon Apr 15 00:00:00 EDT 2019 · Nature Chemical Biology · OSTI ID:1481292

Trachman III, Robert J.; Autour, Alexis; Jeng, Sunny C. Y.; +9 more

A photophysical study of two fluorogen-activating proteins bound to their cognate fluorogens

Conference · Tue Dec 14 00:00:00 EST 2010 · OSTI ID:1481292

Gaiotto, Tiziano; Nguyen, Hau B; Jung, Jaemyeong; +5 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
chemical biology
RNA
structural biology

Title: Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif

Citation Formats

References (62)

Similar Records

Related Subjects