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Bornewasser L, Kath-Schorr S. Preparation of Site-Specifically Spin-Labeled RNA by in Vitro Transcription Using an Expanded Genetic Alphabet. Methods Mol Biol 2022; 2439:223-240. [PMID: 35226325 DOI: 10.1007/978-1-0716-2047-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recent advances in pulsed electron paramagnetic resonance (EPR) spectroscopy enable studying structure and folding of nucleic acids. An efficient introduction of spin labels at specific positions within the oligonucleotide sequence is a prerequisite. We here present a step-by-step guide to synthesize long RNA oligonucleotides bearing spin labels at specific positions within the sequence. RNA preparation is achieved enzymatically via in vitro transcription using an expanded genetic alphabet. Highly structured, several hundred nucleotides long RNAs with two nitroxide spin labels at specific positions can be prepared by this method.
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2
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Zhao M, Börner R, Sigel RKO, Freisinger E. Site-Specific Dual-Color Labeling of Long RNAs. Methods Mol Biol 2021; 2106:253-270. [PMID: 31889263 DOI: 10.1007/978-1-0716-0231-7_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Labeling of large RNAs with reporting entities, e.g., fluorophores, has significant impact on RNA studies in vitro and in vivo. Here, we describe a minimally invasive RNA labeling method featuring nucleotide and position selectivity, which solves the long-standing challenge of how to achieve accurate site-specific labeling of large RNAs with a least possible influence on folding and/or function. We use a custom-designed reactive DNA strand to hybridize to the RNA and transfer the alkyne group onto the targeted adenine or cytosine. Simultaneously, the 3'-terminus of RNA is converted to a dialdehyde moiety under the experimental condition applied. The incorporated functionalities at the internal and the 3'-terminal sites can then be conjugated with reporting entities via bioorthogonal chemistry. This method is particularly valuable for, but not limited to, single-molecule fluorescence applications. We demonstrate the method on an RNA construct of 275 nucleotides, the btuB riboswitch of Escherichia coli.
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Affiliation(s)
- Meng Zhao
- Department of Chemistry, University of Zurich, Zurich, Switzerland
- Department of Physics, University of Alberta, Edmonton, AB, Canada
| | - Richard Börner
- Department of Chemistry, University of Zurich, Zurich, Switzerland
- Laserinstitut Hochschule Mittweida, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Eva Freisinger
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
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3
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Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods. Methods 2020; 183:93-107. [DOI: 10.1016/j.ymeth.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
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Domnick C, Eggert F, Wuebben C, Bornewasser L, Hagelueken G, Schiemann O, Kath‐Schorr S. EPR Distance Measurements on Long Non-coding RNAs Empowered by Genetic Alphabet Expansion Transcription. Angew Chem Int Ed Engl 2020; 59:7891-7896. [PMID: 31981397 PMCID: PMC7318606 DOI: 10.1002/anie.201916447] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/22/2020] [Indexed: 11/26/2022]
Abstract
We present herein a novel nitroxide spin label-containing RNA triphosphate TPT3NO and its application for site-specific spin-labeling of RNA through in vitro transcription using an expanded genetic alphabet. Our strategy allows the facile preparation of spin-labeled RNAs with sizes ranging from short RNA oligonucleotides to large, complex RNA molecules with over 370 nucleotides by standard in vitro transcription. As a proof of concept, inter-spin distance distributions are measured by pulsed electron paramagnetic resonance (EPR) spectroscopy in short self-complementary RNA sequences and in a well-studied 185 nucleotide non-coding RNA, the B. subtilis glmS ribozyme. The approach is then applied to probe for the first time the folding of the 377 nucleotide A-region of the long non-coding RNA Xist, by PELDOR.
