Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET

Jeng, Sunny C.Y.; Trachman, III, Robert J.; Weissenboeck, Florian; Truong, Lynda; Link, Katie A.; Jepsen, Mette D.E.; Knutson, Jay R.; Andersen, Ebbe S.; Ferré-D'Amaré, Adrian R.; Unrau, Peter J.

doi:10.1261/rna.078220.120

Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET

Journal Article · Mon Dec 28 23:00:00 EST 2020 · RNA

DOI:https://doi.org/10.1261/rna.078220.120· OSTI ID:1837277

Jeng, Sunny C.Y. ^[1]; Trachman, III, Robert J. ^[2]; Weissenboeck, Florian ^[1]; Truong, Lynda ^[2]; Link, Katie A. ^[2]; Jepsen, Mette D.E. ^[3]; Knutson, Jay R. ^[2]; Andersen, Ebbe S. ^[3]; Ferré-D'Amaré, Adrian R. ^[2]; Unrau, Peter J. ^[1]

Simon Fraser Univ., Burnaby, BC (Canada)
National Heart, Lung, and Blood Institute, Bethesda, MD (United States)
Aarhus Univ. (Denmark)

To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor–acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. In this work, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH); European Research Council (ERC); Independent Research Fund Denmark

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1837277

Alternate ID(s):: OSTI ID: 1839755

Journal Information:: RNA, Journal Name: RNA Journal Issue: 4 Vol. 27; ISSN 1355-8382

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (59)