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Affiliation(s)
- Christof Domnick
- Life & Medical Sciences InstituteChemical Biology & Medicinal Chemistry UnitUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Frank Eggert
- Life & Medical Sciences InstituteChemical Biology & Medicinal Chemistry UnitUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Christine Wuebben
- Institute for Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Lisa Bornewasser
- Life & Medical Sciences InstituteChemical Biology & Medicinal Chemistry UnitUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Gregor Hagelueken
- Institute for Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Olav Schiemann
- Institute for Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Stephanie Kath‐Schorr
- Life & Medical Sciences InstituteChemical Biology & Medicinal Chemistry UnitUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
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5
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Domnick C, Eggert F, Wuebben C, Bornewasser L, Hagelueken G, Schiemann O, Kath‐Schorr S. EPR Distance Measurements on Long Non‐coding RNAs Empowered by Genetic Alphabet Expansion Transcription. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916447] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christof Domnick
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Frank Eggert
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Christine Wuebben
- Institute for Physical and Theoretical Chemistry University of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Lisa Bornewasser
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Gregor Hagelueken
- Institute for Physical and Theoretical Chemistry University of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Olav Schiemann
- Institute for Physical and Theoretical Chemistry University of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Stephanie Kath‐Schorr
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
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Ehrenberger MA, Vieyra A, Esquiaqui JM, Fanucci GE. Ion-dependent mobility effects of the Fusobacterium nucleatum glycine riboswitch aptamer II via site-directed spin-labeling (SDSL) electron paramagnetic resonance (EPR). Biochem Biophys Res Commun 2019; 516:839-844. [PMID: 31262445 DOI: 10.1016/j.bbrc.2019.06.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 06/19/2019] [Indexed: 01/31/2023]
Abstract
Site-directed spin-labeling (SDSL) with continuous wave electron paramagnetic resonance (cw-EPR) spectroscopy was utilized to probe site-specific changes in backbone dynamics that accompany folding of the isolated 84 nucleotide aptamer II domain of the Fusobacterium nucleatum (FN) glycine riboswitch. Spin-labels were incorporated using splinted ligation strategies. Results show differential dynamics for spin-labels incorporated into the backbone at a base-paired and loop region. Additionally, the addition of a biologically relevant concentration of 5 mM Mg2+, to an RNA solution with 100 mM K+, folds and compacts the structure, inferred by a reduction in spin-label mobility. Furthermore, when controlling for ionic strength, Mg2+ added to the RNA induces more folding/less flexibility at the two sites than RNA with K+ alone. Addition of glycine does not alter the dynamics of this singlet aptamer II, indicating that the full length riboswitch construct may be needed for glycine binding and induced conformational changes. This work adds to our growing understanding of how splinted-ligation SDSL can be utilized to interrogate differential dynamics in large dynamic RNAs, providing insights into how RNA folding and structure is differentially stabilized by monovalent versus divalent cations.
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Affiliation(s)
- Michelle A Ehrenberger
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States
| | - Aleida Vieyra
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States
| | - Jackie M Esquiaqui
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States.
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Domnick C, Hagelueken G, Eggert F, Schiemann O, Kath-Schorr S. Posttranscriptional spin labeling of RNA by tetrazine-based cycloaddition. Org Biomol Chem 2019; 17:1805-1808. [DOI: 10.1039/c8ob02597e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Spin labeling of in vitro transcribed RNA by iEDDA click chemistry is demonstrated. This allows the determination of distance distributions between two nitroxide spin labels by PELDOR in a self-complementary RNA duplex.
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Affiliation(s)
- Christof Domnick
- Life & Medical Sciences Institute
- Chemical Biology & Medicinal Chemistry Unit
- University of Bonn
- 53121 Bonn
- Germany
| | - Gregor Hagelueken
- Institute for Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Frank Eggert
- Life & Medical Sciences Institute
- Chemical Biology & Medicinal Chemistry Unit
- University of Bonn
- 53121 Bonn
- Germany
| | - Olav Schiemann
- Institute for Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Stephanie Kath-Schorr
- Life & Medical Sciences Institute
- Chemical Biology & Medicinal Chemistry Unit
- University of Bonn
- 53121 Bonn
- Germany
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Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink–Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling. Biochemistry 2016; 55:4295-305. [DOI: 10.1021/acs.biochem.6b00287] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jackie M. Esquiaqui
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Eileen M. Sherman
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Jing-Dong Ye
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Gail E. Fanucci
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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Babaylova ES, Malygin AA, Lomzov AA, Pyshnyi DV, Yulikov M, Jeschke G, Krumkacheva OA, Fedin MV, Karpova GG, Bagryanskaya EG. Complementary-addressed site-directed spin labeling of long natural RNAs. Nucleic Acids Res 2016; 44:7935-43. [PMID: 27269581 PMCID: PMC5027493 DOI: 10.1093/nar/gkw516] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/30/2016] [Indexed: 12/21/2022] Open
Abstract
Nanoscale distance measurements by pulse dipolar Electron paramagnetic resonance (EPR) spectroscopy allow new insights into the structure and dynamics of complex biopolymers. EPR detection requires site directed spin labeling (SDSL) of biomolecule(s), which remained challenging for long RNAs up-to-date. Here, we demonstrate that novel complementary-addressed SDSL approach allows efficient spin labeling and following structural EPR studies of long RNAs. We succeeded to spin-label Hepatitis C Virus RNA internal ribosome entry site consisting of ≈330 nucleotides and having a complicated spatial structure. Application of pulsed double electron–electron resonance provided spin–spin distance distribution, which agrees well with the results of molecular dynamics (MD) calculations. Thus, novel SDSL approach in conjunction with EPR and MD allows structural studies of long natural RNAs with nanometer resolution and can be applied to systems of biological and biomedical significance.
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Affiliation(s)
- Elena S Babaylova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Olesya A Krumkacheva
- Novosibirsk State University, Novosibirsk 630090, Russia International Tomography Center SB RAS, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- Novosibirsk State University, Novosibirsk 630090, Russia International Tomography Center SB RAS, Novosibirsk 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Novosibirsk State University, Novosibirsk 630090, Russia N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
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Beasley KN, Sutch BT, Hatmal MM, Langen R, Qin PZ, Haworth IS. Computer Modeling of Spin Labels: NASNOX, PRONOX, and ALLNOX. Methods Enzymol 2015; 563:569-93. [PMID: 26478499 DOI: 10.1016/bs.mie.2015.07.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Measurement of distances between spin labels using electron paramagnetic resonance with the double electron-electron resonance (DEER) technique is an important method for evaluation of biomolecular structures. Computation of interlabel distances is of value for experimental planning, validation of known structures using DEER-measured distances, and determination of theoretical data for comparison with experiment. This requires steps of building labels at two defined sites on proteins, DNA or RNA; calculation of allowable label conformers based on rotation around torsional angles; computation of pairwise interlabel distances on a per conformer basis; and calculation of an average distance between the two label ensembles. We have described and validated two programs for this purpose: NASNOX, which permits computation of distances between R5 labels on DNA or RNA; and PRONOX, which similarly computes distances between R1 labels on proteins. However, these programs are limited to a specific single label and single target types. Therefore, we have developed a program, which we refer to as ALLNOX (Addition of Labels and Linkers), which permits addition of any label to any site on any target. The main principle in the program is to break the molecular system into a "label," a "linker," and a "target." The user can upload a "label" with any chemistry, define a "linker" based on a SMILES-like string, and then define the "target" site. The flexibility of ALLNOX facilitates theoretical evaluation of labels prior to synthesis and accommodates evaluation of experimental data in biochemical complexes containing multiple molecular types.
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Affiliation(s)
- Kathleen N Beasley
- Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA
| | - Brian T Sutch
- Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA
| | - Ma'mon M Hatmal
- Department of Laboratory Medical Sciences, Faculty of Allied Health Sciences, Hashemite University, Zarqa, Jordan
| | - Ralf Langen
- Department of Biochemistry, University of Southern California, Los Angeles, California, USA
| | - Peter Z Qin
- Department of Chemistry and Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Ian S Haworth
- Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA; Department of Biochemistry, University of Southern California, Los Angeles, California, USA.
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