Supramolecular Fluorescence Resonance Energy Transfer in Nucleobase‐Modified Fluorogenic RNA Aptamers Steinmetzger, Christian; Bäuerlein, Carmen; Höbartner, Claudia Angewandte Chemie International Edition, Vol. 59, Issue 17 https://doi.org/10.1002/anie.201916707	journal	March 2020
Following the messenger: Recent innovations in live cell single molecule fluorescence imaging Schmidt, Andreas; Gao, Guoming; Little, Saffron R. WIREs RNA, Vol. 11, Issue 4 https://doi.org/10.1002/wrna.1587	journal	January 2020
Resonance Energy Transfer: Methods and Applications Wu, P. G.; Brand, L. Analytical Biochemistry, Vol. 218, Issue 1 https://doi.org/10.1006/abio.1994.1134	journal	April 1994
More than just scanning: the importance of cap-independent mRNA translation initiation for cellular stress response and cancer Lacerda, Rafaela; Menezes, Juliane; Romão, Luísa Cellular and Molecular Life Sciences, Vol. 74, Issue 9 https://doi.org/10.1007/s00018-016-2428-2	journal	December 2016
Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H–13C residual dipolar coupling on refinement Tolbert, Blanton S.; Miyazaki, Yasuyuki; Barton, Shawn Journal of Biomolecular NMR, Vol. 47, Issue 3 https://doi.org/10.1007/s10858-010-9424-x	journal	June 2010
Fluorescence lifetime imaging Lakowicz, Joseph R.; Szmacinski, Henryk; Nowaczyk, Kazimierz Analytical Biochemistry, Vol. 202, Issue 2 https://doi.org/10.1016/0003-2697(92)90112-K	journal	May 1992
[18] Fluorescence resonance energy transfer and nucleic acids Clegg, Robert M. DNA Structures Part A: Synthesis and Physical Analysis of DNA https://doi.org/10.1016/0076-6879(92)11020-J	book	January 1992
Measuring protein conformational changes by FRET/LRET Heyduk, Tomasz Current Opinion in Biotechnology, Vol. 13, Issue 4 https://doi.org/10.1016/S0958-1669(02)00332-4	journal	August 2002
Fretting about FRET: Failure of the Ideal Dipole Approximation Muñoz-Losa, Aurora; Curutchet, Carles; Krueger, Brent P. Biophysical Journal, Vol. 96, Issue 12 https://doi.org/10.1016/j.bpj.2009.03.052	journal	June 2009
Cy3-DNA Stacking Interactions Strongly Depend on the Identity of the Terminal Basepair Spiriti, Justin; Binder, Jennifer K.; Levitus, Marcia Biophysical Journal, Vol. 100, Issue 4 https://doi.org/10.1016/j.bpj.2011.01.014	journal	February 2011
Measurement of the Change in Twist at a Helical Junction in RNA Using the Orientation Dependence of FRET Fessl, Tomáš; Lilley, David M. J. Biophysical Journal, Vol. 105, Issue 9 https://doi.org/10.1016/j.bpj.2013.09.042	journal	November 2013
The Kink Turn, a Key Architectural Element in RNA Structure Huang, Lin; Lilley, David M. J. Journal of Molecular Biology, Vol. 428, Issue 5 https://doi.org/10.1016/j.jmb.2015.09.026	journal	February 2016
Bacterial Riboswitches Cooperatively Bind Ni 2+ or Co 2+ Ions and Control Expression of Heavy Metal Transporters Furukawa, Kazuhiro; Ramesh, Arati; Zhou, Zhiyuan Molecular Cell, Vol. 57, Issue 6 https://doi.org/10.1016/j.molcel.2015.02.009	journal	March 2015
Analysis of X-ray and neutron scattering from biomacromolecular solutions Petoukhov, Maxim V.; Svergun, Dmitri I. Current Opinion in Structural Biology, Vol. 17, Issue 5 https://doi.org/10.1016/j.sbi.2007.06.009	journal	October 2007
Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair Trachman, Robert J.; Cojocaru, Razvan; Wu, Di Structure, Vol. 28, Issue 7 https://doi.org/10.1016/j.str.2020.04.007	journal	July 2020
The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins Rodriguez, Erik A.; Campbell, Robert E.; Lin, John Y. Trends in Biochemical Sciences, Vol. 42, Issue 2 https://doi.org/10.1016/j.tibs.2016.09.010	journal	February 2017
Structural Principles of Fluorescent RNA Aptamers Trachman, Robert J.; Truong, Lynda; Ferré-D'Amaré, Adrian R. Trends in Pharmacological Sciences, Vol. 38, Issue 10 https://doi.org/10.1016/j.tips.2017.06.007	journal	October 2017
Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers Trachman, Robert J.; Ferré-D'Amaré, Adrian R. Quarterly Reviews of Biophysics, Vol. 52 https://doi.org/10.1017/S0033583519000064	journal	January 2019
The czcD (NiCo) Riboswitch Responds to Iron(II) Xu, Jiansong; Cotruvo, Joseph A. Biochemistry, Vol. 59, Issue 15 https://doi.org/10.1021/acs.biochem.0c00074	journal	April 2020
Crystal Structures of the Mango-II RNA Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of Variants with Improved Selectivity and Brightness Trachman, Robert J.; Abdolahzadeh, Amir; Andreoni, Alessio Biochemistry, Vol. 57, Issue 26 https://doi.org/10.1021/acs.biochem.8b00399	journal	May 2018
The Structure of Cyanine 5 Terminally Attached to Double-Stranded DNA: Implications for FRET Studies Iqbal, Asif; Wang, Lihua; Thompson, Katherine C. Biochemistry, Vol. 47, Issue 30 https://doi.org/10.1021/bi800773f	journal	July 2008
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
Orientation Control of Fluorescence Resonance Energy Transfer Using DNA as a Helical Scaffold Lewis, Frederick D.; Zhang, Ligang; Zuo, Xiaobing Journal of the American Chemical Society, Vol. 127, Issue 28 https://doi.org/10.1021/ja0524402	journal	June 2005
Plug-and-Play Fluorophores Extend the Spectral Properties of Spinach Song, Wenjiao; Strack, Rita L.; Svensen, Nina Journal of the American Chemical Society, Vol. 136, Issue 4 https://doi.org/10.1021/ja410819x	journal	January 2014
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
Nucleic Acid Base Analog FRET-Pair Facilitating Detailed Structural Measurements in Nucleic Acid Containing Systems Börjesson, Karl; Preus, Søren; El-Sagheer, Afaf H. Journal of the American Chemical Society, Vol. 131, Issue 12 https://doi.org/10.1021/ja806944w	journal	April 2009
RNA-Based Fluorescent Biosensors for Live Cell Imaging of Second Messenger Cyclic di-AMP Kellenberger, Colleen A.; Chen, Chen; Whiteley, Aaron T. Journal of the American Chemical Society, Vol. 137, Issue 20 https://doi.org/10.1021/jacs.5b00275	journal	May 2015
Fluorescence Properties and Photophysics of the Sulfoindocyanine Cy3 Linked Covalently to DNA Sanborn, Matthew E.; Connolly, Brian K.; Gurunathan, Kaushik The Journal of Physical Chemistry B, Vol. 111, Issue 37 https://doi.org/10.1021/jp072912u	journal	September 2007
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
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
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
Observation of internal cleavage and ligation reactions of a ribozyme Nahas, Michelle K.; Wilson, Timothy J.; Hohng, Sungchul Nature Structural & Molecular Biology, Vol. 11, Issue 11 https://doi.org/10.1038/nsmb842	journal	October 2004
Development of a genetically encodable FRET system using fluorescent RNA aptamers Jepsen, Mette D. E.; Sparvath, Steffen M.; Nielsen, Thorbjørn B. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-017-02435-x	journal	January 2018
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
Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch Suddala, Krishna C.; Price, Ian R.; Dandpat, Shiba S. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12230-5	journal	September 2019
Live cell imaging of single RNA molecules with fluorogenic Mango II arrays Cawte, Adam D.; Unrau, Peter J.; Rueda, David S. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14932-7	journal	March 2020
Structure and functional reselection of the Mango-III fluorogenic RNA aptamer Trachman, Robert J.; Autour, Alexis; Jeng, Sunny C. Y. Nature Chemical Biology, Vol. 15, Issue 5 https://doi.org/10.1038/s41589-019-0267-9	journal	April 2019
Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids Iqbal, A.; Arslan, S.; Okumus, B. Proceedings of the National Academy of Sciences, Vol. 105, Issue 32 https://doi.org/10.1073/pnas.0801707105	journal	August 2008
A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate Tan, E.; Wilson, T. J.; Nahas, M. K. Proceedings of the National Academy of Sciences, Vol. 100, Issue 16 https://doi.org/10.1073/pnas.1233536100	journal	July 2003
Energy transfer: a spectroscopic ruler. Stryer, L.; Haugland, R. P. Proceedings of the National Academy of Sciences, Vol. 58, Issue 2 https://doi.org/10.1073/pnas.58.2.719	journal	August 1967
Fluorescence lifetime imaging of free and protein-bound NADH. Lakowicz, J. R.; Szmacinski, H.; Nowaczyk, K. Proceedings of the National Academy of Sciences, Vol. 89, Issue 4 https://doi.org/10.1073/pnas.89.4.1271	journal	February 1992
Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer. Gohlke, C.; Murchie, A. I.; Lilley, D. M. Proceedings of the National Academy of Sciences, Vol. 91, Issue 24 https://doi.org/10.1073/pnas.91.24.11660	journal	November 1994
Internally labeled Cy3/Cy5 DNA constructs show greatly enhanced photo-stability in single-molecule FRET experiments Lee, Wonbae; von Hippel, Peter H.; Marcus, Andrew H. Nucleic Acids Research, Vol. 42, Issue 9 https://doi.org/10.1093/nar/gku199	journal	March 2014
iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications Autour, Alexis; Westhof, Eric; Ryckelynck, Michael Nucleic Acids Research, Vol. 44, Issue 6 https://doi.org/10.1093/nar/gkw083	journal	March 2016
Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes Kashida, Hiromu; Kurihara, Ayako; Kawai, Hayato Nucleic Acids Research, Vol. 45, Issue 11 https://doi.org/10.1093/nar/gkx200	journal	March 2017
Automated matching of high- and low-resolution structural models Kozin, M. B.; Svergun, D. I. Journal of Applied Crystallography, Vol. 34, Issue 1, p. 33-41 https://doi.org/10.1107/S0021889800014126	journal	February 2001
Uniqueness of ab initio shape determination in small-angle scattering Volkov, Vladimir V.; Svergun, Dmitri I. Journal of Applied Crystallography, Vol. 36, Issue 3, p. 860-864 https://doi.org/10.1107/S0021889803000268	journal	April 2003
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
DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering Franke, Daniel; Svergun, Dmitri I. Journal of Applied Crystallography, Vol. 42, Issue 2, p. 342-346 https://doi.org/10.1107/S0021889809000338	journal	January 2009
Determination of the regularization parameter in indirect-transform methods using perceptual criteria Svergun, D. I. Journal of Applied Crystallography, Vol. 25, Issue 4, p. 495-503 https://doi.org/10.1107/S0021889892001663	journal	August 1992
CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates Svergun, D.; Barberato, C.; Koch, M. H. J. Journal of Applied Crystallography, Vol. 28, Issue 6 https://doi.org/10.1107/S0021889895007047	journal	December 1995
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Co-crystal structure of the i Mango-III fluorescent RNA aptamer using an X-ray free-electron laser Trachman, Robert J.; Stagno, Jason R.; Conrad, Chelsie Acta Crystallographica Section F Structural Biology Communications, Vol. 75, Issue 8 https://doi.org/10.1107/S2053230X19010136	journal	August 2019
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
Fluorophore ligand binding and complex stabilization of the RNA Mango and RNA Spinach aptamers Jeng, Sunny C. Y.; Chan, Hedy H. Y.; Booy, Evan P. RNA, Vol. 22, Issue 12 https://doi.org/10.1261/rna.056226.116	journal	October 2016
A divalent cation-dependent variant of the glmS ribozyme with stringent Ca ²⁺ selectivity co-opts a preexisting nonspecific metal ion-binding site Lau, Matthew W. L.; Trachman, Robert J.; Ferré-D'Amaré, Adrian R. RNA, Vol. 23, Issue 3 https://doi.org/10.1261/rna.059824.116	journal	December 2016
Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI Fernandez-Millan, Pablo; Autour, Alexis; Ennifar, Eric RNA, Vol. 23, Issue 12 https://doi.org/10.1261/rna.063008.117	journal	September 2017
A Guide to Fluorescent Protein FRET Pairs Bajar, Bryce; Wang, Emily; Zhang, Shu Sensors, Vol. 16, Issue 9 https://doi.org/10.3390/s16091488	journal	September 2016

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
FRET
G-quadruplex
RNA
fluorescent aptamer
helical junction
riboswitch

Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET

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